├── .gitignore
├── readme.org
├── denote-explore-network.html
├── denote-explore.org
├── LICENSE
├── denote-explore.texi
└── denote-explore.info


/.gitignore:
--------------------------------------------------------------------------------
1 | /test/
2 | /dev/
3 | 


--------------------------------------------------------------------------------
/readme.org:
--------------------------------------------------------------------------------
  1 | #+title:  Denote Explorer: Explore your Denote Digital Garden
  2 | #+author: Peter Prevos
  3 | 
  4 | The Denote-Explorer package provides auxiliary functions to maintain and explore your collection of Denote files. Denote-Explore provides three groups of Emacs commands:
  5 | 
  6 | 1. /Summary statistics/: Count and visualise notes, attachments and keywords.
  7 | 2. /Random walks/: Generate new ideas using serendipity.
  8 | 3. /Janitor/: Manage your denote collection.
  9 | 4. /Knowledge graphs/: Visualise your Denote network  as a network graph.
 10 | 
 11 | Read the [[https://lucidmanager.org/productivity/denote-explore][Denote-Explorer manual]] for a comprehensive explanation of all functionality (=C-h R denote-explore=).
 12 | 
 13 | Visualising networks of Denote files with SVG or PDF files will require the [[https://graphviz.org/][GraphViz]] package to be available. The D3.js visualisation type downloads an external JavaScript file from [[https://d3js.org/][d3js.org]].
 14 | 
 15 | Denote-Explore package is available on MELPA and is easily installed with the ~use-package~ macro.
 16 | 
 17 | The configuration below customises all available variables and binds all available commands to the =C-c e= prefix. Modify this configuration to suit your needs, as one person's sensible defaults are another person's nightmare. To get started you don't need to configure anything, so ~(use-package denote-explore)~ is sufficient. 
 18 | 
 19 | #+begin_src elisp
 20 |   (use-package denote-explore
 21 |     :custom
 22 |     ;; Where to store network data and in which format
 23 |     (denote-explore-network-directory "<your preferred folder>")
 24 |     (denote-explore-network-filename "denote-network")
 25 |     (denote-explore-network-keywords-ignore "<keywords list>")
 26 |     (denote-explore-network-regex-ignore "<regex>")
 27 |     (denote-explore-network-format 'd3.js)
 28 |     (denote-explore-network-d3-colours 'SchemeObservable10)
 29 |     (denote-explore-network-d3-js "https://d3js.org/d3.v7.min.js")
 30 |     (denote-explore-network-d3-template "<file path>")
 31 |     (denote-explore-network-graphviz-header "<header strings>")
 32 |     (denote-explore-network-graphviz-filetype 'svg)
 33 |     :bind
 34 |     (;; Statistics
 35 |      ("C-c e s n" . denote-explore-count-notes)
 36 |      ("C-c e s k" . denote-explore-count-keywords)
 37 |      ("C-c e s e" . denote-explore-barchart-filetypes)
 38 |      ("C-c e s w" . denote-explore-barchart-keywords)
 39 |      ("C-c e s t" . denote-explore-barchart-timeline)
 40 |      ;; Random walks
 41 |      ("C-c e w n" . denote-explore-random-note)
 42 |      ("C-c e w r" . denote-explore-random-regex)
 43 |      ("C-c e w l" . denote-explore-random-link)
 44 |      ("C-c e w k" . denote-explore-random-keyword)
 45 |      ;; Denote Janitor
 46 |      ("C-c e j d" . denote-explore-duplicate-notes)
 47 |      ("C-c e j D" . denote-explore-duplicate-notes-dired)
 48 |      ("C-c e j l" . denote-explore-missing-links)
 49 |      ("C-c e j z" . denote-explore-zero-keywords)
 50 |      ("C-c e j s" . denote-explore-single-keywords)
 51 |      ("C-c e j r" . denote-explore-rename-keywords)
 52 |      ("C-c e j y" . denote-explore-sync-metadata)
 53 |      ("C-c e j i" . denote-explore-isolated-files)
 54 |      ;; Visualise denote
 55 |      ("C-c e n" . denote-explore-network)
 56 |      ("C-c e r" . denote-explore-network-regenerate)
 57 |      ("C-c e d" . denote-explore-barchart-degree)
 58 |      ("C-c e b" . denote-explore-barchart-backlinks)))
 59 | #+end_src
 60 | 
 61 | Alternatively, you can install it directly from GitHub:
 62 | 
 63 | #+begin_src elisp :eval no
 64 |   (unless (package-installed-p 'denote-explore)
 65 |     (package-vc-install
 66 |      '(denote-explore
 67 |        :url "https://github.com/pprevos/denote-explore/")))
 68 | #+end_src
 69 | 
 70 | * Change Log
 71 | Major version numbers coincide with Denote major versions.
 72 | 
 73 | ** Version 4.1
 74 | - Minor compatibility issues with Denote 4.1. No upgrades.
 75 | 
 76 | ** Version 4.01
 77 | - Various bug fixes and refactoring
 78 | - Added ~denote-explore-random-signature~ function
 79 | - Add ability to ignore files by keyword for determining isolatedness ([[https://github.com/pprevos/denote-explore/pull/41][Pull request 41]])
 80 | - Added ~denote-explore-list-keywords~ function ([[https://github.com/pprevos/denote-explore/pull/42][Pull request 42]])
 81 | 
 82 | ** Version 4.0
 83 | - Compatibility check with Denote 4
 84 |   - Minor update to denoter-explore-sync-metadata
 85 |   - Updated denote-explore-rename-keyword
 86 | - Clarifications in the manual
 87 | - Added error message when 'missing' link is not found in buffer
 88 | - Clarifications in the manual
 89 | 
 90 | ** Version 3.3.3
 91 | - Fixed bug in keyword renaming function. 
 92 | 
 93 | ** version 3.3.2
 94 | - Refactoring of missing links functionality
 95 | - Added table of missing file links in Denote files
 96 | - Renamed ~denote-explore-dead-links~ to ~denote-explore-missing-links~
 97 | 
 98 | ** Version 3.3.1
 99 | - Fixed issues in the manual.
100 | - Clarified duplicate detection.
101 | - Fixed bug in ~denote-explore-barchart-backlinks~.
102 | - Added ~denote-explore-random-regex-ignore~ variable to exclude files from random walks.
103 | 
104 | ** Version 3.3
105 | + Knowledge Graphs
106 |   - New visualisation type: Sequences of Denote signatures
107 |     - Changed GraphViz geometry for sequence graphs
108 |   - Full rewrite of most functions.
109 |     - Increased efficiency in detecting edges (links between files)
110 |     - Ability to draw graphs without attachments by using the universal argument when generating and regenerating graphs
111 |   - D3.js Visualisations
112 |     - New slider to change the number of node labels (from none to every node)
113 |     - Added number of isolated notes to info tooltip (when isolated nodes > 0)
114 | + Janitor
115 |   - New function ~denote-explore-dead-links~ to find dead links
116 |   - Optimised single and zero keywords detection
117 |   - Change behaviour and optimisation for ~denote-explore-isolated-notes~
118 |   - ~denote-explore-sort-keywords~ replaced by ~denote-explore-sync-metadata~
119 |   - Refactored ~denote-explore-rename-keyword~
120 |   - Renamed duplicate notes functions to remove double verb and UI improvements.
121 |   - ~denote-explore-sync-metadata~ bug fix
122 | + Statistics
123 |   - New function ~denote-explore-barchart-timeline~ to show number of nodes and/or attachment created per year
124 |   - The File type bar chart can also show only attachments.
125 |   - ~denote-explore-barchart-degree~ allows text-only option
126 |   - Added all used keywords to ~denote-explore-count-keywords~
127 |   - Fixed bug in random walk functions
128 | 
129 | ** Version 3.2
130 | - First version formally registered (for inclusion in Guin)
131 | - D3.js Visualisation
132 |   - Community graphs can filter out nodes where degree = 0 (isolated notes)
133 |   - Preview images and PDF files in tooltips
134 | - Updated manual
135 | - Bug fixes
136 |   - GraphViz network
137 |   - D3.js file type legend colours
138 |   - Random walk functions
139 | - Updated code commentary
140 | - Updated counting and related bar chart functions
141 | 
142 | ** Version 3.1
143 | - Removed dependency on R for D3.js graphs. D3 now uses a template in which a JSON file is inserted. This format is now the default.
144 | - Fixed bugs in renaming functions
145 | - Protection against using quotation marks in note title when visualising networks in GraphViz.
146 | - Fixed backlinks barchart visualisation
147 | - Updates documentation strings.
148 | 
149 | ** Version 3.0
150 | - Compatability with Denote 3.0 
151 | - Renamed barchart functions to all start with ~denote-explore-barchart-~.
152 | - Using universal argument with ~denote-explore-barchart-extensions~ visualises only attachment file types.
153 | - All functions that rename files updated for compatability with Denote 3.0
154 | - Enhanced info manual
155 |   
156 | ** Version 1.6
157 | - New functions:
158 |   - ~denote-explore-backlinks-barchart~ to view top-n notes with backlinks
159 |   - ~denote-explore-random-regex~ to jump to random note matching a regular expression.
160 |   - ~denote-explore-identify-duplicate-notes-dired~: View notes with duplicates ID in Dired.
161 |   
162 | ** Version 1.5.1
163 | - Fixed various compilation errors.
164 | - Enhanced output for ~denote-explore-identify-duplicate-notes~
165 | - Update customization types for note ignore variables
166 | - Updated ~defgroup~ definition and ~defcustom~ types
167 | 
168 | ** Version 1.5
169 | - Published Info mode manual
170 | - Clarified obsolete variables and functions
171 | - ~denote-explore-network-keywords~ no longer interactive
172 | - Updates to Denote functions
173 | 
174 | ** Version 1.4.2
175 | - Geneal code refactoring with assistance from Prot
176 | - Added ability to filter keywords network by minimum weight of edges
177 | - Added ability for free text in ~denote-explore-network-graphviz-filetype~
178 | - GEXF format now includes the total degree for each node
179 | - Enforced consistency with use of universal argument (its use will include attachments)
180 | - ~denote-explore--retrieve-title~ deprecated. Now using Denote function.
181 | - Updated manual with clarifications
182 | 
183 | ** Version 1.4.1
184 | - Fixed bugs with random links and keywords from nil file-name
185 | - New variable ~denote-explore-network-regex-ignore~ to ignore files matching a regular expression when creating neighbourhood or community graphs.
186 | 
187 | ** Version 1.4
188 | + Network visualisation
189 |   - SVG output includes links to source file.
190 |   - Configure [[https://graphviz.org/docs/outputs/][GraphViz output format]] with ~denote-explore-network-graphviz-filetype~ (SVG (default) or PDF advised). 
191 |   - Improved scaling of GraphViz graphics.
192 |   - ~denote-explore-network-regenerate~ recreates the previous graph
193 | + New functions:
194 |   - ~denote-explore-isolated-notes~ to select Denote files without any links or backlinks.
195 |   - ~denote-explore-degree-barchart~ draws the distribution of total number of (back)links per file ([[https://en.wikipedia.org/wiki/Degree_distribution][Degree distribution - Wikipedia]]).
196 | + Updated functions:
197 |   - ~denote-explore-rename-keyword~ allows renaming more than one keyword to a new version.
198 |   - ~denote-explore-sync-metadata~ enforces renaming confirmation.
199 | + Minor bug fixes.
200 | 
201 | ** Version 1.3
202 | - Complete rewrite of the graph visualisation functionality. Now includes three formats (JavaScript, GraphViz and GEXF) and three graph types (notes that match a regular expression, note neighbourhood and keyword graph).
203 | - Fixed bugs in =denote-explore--retrieve-title= and =denote-explore--retrieve-keywords=.
204 | - Enhanced function and variable documentation.
205 | 
206 | ** Version 1.2
207 | - Removed =pandoc= dependency in network generation.
208 | -  ~denote-explore-identify-duplicate-notes~ replaces ~denote-explore-identify-duplicate-identifiers~. This new version either detects duplicate identifiers, or duplicate file names (using the universal argument). Comparing duplicate filenames ignores any duplicate identifiers caused by exporting Org mode files.
209 | 
210 | ** Version 1.1
211 | - Added helper function to call R script for network visualisation.
212 | - =denote-explore-dashboard.el= deprecated.
213 | - Added to MELPA.
214 | 
215 | ** Version 1.0
216 | This version is a complete rewrite of the code to improve coding quality and compatibility with internal changes since Denote version 2.2.
217 | 
218 | Also major changes to the network visualisation, which can now take a regular expression for partial networks. Most of the code is now undertaken in Emacs Lisp, which saves the network in JSON format.
219 | 
220 | The functionality for a Dashboard widget has been moved to a separate file to not enforce the requirements for those users not seeking to implement the widget.
221 | 
222 | New functionality since the previous version:
223 | - ~denote-explore-identify-duplicate-identifiers~: Provide a list of duplicate identifiers.
224 | - ~denote-explore-single-keywords~: Select a note or attachment with a keyword that is only used once.
225 | - ~denote-explore-zero-keywords~: Select a note or attachment without any keywords.
226 | - ~denote-explore-sort-keywords~: Order the keywords of all Denote notes and attachments alphabetically.
227 | - ~denote-explore-rename-keyword~: Rename or remove a keyword across the whole Denote collection.
228 | - ~denote-explore-sync-metadata~: Synchronise the filenames with the metadata for all Denote files.
229 | 
230 | * Ideas for future development
231 | Some random ideas for future development. Feel free to suggest other ideas.
232 | 
233 | - [ ] Functions to rename Denote attachments using EXIF metadata.
234 | - [ ] Store the Denote metadata in a [[https://www.gnu.org/software/emacs/manual/html_node/elisp/Hash-Tables.html][hash table]] that is updated after every modification to a Denote file for more efficient visualisation.
235 | - [ ] Ring of previously-generated networks instead of overwriting ~denote-explore-network-previous~
236 | - [ ] Use [[https://github.com/alphapapa/org-graph-view/][org-graph-view]] for live neighbourhood view of the current buffer
237 | - [ ] [[https://graphviz.org/pdf/cluster.1.pdf][Community detection]]?
238 | - [ ] Create a Denote widget for the Emacs Dashboard with links to statistics.
239 | 


--------------------------------------------------------------------------------
/denote-explore-network.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html>
  3 |   <head>
  4 |     <meta charset="utf-8">
  5 |     <title>Denote Explore {{graph-type}} Network</title>
  6 |     <style>
  7 |       body {
  8 |           font-family: sans-serif;
  9 |           margin: 0;
 10 |           padding: 0;
 11 |           display: flex;
 12 |           justify-content: center;
 13 |           align-items: center;
 14 |           height: 100vh;
 15 |           background-color: #f8f8f8;
 16 |       }
 17 | 
 18 |       svg {
 19 |           border: 0px solid #ccc;
 20 | 	  z-index: 1;
 21 |       }
 22 | 
 23 |       .tooltip {
 24 |           position: absolute;
 25 |           background-color: white;
 26 |           border: 1px solid #ddd;
 27 |           border-radius: 8px;
 28 |           padding: 15px;
 29 |           box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
 30 |           pointer-events: none;
 31 |           line-height: 1.4;
 32 |           max-width: 600px;
 33 | 	  z-index: 1000;
 34 |       }
 35 | 
 36 |       .lighter {
 37 | 	  color: #888;
 38 |       }
 39 | 
 40 |       .tooltip .title {
 41 |           font-weight: bold;
 42 |           margin-bottom: 10px;
 43 | 	  font-size: 28px;
 44 |       }
 45 | 
 46 |       .tooltip .keywords {
 47 |           display: flex;
 48 |           flex-wrap: wrap;
 49 |           gap: 5px;
 50 |           margin-top: 5px;
 51 |       }
 52 | 
 53 |       .tooltip .keywords span {
 54 |           background-color: #e0e7ff;
 55 |           color: #3b82f6;
 56 |           padding: 2px 8px;
 57 |           border-radius: 4px;
 58 |           font-size: 18px;
 59 |       }
 60 | 
 61 |       .tooltip .metadata {
 62 |           margin-top: 10px;
 63 |           font-size: 18px;
 64 |           color: #333;
 65 |       }
 66 | 
 67 |       .hidden {
 68 |           display: none;
 69 |       }
 70 | 
 71 |       .info-button {
 72 | 	  position: fixed;
 73 | 	  top: 10px;
 74 | 	  left: 10px;
 75 | 	  width: 50px;
 76 | 	  height: 50px;
 77 | 	  background-color: #007BFF;
 78 | 	  color: white;
 79 | 	  font-size: 24px;
 80 | 	  font-weight: bold;
 81 | 	  text-align: center;
 82 | 	  line-height: 50px;
 83 | 	  border-radius: 25px;
 84 | 	  cursor: pointer;
 85 | 	  z-index: 1000;
 86 | 	  box-shadow: 0px 4px 6px rgba(0, 0, 0, 0.2);
 87 | 	  transition: transform 0.2s, box-shadow 0.2s;
 88 |       }
 89 | 
 90 |       .info-button:hover {
 91 | 	  transform: scale(1.1); /* Slightly enlarges on hover */
 92 | 	  box-shadow: 0px 6px 8px rgba(0, 0, 0, 0.3); /* More pronounced shadow */
 93 |       }
 94 | 
 95 |       .info-button:active {
 96 | 	  transform: scale(0.95); /* Slightly shrinks when clicked */
 97 | 	  box-shadow: 0px 2px 4px rgba(0, 0, 0, 0.3); /* Subtle shadow on click */
 98 |       }
 99 | 
100 |       #info-button:hover .info-tooltip {
101 | 	  display: block; /* Show on hover */
102 |       }
103 | 
104 |       .info-tooltip {
105 | 	  position: absolute;
106 | 	  top: 60px;
107 | 	  left: 10px;
108 | 	  background-color: white;
109 | 	  color: black;
110 | 	  border: 1px solid #ddd;
111 | 	  border-radius: 8px;
112 | 	  padding: 15px;
113 | 	  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
114 | 	  max-width: 600px; /* Prevents it from growing too wide */
115 | 	  overflow: auto;
116 | 	  display: none;
117 | 	  z-index: 99999;
118 |       }
119 | 
120 |       .info-tooltip .title {
121 | 	  font-weight: bold;
122 | 	  margin-bottom: 10px;
123 | 	  font-size: 24px;
124 |       }
125 | 
126 |       .info.tooltip .metadata {
127 | 	  margin-top: 10px;
128 | 	  font-size: 22px;
129 | 	  color: #555;
130 |       }
131 | 
132 |       #keyword-chart svg {
133 | 	  font-family: sans-serif;
134 |       }
135 | 
136 |       .legend-container .chart-container {
137 | 	  margin-bottom: 10px;
138 | 	  padding: 10px;
139 | 	  border: 1px solid #ddd;
140 | 	  border-radius: 8px;
141 | 	  background-color: #f8f8f8;
142 |       }
143 | 
144 |       .metadata-container {
145 | 	  margin-bottom: 10px;
146 | 	  padding: 10px;
147 | 	  border: 1px solid #ddd;
148 | 	  border-radius: 8px;
149 | 	  background-color: #f8f8f8; /* Matches the existing tooltip and legend background */
150 | 	  font-size: 18px; /* Matches the metadata text size */
151 |       }
152 | 
153 |       .metadata {
154 | 	  margin-bottom: 10px; /* Adjust spacing as needed */
155 | 	  font-size: 18px; /* Optional: Adjust font size */
156 |       }
157 | 
158 |     </style>
159 |   </head>
160 |   <body>
161 |     <!-- Info Button -->
162 |     <div id="info-button" class="info-button" title="Click for more information">ℹ</div>
163 |     <!-- Tooltip Container -->
164 |     <div class="info-tooltip"></div>
165 | </div>
166 |     <script src="{{d3-js}}"></script>
167 |     <script>
168 |       const data = {{json-content}}
169 | 
170 |       const width = 1440;
171 |       const height = 900;
172 |       const fontSize = 18;
173 |       const color = d3.scaleOrdinal(d3.{{d3-colourscheme}});
174 |       const links = data.edges; // Array of edges
175 |       const nodes = data.nodes; // Array of nodes
176 |       // Variable to hold the current minimum degree tag value
177 |       let minDegreeTag = 2;
178 | 
179 |       // Create a tooltip div
180 |       const tooltip = d3.select("body")
181 | 	    .append("div")
182 | 	    .attr("class", "tooltip hidden");
183 | 
184 |       // Create a zoom behaviour
185 |       const zoom = d3.zoom()
186 | 	    .scaleExtent([0.1, 4]) // Zoom scale limits
187 | 	    .on("zoom", (event) => {
188 | 		svgGroup.attr("transform", event.transform); // Apply zoom
189 | 	    });
190 | 
191 |       // Create the SVG container with zoom functionality
192 |       const svg = d3.select('body').append("svg")
193 | 	    .attr("width", width)
194 | 	    .attr("height", height)
195 | 	    .attr("viewBox", [0, 0, width, height])
196 | 	    .attr("style", "max-width: 100%; height: auto;")
197 | 	    .call(zoom);
198 | 
199 |       const svgGroup = svg.append("g"); // Group to apply zoom transformations
200 |       const radiusScale = d3.scaleLinear()
201 | 	    .domain(d3.extent(nodes, d => d.degree)) // Node degree range
202 |       .range([7, 30]); // Radius range for nodes
203 | 
204 |       // Define a weight scale for edge stroke width (Keywords only)
205 |       const isKeywordType = data.meta.type === "Keywords";
206 |       const maxWeight = d3.max(links, d => d.weight || 1);
207 | 
208 |       // Define the weight scale with interpolation
209 |       const weightScale = d3.scaleLinear()
210 | 	    .domain([1, maxWeight]) // Map the range of weights
211 | 	    .range(isKeywordType ? [2, 30] : [1, 1]); // Adjust the range
212 | 
213 |       const arrowMarkers = svg.append("defs");
214 | 
215 |       // Pre-calculate refX for edges
216 |       links.forEach((d, i) => {
217 |       const targetNode = nodes.find(node => node.id === d.target);
218 |       const targetRadius = isKeywordType ? 15 : radiusScale(targetNode.degree); // Use constant radius if isKeywordType is true
219 |       d.refX = targetRadius + 2; // Dynamically calculate refX for alignment, with padding
220 |       });
221 | 
222 |       // Define arrow markers dynamically based on line weight
223 |       links.forEach((d, i) => {
224 |       arrowMarkers.append("marker")
225 |       .attr("id", `arrow-${i}`)
226 |       .attr("viewBox", "0 -5 10 10")
227 |       .attr("refX", d.refX) // Use the pre-calculated refX
228 |       .attr("refY", 0)
229 |       .attr("markerWidth", 10) // Adjust arrow size
230 |       .attr("markerHeight", 5) // Adjust arrow size
231 |       .attr("orient", "auto")
232 |       .append("path")
233 |       .attr("d", "M0,-5L10,0L0,5") // Arrow shape
234 |       .attr("fill", "#999")
235 |       .attr("stroke", "none");
236 |       });
237 | 
238 |       // Add links and use dynamically created markers
239 |       const link = svgGroup.append("g")
240 |       .attr("stroke", "#999")
241 |       .attr("stroke-opacity", 0.6)
242 |       // Binding and joining data
243 |       .selectAll("line")
244 |       .data(links)
245 |       .join("line")
246 |       // Styling the links
247 |       .attr("stroke-width", d => weightScale(d.weight || 1))
248 |       // Add arrow markers
249 |       .attr("marker-end", (d, i) => data.meta.directed ? `url(#arrow-${i})` : null)
250 | 
251 |       // Add hover interaction for edges
252 |       .on("mouseover", (event, d) => {
253 |       if (data.meta.type === "Keywords") {
254 |       // Generate content for the tooltip
255 |       const tooltipContent = `
256 |       <div class="metadata">From: ${d.source.name}</div>
257 |       <div class="metadata">To: ${d.target.name}</div>
258 |       <div class="metadata">Weight: ${d.weight || 'undefined'}</div>
259 |       `;
260 |       tooltip
261 |       .classed("hidden", false)
262 |       .html(tooltipContent)
263 |       .style("left", (event.pageX + 10) + "px")
264 |       .style("top", (event.pageY + 10) + "px");
265 |       }
266 |       })
267 |       .on("mouseout", () => {
268 |       tooltip.classed("hidden", true);
269 |       });
270 | 
271 |       // Add nodes
272 |       const node = svgGroup.append("g")
273 |       .attr("stroke", "none")
274 |       .selectAll("circle")
275 |       .data(nodes)
276 |       .join("circle")
277 |       .attr("r", d => isKeywordType ? 15 : radiusScale(d.degree))
278 |       .attr("fill", d => color(d.type))
279 |       .on("click", (event, d) => {
280 |       if (!isKeywordType) { // Only open hyperlink if isKeywordType is false
281 |       window.open(d.filename, "_blank");
282 |       }
283 |       })
284 |       .on("mouseover", (event, d) => {
285 |       // Check if the filename is an image or a PDF
286 |       const isImage = /\.(jpg|jpeg|png|gif|svg)$/i.test(d.filename);
287 |       const isPDF = /\.pdf$/i.test(d.filename);
288 |       // Generate tooltip content based on meta.type
289 |       const tooltipContent = data.meta.type === "Keywords"
290 |       ? `
291 |       <div class="title">${d.name}</div>
292 |       <div class="metadata">Degree: ${d.degree}</div>
293 |       `:
294 |       // Tooltip for other types
295 |       `
296 |       <div class="title">${d.name}</div>
297 |       <div class="metadata">ID: ${d.id.replace('T', '<span class="lighter">T</span>')}</div>
298 |       <div class="metadata">Degree: ${d.degree}, Backlinks: ${d.backlinks}</div>
299 |       <div class="metadata">Type: ${d.type}</div>
300 |       ${d.signature ? `<div class="metadata">Signature: ${d.signature}</div>` : ''}
301 |       <div class="keywords">${d.keywords && d.keywords.length > 0 ? d.keywords.map(keyword =>
302 |         `<span>${keyword}</span>`).join('') :
303 |         '<div class="metadata">No keywords</div>'}</div>
304 |       ${isImage
305 |       ? `<img src="${d.filename}" alt="${d.name}"
306 | 	  onload="if(this.naturalHeight > this.naturalWidth) this.style.maxHeight='500px';"
307 | 	  style="max-width: 100%; height: auto; margin-top: 10px;">`
308 |         : isPDF
309 |       ? `<iframe src="${d.filename}?toolbar=0&navpanes=0&scrollbar=0#view=FitH"
310 | 		 style="width: 100%; height: 500px; margin-top: 10px; border: none;"></iframe>`
311 |           : ''
312 |         }
313 |       `;
314 |     // Display the tooltip and set its initial content
315 |     tooltip
316 |         .classed("hidden", false)
317 |         .html(tooltipContent);
318 | 
319 |     // Calculate tooltip dimensions
320 |     const tooltipNode = tooltip.node();
321 |     const tooltipWidth = tooltipNode.offsetWidth;
322 |     const tooltipHeight = tooltipNode.offsetHeight;
323 | 
324 |     // Get viewport dimensions
325 |     const viewportWidth = window.innerWidth;
326 |     const viewportHeight = window.innerHeight;
327 | 
328 |     // Calculate mouse position
329 |     let tooltipX = event.pageX + 10; // Default offset
330 |     let tooltipY = event.pageY + 10;
331 | 
332 |     // Adjust position to fit within the viewport
333 |     if (tooltipX + tooltipWidth > viewportWidth) {
334 |         tooltipX = viewportWidth - tooltipWidth - 10; // Align with the right edge
335 |     }
336 |     if (tooltipY + tooltipHeight > viewportHeight) {
337 |         tooltipY = viewportHeight - tooltipHeight - 10; // Align with the bottom edge
338 |     }
339 | 
340 |     // Set tooltip position
341 |     tooltip
342 |         .style("left", `${tooltipX}px`)
343 |         .style("top", `${tooltipY}px`);
344 | })
345 | .on("mouseout", () => {
346 |     tooltip.classed("hidden", true);
347 | });
348 |       // Add drag behavior
349 |       node.call(d3.drag()
350 |       .on("start", dragstarted)
351 |       .on("drag", dragged)
352 |       .on("end", dragended));
353 | 
354 |       // Add labels for nodes with degree > minDegreeTag
355 |       const labels = svgGroup.append("g")
356 |       .selectAll("text")
357 |       .data(nodes.filter(d => d.degree > minDegreeTag)) // Filter nodes based on degree
358 |       .join("text")
359 |       .attr("dx", 10)
360 |       .attr("dy", ".35em")
361 |       .style("font-size", `${fontSize}px`)
362 |       .style("font-family", "sans-serif")
363 |       .style("fill", "#333")
364 |       .text(d => d.name);
365 | 
366 |       // Set up force simulation
367 |       const simulation = d3.forceSimulation(nodes)
368 |       .force("link", d3.forceLink(links).id(d => d.id).distance(20)) // Link force
369 |       .force("charge", d3.forceManyBody().strength(-20)) // Repel nodes
370 |       .force("center", d3.forceCenter(width / 2, height / 2)) // Centering force
371 |       .force("collide", d3.forceCollide(50)) // Spread out nodes
372 |       .force("x", d3.forceX(width / 2).strength(0.05)) // Keep nodes near center
373 |       .force("y", d3.forceY(height / 2).strength(0.05))
374 |       .on("tick", ticked);
375 | 
376 |       // Update positions on each tick
377 |       function ticked() {
378 |       link
379 |       .attr("x1", d => d.source.x)
380 |       .attr("y1", d => d.source.y)
381 |       .attr("x2", d => {
382 |       const dx = d.target.x - d.source.x;
383 |       const dy = d.target.y - d.source.y;
384 |       const distance = Math.sqrt(dx * dx + dy * dy) || 1; // Avoid division by zero
385 |       const targetRadius = isKeywordType ? 15 : radiusScale(d.target.degree);
386 |       const offsetX = (dx / distance) * targetRadius;
387 |       return d.target.x - offsetX;
388 |       })
389 |       .attr("y2", d => {
390 |       const dx = d.target.x - d.source.x;
391 |       const dy = d.target.y - d.source.y;
392 |       const distance = Math.sqrt(dx * dx + dy * dy) || 1; // Avoid division by zero
393 |       const targetRadius = radiusScale(d.target.degree); // Exact node radius
394 |       const offsetY = (dy / distance) * targetRadius;
395 |       return d.target.y - offsetY;
396 |       });
397 | 
398 |       node
399 |       .attr("cx", d => d.x)
400 |       .attr("cy", d => d.y);
401 | 
402 |       labels
403 |       .attr("x", d => d.x)
404 |       .attr("y", d => d.y);
405 |       }
406 | 
407 |       // Drag event handlers
408 |       function dragstarted(event) {
409 |       if (!event.active) simulation.alphaTarget(0.3).restart();
410 |       event.subject.fx = event.subject.x;
411 |       event.subject.fy = event.subject.y;
412 |       }
413 | 
414 |       function dragged(event) {
415 |       event.subject.fx = event.x;
416 |       event.subject.fy = event.y;
417 |       }
418 | 
419 |       function dragended(event) {
420 |       if (!event.active) simulation.alphaTarget(0);
421 |       event.subject.fx = null;
422 |       event.subject.fy = null;
423 |       }
424 | 
425 | 
426 |       const infoButton = document.getElementById("info-button");
427 |       const infoTooltip = document.querySelector(".info-tooltip");
428 | 
429 |       // Generate Tooltip Content
430 |       function generateTooltipContent() {
431 | 	  infoTooltip.innerHTML = "";
432 | 
433 | 	  // Add title
434 | 	  const title = document.createElement("div");
435 | 	  title.className = "title";
436 | 	  title.textContent = `Denote ${data.meta.type} Network`;
437 | 	  infoTooltip.appendChild(title);
438 | 
439 | 	  // Add metadata container
440 | 	  const metadataContainer = document.createElement("div");
441 | 	  metadataContainer.className = "metadata-container";
442 | 
443 | 	  if (data.meta.type === "Community") {
444 | 	      const graphParameter = document.createElement("div");
445 | 	      graphParameter.className = "metadata";
446 | 	      graphParameter.textContent = `Regular expression: "${data.meta.parameters[0]}"`;
447 | 	      metadataContainer.appendChild(graphParameter);
448 | 	  }
449 | 
450 | 	  if (data.meta.type === "Keywords") {
451 | 	      const graphParameter = document.createElement("div");
452 | 	      graphParameter.className = "metadata";
453 | 	      graphParameter.textContent = `Minimum links: ${data.meta.parameters}`;
454 | 	      metadataContainer.appendChild(graphParameter);
455 | 	  }
456 | 
457 | 	  if (data.meta.type === "Neighbourhood") {
458 | 	      const graphParameter = document.createElement("div");
459 | 	      graphParameter.className = "metadata";
460 | 
461 | 	      const rootLine = document.createElement("div");
462 | 	      rootLine.textContent = `Root: ${data.meta.parameters[0]}`;
463 | 	      rootLine.style.marginBottom = "5px";
464 | 	      graphParameter.appendChild(rootLine);
465 | 
466 | 	      const depthLine = document.createElement("div");
467 | 	      depthLine.textContent = `Depth: ${data.meta.parameters[1]}`;
468 | 	      graphParameter.appendChild(depthLine);
469 | 	      metadataContainer.appendChild(graphParameter);
470 | 	  }
471 | 
472 | 	  // Number of nodes
473 | 	  const nodeCount = document.createElement("div");
474 | 	  nodeCount.className = "metadata";
475 | 	  nodeCount.textContent = `${data.nodes.length} nodes`;
476 | 	  metadataContainer.appendChild(nodeCount);
477 | 
478 | 	  // Number of edges
479 | 	  const edgeCount = document.createElement("div");
480 | 	  edgeCount.className = "metadata";
481 | 	  edgeCount.textContent = `${data.edges.length} ${data.edges.length === 1 ? "edge" : "edges"}`;
482 | 	  metadataContainer.appendChild(edgeCount);
483 | 
484 | 	  // Network Density
485 | 	  const density = document.createElement("div");
486 | 	  density.className = "metadata";
487 | 	  const edges = data.edges.length;
488 | 	  const nodes = data.nodes.length;
489 | 	  if (nodes > 1) {
490 | 	      // Number of actual edges divided by the possible edges
491 | 	      const calculatedDensity = (2 * edges) / (nodes * (nodes - 1));
492 | 	      density.textContent = `Density: ${calculatedDensity.toFixed(3)}`;
493 | 	  } else {
494 | 	      density.textContent = "Density: N/A (insufficient nodes)";
495 | 	  }
496 | 	  metadataContainer.appendChild(density);
497 | 
498 | 	  infoTooltip.appendChild(metadataContainer);
499 | 
500 | 	  // Calculate the number of singular nodes
501 | 	  const singularNodeCount = data.nodes.filter(node => node.degree === 0).length;
502 | 
503 | 	  // Add a toggle button
504 | 	  if (data.meta.type === "Community" && singularNodeCount !== 0) {
505 | 	      const buttonContainer = document.createElement("div");
506 | 	      buttonContainer.className = "metadata-container";
507 | 
508 | 	      const toggleButton = document.createElement("button");
509 | 	      toggleButton.textContent = "Hide isolated nodes";
510 | 	      toggleButton.style.marginTop = "10px";
511 | 	      toggleButton.style.padding = "10px 20px";
512 | 	      toggleButton.style.borderRadius = "5px";
513 | 	      toggleButton.style.border = "1px solid #darkgrey";
514 | 	      toggleButton.style.backgroundColor = "darkgrey";
515 | 	      toggleButton.style.color = "white";
516 | 	      toggleButton.style.cursor = "pointer";
517 | 	      toggleButton.style.fontSize = "18px";
518 | 
519 | 	      // Toggle button click event
520 | 	      toggleButton.addEventListener("click", () => {
521 | 		  // Find all nodes with degree = 0
522 | 		  const isolatedNodes = d3.selectAll("circle")
523 | 			.filter(d => d.degree === 0);
524 | 
525 | 		  // Determine if they are currently visible
526 | 		  const isVisible = isolatedNodes.style("display") !== "none";
527 | 
528 | 		  // Toggle their visibility
529 | 		  isolatedNodes.style("display", isVisible ? "none" : "block");
530 | 
531 | 		  // Update the button text
532 | 		  toggleButton.textContent = isVisible ? "Show Isolated Nodes" : "Hide Isolated Nodes";
533 | 	      });
534 | 
535 | 	      // Create a comment element to display the count
536 | 	      const singularNodeComment = document.createElement("div");
537 | 	      singularNodeComment.className = "metadata";
538 | 	      singularNodeComment.textContent = `${singularNodeCount} isolated notes`;
539 | 
540 | 	      // Append this comment above the toggle button
541 | 	      buttonContainer.appendChild(singularNodeComment);
542 | 
543 | 	      buttonContainer.appendChild(toggleButton);
544 | 	      infoTooltip.appendChild(buttonContainer);
545 | 	  }
546 | 
547 | 
548 | 	  // Add legend container
549 | 	  const legendContainer = document.createElement("div");
550 | 	  legendContainer.className = "metadata-container";
551 | 	  legendContainer.style.marginTop = "10px";
552 | 
553 | 	  const legendTitle = document.createElement("div");
554 | 	  legendTitle.style.fontWeight = "bold";
555 | 	  legendTitle.style.marginBottom = "10px";
556 | 	  legendTitle.textContent = "File Types";
557 | 	  legendContainer.appendChild(legendTitle);
558 | 
559 | 	  // Generate legend and bar chart dynamically for non-keyword types
560 | 	  if (!isKeywordType) {
561 | 	      const typeCounts = data.nodes.reduce((acc, node) => {
562 | 		  acc[node.type] = (acc[node.type] || 0) + 1;
563 | 		  return acc;
564 | 	      }, {});
565 | 
566 | 	      const legendData = Object.entries(typeCounts).map(([type, count]) => ({
567 | 		  type,
568 | 		  count,
569 | 	      }));
570 | 
571 | 	      legendData.forEach((entry) => {
572 | 		  const legendItem = document.createElement("div");
573 | 		  legendItem.style.display = "flex";
574 | 		  legendItem.style.alignItems = "center";
575 | 		  legendItem.style.marginBottom = "5px";
576 | 
577 | 		  const colorBox = document.createElement("div");
578 | 		  colorBox.style.width = "15px";
579 | 		  colorBox.style.height = "15px";
580 | 		  colorBox.style.marginRight = "10px";
581 | 		  colorBox.style.backgroundColor = d3.{{d3-colourscheme}}[legendData.indexOf(entry)];
582 | 		  legendItem.appendChild(colorBox);
583 | 
584 | 		  const text = document.createElement("span");
585 | 		  text.style.fontSize = `${fontSize}px`;
586 | 		  text.textContent = `${entry.type} (${entry.count})`;
587 | 		  legendItem.appendChild(text);
588 | 
589 | 		  legendContainer.appendChild(legendItem);
590 | 	      });
591 | 
592 | 	      infoTooltip.appendChild(legendContainer);
593 | 
594 |       // Add keyword frequency chart container
595 |       const chartContainer = document.createElement("div");
596 |       chartContainer.className = "metadata-container"; // Match the metadata background style
597 |       chartContainer.style.marginTop = "10px"; // Add spacing between sections
598 | 
599 |       const chartTitle = document.createElement("div");
600 |       chartTitle.style.fontWeight = "bold";
601 |       chartTitle.style.marginBottom = "10px";
602 |       chartTitle.textContent = "Keywords";
603 |       chartContainer.appendChild(chartTitle);
604 | 
605 |       // Bar chart
606 |       const keywordCounts = data.nodes.reduce((acc, node) => {
607 |       (node.keywords || []).forEach((keyword) => {
608 |       acc[keyword] = (acc[keyword] || 0) + 1;
609 |       });
610 |       return acc;
611 |       }, {});
612 | 
613 |       const keywordData = Object.entries(keywordCounts).map(([keyword, count]) => ({
614 |       keyword,
615 |       count,
616 |       }));
617 | 
618 |       // Sort keywordData by count in descending order
619 |       keywordData.sort((a, b) => b.count - a.count);
620 | 
621 |       // Define constants
622 |       const barHeight = 20; // Height of each bar
623 |       const barSpacing = 5; // Space between bars
624 |       const chartWidth = 400;
625 |       const margin = { top: 20, right: 20, bottom: 30, left: 20 }; // Initial margins
626 | 
627 |       // Create a temporary SVG to measure label dimensions
628 |       const tempSVG = d3.select("body").append("svg").attr("class", "temp-svg");
629 | 
630 |       // Calculate max label width for y-axis
631 |       const maxYLabelWidth = d3.max(keywordData, (d) => {
632 |       const textElement = tempSVG
633 |       .append("text")
634 |       .attr("class", "temp-text")
635 |       .style("font-size", `${fontSize}px`)
636 |       .text(d.keyword);
637 |       const textWidth = textElement.node().getBBox().width;
638 |       textElement.remove();
639 |       return textWidth;
640 |       });
641 | 
642 |       // Calculate max label height for x-axis
643 |       const maxXLabelHeight = d3.max(keywordData, (d) => {
644 |       const textElement = tempSVG
645 |       .append("text")
646 |       .attr("class", "temp-text")
647 |       .style("font-size", `${fontSize}px`)
648 |       .text(d.count * 2);
649 |       const textHeight = textElement.node().getBBox().height;
650 |       textElement.remove();
651 |       return textHeight;
652 |       });
653 |       tempSVG.remove(); // Clean up the temporary SVG
654 | 
655 |       // Update margins dynamically
656 |       margin.left = maxYLabelWidth + 20; // Add padding
657 |       margin.bottom = maxXLabelHeight + 10; // Add padding
658 | 
659 |       // Compute chart height based on number of bars
660 |       const chartHeight = keywordData.length * (barHeight + barSpacing) + margin.top + margin.bottom;
661 | 
662 |       // Update scales
663 |       const x = d3
664 |       .scaleLinear()
665 |       .domain([0, d3.max(keywordData, (d) => d.count)])
666 |       .range([0, chartWidth - margin.left - margin.right]);
667 | 
668 |       const y = d3
669 |       .scaleBand()
670 |       .domain(keywordData.map((d) => d.keyword))
671 |       .range([0, keywordData.length * (barHeight + barSpacing)])
672 |       .padding(0.1); // Padding within the band
673 | 
674 |       // Create SVG
675 |       const chartSVG = d3
676 |       .select(chartContainer)
677 |       .append("svg")
678 |       .attr("width", chartWidth)
679 |       .attr("height", chartHeight);
680 | 
681 |       const chartGroup = chartSVG
682 |       .append("g")
683 |       .attr("transform", `translate(${margin.left}, ${margin.top})`);
684 | 
685 |       // Add bars
686 |       chartGroup
687 |       .selectAll(".bar")
688 |       .data(keywordData)
689 |       .enter()
690 |       .append("rect")
691 |       .attr("class", "bar")
692 |       .attr("x", 0)
693 |       .attr("y", (d, i) => i * (barHeight + barSpacing)) // Use index to calculate position
694 |       .attr("width", (d) => x(d.count))
695 |       .attr("height", barHeight)
696 |       .attr("fill", "lightgrey");
697 | 
698 |       // Add y-axis
699 |       chartGroup
700 |       .append("g")
701 |       .call(d3.axisLeft(y))
702 |       .selectAll("text")
703 |       .style("font-size", `${fontSize}px`);
704 | 
705 |       // Add x-axis
706 |       const maxValue = d3.max(keywordData, d => d.count); // Get the maximum value
707 |       chartGroup
708 |       .append("g")
709 |       .attr("transform", `translate(0, ${chartHeight - margin.top - margin.bottom})`)
710 |       .call(d3.axisBottom(x).tickValues([0, maxValue])) // Set tick values to only 0 and max
711 |       .selectAll("text")
712 |       .style("font-size", `${fontSize}px`);
713 | 
714 |       // Append the chart container to the tooltip or desired location
715 |       infoTooltip.appendChild(chartContainer);
716 |       }
717 |       }
718 | 
719 |       // Toggle tooltip visibility on button click
720 |       infoButton.addEventListener("click", () => {
721 |       if (infoTooltip.style.display === "block") {
722 |       infoTooltip.style.display = "none";
723 |       } else {
724 |       generateTooltipContent();
725 |       infoTooltip.style.display = "block";
726 |       }
727 | 
728 |       });
729 | 
730 | 
731 |       // Label density
732 |       // Add a slider element to the top-right corner
733 |       const sliderContainer = d3.select('body').append('div')
734 | 	    .style('position', 'fixed')
735 | 	    .style('top', '10px')
736 | 	    .style('right', '10px')
737 | 	    .style('z-index', '1000');
738 | 
739 |       sliderContainer.append('label')
740 |     .text('Label density: ')
741 |     .style('margin-right', '10px');
742 | 
743 |       const slider = sliderContainer.append('input')
744 | 	    .attr('type', 'range')
745 | 	    .attr('min', 0)
746 | 	    .attr('max', d3.max(nodes, d => d.degree))
747 | 	    .attr('value', minDegreeTag)
748 | 	    .style('width', '150px')
749 | 	    .on('input', function () {
750 | 		minDegreeTag = d3.max(nodes, d => d.degree) - +this.value;
751 | 		updateLabels();
752 | 	    });
753 | 
754 |       // Function to update labels based on the slider value
755 |       function updateLabels() {
756 | 	  labels = svgGroup.selectAll('text')
757 |               .data(nodes.filter(d => d.degree > minDegreeTag), d => d.id)
758 |               .join(
759 | 		  enter => enter.append('text')
760 |                       .attr('x', d => d.x)
761 |                       .attr('y', d => d.y)
762 |                       .attr('dx', 10)
763 |                       .attr('dy', '.35em')
764 |                       .style('font-size', `${fontSize}px`)
765 |                       .style('font-family', 'sans-serif')
766 |                       .style('fill', '#333')
767 |                       .text(d => d.name),
768 | 		  update => update.attr('x', d => d.x).attr('y', d => d.y),
769 | 		  exit => exit.remove()
770 |               );
771 | 	  simulation.alpha(1).restart();
772 |       }
773 | 
774 |     </script>
775 |   </body>
776 | </html>
777 | 


--------------------------------------------------------------------------------
/denote-explore.org:
--------------------------------------------------------------------------------
  1 | #+title: Denote Explorer: Explore your Denote digital garden
  2 | #+texinfo_dir_category: Emacs misc features
  3 | #+texinfo_dir_title: Denote Explorer: (denote-explore)
  4 | #+texinfo_dir_name: Denote Explorer
  5 | #+texinfo_dir_desc: Explore, visualise and analyse Denote files
  6 | #+texinfo_header: @set MAINTAINERSITE @uref{https://lucidmanager.org/tags/emacs,maintainer webpage}
  7 | #+texinfo_header: @set MAINTAINER Peter Prevos
  8 | #+texinfo_header: @set MAINTAINEREMAIL @email{peter@prevos.net}
  9 | #+texinfo_header: @set MAINTAINERCONTACT @uref{mailto:peter@prevos.net,contact the maintainer}
 10 | 
 11 | The Denote package by Protesilaos (Prot) Stavrou provides extensive functionality for creating, retrieving, managing, and linking files in plain text, Markdown, and Org Mode. The most redeeming qualities of this package are its filename convention and modular simplicity.
 12 | 
 13 | Due to its reliance on file names, you can also use the package to access other file types, such as PDFs or multimedia files (which we call Denote attachments). In this way, Denote becomes a fully-featured personal knowledge management system. 
 14 | 
 15 | The Denote-Explorer package came into existence as my collection of Denote files grew. I created some auxiliary functions to manage and explore my burgeoning Denote files, resulting in four types of commands:
 16 | 
 17 | 1. Descriptive statistics: Count notes, attachments and keywords.
 18 | 2. Random walks: Generate new ideas using serendipity.
 19 | 3. Janitor: Maintain your denote collection.
 20 | 4. Knowledge Graphs: Visualise and analyse your Denote files as a network.
 21 | 
 22 | * Descriptive Statistics
 23 | The Denote-Explorer package distinguishes between Denote files (notes) and attachments. Denote files are either Org Mode, Markdown, or Plain Text. All other files, such as photographs, PDFs, media files, LaTeX, and HTML, are attachments.
 24 | 
 25 | After a day of working hard on your digital knowledge garden, you can count the notes and attachments in your collection. Two functions provide some basic statistics of your Denote files:
 26 | 
 27 | 1. ~denote-explore-count-notes~: Count the number of notes and attachments. With universal argument, only count notes.
 28 | 2. ~denote-explore-count-keywords~: Count the number of distinct Denote keywords. 
 29 | 
 30 | These functions are informative, but a graph says more than a thousand numbers. The built-in =chart.el= package by Eric M. Ludlam is a quaint tool for creating bar charts in a plain text buffer. Two commands are available in Denote-Explorer to visualise basic statistics: 
 31 | 
 32 | 1. ~denote-explore-barchart-filetypes~: Visualise used file extensions. With universal argument =C-u= visualises only attachments.
 33 | 2. ~denote-explore-barchart-keywords~: Visualise the top-n keywords
 34 | 3. ~denote-explore-barchart-timeline~: Visualise notes created by year
 35 | 
 36 | The ~denote-excluded-files-regexp~ variable can contain a regular expression of files excluded from these statistical functions. 
 37 | 
 38 | * Random Walks
 39 | Creativity springs from a medley of experiences, emotions, subconscious musings, and connecting random ideas. Introducing random elements into the creative process generates avenues of thought you might not have travelled otherwise. Random walks through your notes can be beneficial when you're stuck in a rut or just like to walk through your files randomly.
 40 | 
 41 | A random walk is an arbitrary sequence without a defined relationship between the steps. You take a random walk by jumping to a random note, connected or unconnected to the current buffer.
 42 | 
 43 | The Denote-Explorer package provides three commands to inject some randomness into your explorations:
 44 | 
 45 | 1. ~denote-explore-random-note~: Jump to a random Denote file.
 46 | 2. ~denote-explore-random-regex~: Jump to a random Denote file that matches a regular expression.
 47 | 3. ~denote-explore-random-link~: Jump to a random linked note (either forward or backward) or attachments (forward only).
 48 | 4. ~denote-explore-random-keyword~: Jump to a random Denote file with the same selected keyword(s).
 49 | 5. ~denote-explore-random-signature~: Jump to a random Denote file with the same (partial) signature.
 50 | 
 51 | The default state is that these functions jump to any Denote text file (plain text, Markdown or Org-mode). Prefixing the universal argument (=C-u=) includes attachments in the sample for a random jump, otherwise the walk remains within the collection of notes. The ~denote-explore-random-regex-ignore~ variable can contain a regular expression of files excluded from the sample of files to jump to.
 52 | 
 53 | Jumping to a note that matches a regular expression lets you find random notes matching a search string. For example, to find a note you wrote in May 2022, use =^202205= and using =202305.*_journal= jumps to a random journal entry in May 2023.
 54 | 
 55 | Jumping to a randomly linked file naturally only works when the current buffer is a Denote file. A warning appears when the current buffer is an isolated note (no links or backlinks available).
 56 | 
 57 | When jumping to a random file with one or more matching keywords, you can choose one or more keywords from the current buffer, or override the completion options with free text. The asterisk symbol =*= selects all keywords in the completion list. This section process is skipped when the current buffer only has one keyword. When the current buffer is not a Denote file, you can choose any available keyword(s) in your Denote collection.
 58 | 
 59 | Jumping to a random note and matching multiple keywords only works when ~denote-sort-keywords~ is enabled, or when the selected keywords are in the same order as in the target file. You can alphabetise keywords in your Denote files with ~denote-explore-sort-keywords~, explained in the next section.
 60 | 
 61 | * Janitor
 62 | After hoarding Denote files for a while, you may need a janitor to organise your collection. A janitor ensures cleanliness, orderliness, and sanitation in a building, so this role is also perfect for managing to your Denote files. The Denote-Explorer package provides a series of commands to assist with cleaning, organising, and sanitising your files.
 63 | 
 64 | ** Duplicate notes
 65 | The Denote package prevents duplicate identifiers when creating a new note, but when assigning filenames manually, or when exporting org files, duplicates might appear.
 66 | 
 67 | The Denote identifier is a unique string constructed of the note's creation date and time in ISO 8601 format (e.g., =2024035T203312=). Denote either uses the current date and time when generating a new note or the date and time the file was created on the file system.
 68 | 
 69 | The file's creation date and time are not always relevant for attachments. For example, when adding scanned historical records, the identifier might be centuries ago, so it must be added manually.
 70 | 
 71 | The ~denote-explore-identify-duplicate-notes~ command lists all duplicate Denote files in a popup org buffer, which includes links to the suspected duplicate notes and attachments.
 72 | 
 73 | Additionally, the ~denote-explore-identify-duplicate-notes-dired~ command displays files with duplicate identifiers in a Dired buffer. You can directly change filenames in the Dired buffer with ~dired-toggle-read-only~ (=C-x C-q=) or remove individual duplicates with =D= (~dired-do-delete~). Note that this function only shows files in the denote directory and not its subdirectories or symbolic links.
 74 | 
 75 | With the universal argument (=C-u=), these commands ignore any duplicated identifiers created when exporting Denote Org mode files.
 76 | 
 77 | The ~denote-excluded-files-regexp~ variable can contain a regular expression of files excluded from duplicate detection. 
 78 | 
 79 | Be careful when manually changing the identifier of a Denote file, as it can destroy the integrity of your links. Please ensure that the file you rename does not have any links pointing to it. You can use the ~denote-find-link~ and ~denote-find-backlink~ commands to check a file for links, or use the Denote Explorer link checker.
 80 | 
 81 | ** Missing Links
 82 | The Denote identifier keeps links active even when you change the file name, tags or signature. But missing or dead links might still appear in your network of notes when you delete redundant information or you manually change an identifier.
 83 | 
 84 | Using ~denote-explore-missing-links~ lists all links to non-existing notes, attachments and links to other files (such as images) in your Denote directory.
 85 | 
 86 | This function creates a read-only Org mode file with two tables of source documents and the missing linked Denote file or other linked files. You can click on the links to jump to the source file at the missing link location and either remove or edit it. Links will appear in their literal form, i.e. =[[<link>][<description>]]=. You can toggle this behaviour with ~org-toggle-link-display~ to show the formatted links.
 87 | 
 88 | The link contains an Elisp function to open the linked document and find the relevant link. Emacs will ask for confirmation every time you follow such a link. You can disable these warnings by setting ~org-link-elisp-confirm-function~ to =nil=.
 89 | 
 90 | When the missing link is found because perhaps you already removed it, an error message pops up in the echo area.
 91 | 
 92 | The ~denote-excluded-files-regexp~ variable can contain a regular expression of files that are excluded from the search for missing Denote links.
 93 | 
 94 | ** Managing Keywords
 95 | Denote keywords connect notes with similar content. Denote explore provides a few commands to assist with managing your menagerie of keywords.
 96 | 
 97 | First step is to explore the keywords already being used in your collection of notes. The ~denote-explore-list-keywords~ command lists all used Denote keywords in a table, sorted by usage counts. Calling this function with the universal argument (=C-u=), sorts the list alphabetically. This command provides similar functionality to ~denote-explore-barchart-keywords~, but can show all keywords in one buffer. 
 98 | 
 99 | Keywords should not exist in solitude because a category with only one member is not informative. Single keywords can arise because topics need to be fully developed or due to a typo. The ~denote-explore-single-keywords~ command provides a list of file tags that are only used once. The list of single keywords is presented in the minibuffer, from where you can open the relevant note or attachment.
100 | 
101 | You can also find notes or attachments without keywords with the ~denote-explore-zero-keywords~ command. This command lists all notes and attachments without keywords in the minibuffer, so you can open them and consider adding keywords or leaving them as is.
102 | 
103 | You can rename or remove keywords with ~denote-explore-rename-keyword~. Select one or more existing keywords from the completion list and enter the new keyword. This function renames all chosen keywords or removes the original keyword from all existing notes when you enter an empty string as new keyword. This function cycles through all notes and attachments containing one or more selected keywords and asks for confirmation before making any changes. The new keyword list is stored alphabetically. This function uses the front matter as the source of truth for notes and the file name for attachments.
104 | 
105 | The ~denote-excluded-files-regexp~ variable can contain a regular expression of files that are excluded from the purview of these functions.
106 | 
107 | You can also visualise keywords using knowledge graphs described below.
108 | 
109 | ** Synchronising Meta Data
110 | Denote stores the metadata for each note in the filename using its ingenious format. Some of this metadata is copied to the front matter of a note, which can lead to discrepancies between the two metadata sources.
111 | 
112 | The ~denote-explore-sync-metadata~ function checks all notes and asks the user to rename any file where the front matter data differs from the file name. The front matter data is the source of truth for the title and keywords. This function also enforces the alphabetisation of keywords, which assists with finding notes.
113 | 
114 | The ~denote-excluded-files-regexp~ variable can contain a regular expression of files that are excluded from this synchronisation.
115 | 
116 | * Knowledge Graphs
117 | Emacs is a text processor with limited graphical capabilities. However, committing your ideas to text requires a linear way of thinking since you can only process one word at a time. Visual thinking through tools such as mind maps or network diagrams is another way to approach your ideas. One of the most common methods to visualise interlinked documents is in a network or a personal knowledge graph, or in more general terms, a network diagram.
118 | 
119 | ** Principles of Knowledge Graphs
120 | Denote implements a linking mechanism that connects notes (either Org, Markdown, or plain text files) to other notes or attachments. This mechanism allows the user to visualise all notes as a network diagram.
121 | 
122 | Network visualisation in Denote is not just a feature but a powerful tool that visualises how notes are linked, helping you discover previously unseen connections between your thoughts and enhancing your creative process.
123 | 
124 | It's important to note that Denote-Explorer does not offer live previews of your note collection. This deliberate choice prevents the 'dopamine traps' of seeing your thoughts develop in real-time. Instead, Denote-Explorer provides a focused tool for the surgical dissection of your second brain, while the main user interface remains text-based.
125 | 
126 | A network diagram has nodes (vertices) and edges. Each node represents a note or an attachment, and each edge represents a link between them. A link between file is directed and the arrow indicates the source and target of the link. The diagram below shows the basic principle of a knowledge graph. In the actual output, nodes are circles.
127 | 
128 | #+begin_example
129 | ┌──────────────┐        ┌──────────────┐
130 | │     node     │  edge  │     node     │
131 | │    (note)    ├───────►│    (note)    │
132 | │ (attachment) │ (link) │ (attachment) │
133 | └──────────────┘        └──────────────┘
134 | #+end_example
135 | 
136 | Denote-Explorer provides three types of network diagrams to explore the relationships between your thoughts:
137 | 
138 | 1. Community: Notes matching a regular expression
139 | 2. Neighbourhood: Search n-deep in a selected note
140 | 3. Sequence: Visualise a hierarchical sequence
141 | 4. Keywords: Relationships between keywords
142 | 
143 | The package exports and displays these in one of three formats, with JSON displayed in HTML / D3.js files as the default. Other options are GraphViz and GEXF.
144 | 
145 | You create a network with the ~denote-explore-network~ command. This command will ask the user to select the type of network to create. Each network type requires additional inputs to analyse to a defined part of your Denote files.
146 | 
147 | The ~denote-explore-network-regenerate~ command recreates the previous graph with the same parameters, which is useful when changing the structure of your notes and you like to see the result visualised without having to re-enter the parameters.
148 | 
149 | Using the universal argument =C-u= before issuing these two command (re)generates a network excluding attachments. The ~denote-excluded-files-regexp~ variable can contain a regular expression of files that are excluded from visualisation.
150 | 
151 | ** Community of Notes
152 | A community graph displays all notes matching a regular expression and their connections. The example below indicates the community that contains the =_emacs= regular expression, within the dashed line. The algorithm prunes any links to non-matching notes, which in the example below is the note with the =_vim= keyword.
153 | 
154 | #+begin_example
155 | ┌ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┐        
156 |    _emacs community        
157 | │ ┌──────┐  ┌──────┐ │  ┌────┐        
158 |   │_emacs│  │_emacs│───►│_vim│       
159 | │ └──┬───┘  └──────┘ │  └────┘        
160 |      │                       
161 | │    ▼               │        
162 |   ┌──────┐              
163 | │ │_emacs│           │
164 |   └──────┘            
165 | └ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┘        
166 | #+end_example
167 | 
168 | To generate a community graph, use ~denote-explore-network~, choose 'Community' and enter a regular expression. When no matching files are found or there are only solitary nodes, then the network is not generated and you will see this warning: =No Denote files or (back)links found for regex=.
169 | 
170 | The ~denote-explore-network-regex-ignore~ variable defines a regular expression to exclude certain notes from community networks. For example, if you create meta notes with long lists of dynamic links and they have the =_meta= keyword, then you could exclude these nodes by customising this variable to the relevant regular expression.
171 | 
172 | ** Note Neighbourhood
173 | The neighbourhood of a note consists of all files linked to it at one or more steps deep. The algorithm selects members of the graph from linked and back-linked notes. This visualisation effectively creates the possible paths you can follow with the ~denote-explore-random-link~ function discussed in the Random Walks section above.
174 | 
175 | The illustration below shows the principle of the linking depth. Notes B and C are at linking depth 1 from A and notes D and E are at depth 2 from A.
176 | 
177 | #+begin_example
178 | Depth 1      2
179 |      ┌─┐    ┌─┐ 
180 |   ┌─►│B│◄───┤D│ 
181 |   │  └─┘    └─┘ 
182 |  ┌┴┐            
183 |  │A│            
184 |  └─┘            
185 |   ▲  ┌─┐    ┌─┐ 
186 |   └──┤C├───►│E│ 
187 |      └─┘    └─┘
188 | #+end_example
189 | 
190 | To generate a neighbourhood graph from the current Denote note buffer, use ~denote-explore-network~ and enter the graph's depth. The user enters the required depth, and the software searches all notes linked to the current buffer at that depth. When building this graph from a buffer that is not a Denote file, the system also asks to select a source file (A in the diagram). The system issues a warning when you select a note without links or backlinks. You can identify Denote files without any links with the ~denote-explore-isolated-notes~ function describe above.
191 | 
192 | The complete set of your Denote files is most likely a disconnected Graph, meaning that there is no one path that connects all nodes. Firstly, there will be isolated notes. There will also exist isolated neighbourhoods of notes that connect to each other but not to other files.
193 | 
194 | A depth of more than three links is usually not informative because the network can become to large to read, or you hit the edges of your island of connected notes.
195 | 
196 | The ~denote-explore-network-regex-ignore~ variable lets you define a regular expression of notes exclude from neighbourhood networks. 
197 | 
198 | ** Sequences Network
199 | Denote signatures can define a hierarchical sequence of notes, using a family analogy. For example a note with signature =1=a= is the child of a note with signature =1= and a note with signature =1=b= is its sibling. The note with signature =1=a=1= is the child of =1=a= and the grandchild of =1=, and so forth. In a sequence network, links exist independent of any Denote links inside a note, the relationship is only based on the hierarchy of the signatures.
200 | 
201 | #+begin_example
202 | ┌─────┐    ┌─────┐    ┌─────┐  
203 | |  1  ├───►│ 1=a ├───►│1=a=1│ 
204 | └──┬──┘    └─────┘    └─────┘
205 |    │       ┌─────┐ 
206 |    └──────►│ 1=b │ 
207 |            └─────┘
208 | #+end_example
209 | 
210 | The content of the signatures can be either numbers or letters as the order of children is not taken into consideration. These sequences can go on to many generations, building a family tree of your notes. These sequences are the basic building block of the popular Zettelkasten methodology.
211 | 
212 | The Denote-Sequence package provides specialised functions to manage hierarchical connections between files, [[info:denote-sequence][info denote-sequence]]. 
213 | 
214 | To generate a sequence graph, use ~denote-explore-network~ and select the signature of the root node (note =1= in the diagram). When not selecting any signature, all Denote files with a signature are included in the visualisation.
215 | 
216 | The ~denote-explore-network-regex-ignore~ variable lets you define a regular expression of notes exclude from neighbourhood networks.
217 | 
218 | ** Keyword Network
219 | The last available method to visualise your Denote collection is to develop a network of keywords. Two keywords are connected when used in the same note.
220 | 
221 | All keywords in a note form a complete network. The union of all complete networks from all files in your Denote collection defines the keywords network. The relationship between two keywords can exist in multiple notes, so the links between keywords are weighted. The line thickness between two keywords indicates the frequency (weight) of their relationship.
222 | 
223 | While the first two graph types are directed (arrows indicate the direction of links), the keyword network is undirected. These links are bidirectional associations between keywords. The diagram below shows three notes, two with two keywords and one with three keywords. Each notes forms a small complete network that links all keywords.
224 | 
225 | #+begin_example
226 | ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐
227 | │_kwd1├─┤_kwd2│   │_kwd1├─┤_kwd2│   │_kwd3├─┤_kwd4│
228 | └─────┘ └─────┘   └─┬───┘ └───┬─┘   └─────┘ └─────┘
229 |                     │ ┌─────┐ │  
230 |                     └─┤_kwd3├─┘  
231 |                       └─────┘    
232 | #+end_example
233 | 
234 | The union of these three networks forms the keyword network for this collection of notes. The example generates the following keyword network.
235 | 
236 | #+begin_example
237 | ┌─────┐ ┌─────┐                                
238 | │_kwd1├─┤_kwd2│                                
239 | └─┬───┘ └───┬─┘                                
240 |   │         │                                  
241 |   │ ┌─────┐ │  ┌─────┐                         
242 |   └─┤_kwd3├─┴──┤_kwd4│                         
243 |     └─────┘    └─────┘                         
244 | #+end_example
245 | 
246 | When generating this graph type, you will need to enter a minimum edge weight (n). The graph then will only show those keywords that are at least n times associated with each other. The default is one.
247 | 
248 | Some keywords might have to be excluded from this graph because they skew the results. For example, when using the Citar-Denote package, you might like to exclude the =bib= keyword from the diagram because it is only used to minimise the search space for bibliographic notes and has no further semantic value. The ~denote-explore-network-keywords-ignore~ variable lists keywords ignored in this visualisation.
249 | 
250 | ** Network Layout and Presentation
251 | Emacs cannot independently generate graphics and thus relies on external software. This package can use three external mechanisms to create graphs (configurable with ~denote-explore-network-format~), set to D3.js / JSON output by default. Other available formats are GraphViz SVG and GEXF, discussed in detail below.
252 | 
253 | The Denote-Explorer network algorithm consists of four steps:
254 | 
255 | 1. The ~denote-explore-network~ function determines the relevant functions based on user input.
256 | 2. The code generates a nested association list for the selected graph:
257 |    - Metadata e.g.: =(meta (directed . t) (type . "Neighbourhood") (parameters "20210104T194405" 2))=
258 |    - Association list of nodes, e.g., =(((id . "20210104T194405") (name . "Platonic Solids") (keywords "geometry" "esotericism") (type . "org") (degree . 4)) ...)=. In the context of Denote, the degree of a network node is the unweighted sum of links and backlinks in a note. 
259 |    - Association list of edges and their weights: =(((source . "20220529T190246") (target . "20201229T143000") (weight . 1)) ...)=. The weight of an edge indicates the number of time the two files are linked, or the number of times two keywords appear in the same note in case of a keyword graph.
260 | 3. The package encodes the association list to a either a JSON, GraphViz DOT, or GEXF file. The location and name of this file is configurable with the  ~denote-explore-network-directory~ and ~denote-explore-network-filename~ variables.
261 | 4. Relevant external software displays the result (in most cases a web browser).
262 | 
263 | ** D3.js
264 | [[https://d3js.org/][D3.js]] is a JavaScript library for visualising data. This method provides an aesthetically pleasing and interactive view of the structure of your notes. Denote-Explorer stores the desired network as a JSON file. This JSON file is merged with a HTML / JavaScript template to visualise the network. Emacs invokes your default internet browser to view the network. 
265 | 
266 | Hover over any node to reveal its name and relevant metadata. For neighbourhood and community graphs, when the note is an image or PDF file, a preview appears in the tooltip. Clicking on a node opens the relevant file in the browser, or whatever application the browser associates with the relevant file type.
267 | 
268 | For community and neighbourhood graphs, the diameter of nodes is proportional to their degree. Thus, the most linked note in your query will be the most visible. The colours indicate the file type of each node. The size of nodes in a network graph is the same for all.
269 | 
270 | For nodes with a degree greater than two, the name is displayed outside the node.
271 | 
272 | In keyword graphs, the thickness of the edges indicates the number of times two keywords are associated with each other.
273 | 
274 | The info button shows the type of network and provides some basic statistics, such as the number of nodes (files) and edges (links) and the network density. The density of a network is the ratio between the number of edges and the potential number of edges. A density of zero, as such means that no nodes are connected. In a network with a density of one all nodes are connected to each other.
275 | 
276 | For community graphs the panel also provides the option to show or hide isolated nodes to increase clarity. Neighbourhood and keyword graphs by their definition do not have isolated nodes.
277 | 
278 | For community and neighbourhood graphs, the info panel also shows the distribution of keywords for the visualised network.
279 | 
280 | You can customise the output of the network files by modifying the template. The ~denote-explore-network-d3-template~ variable contains the location of the HTML/JavaScript template file so you can craft your own versions. This file contains several shortcodes:
281 | 
282 | - ={{graph-type}}=: Type of graph, community, neighbourhood or network
283 | - ={{d3-js}}=: Content of the ~denote-explore-network-d3-js~ variable, which contains the URL of the D3 source code, which has to be version 7 or above. The default template fetches the JavaScript code from the =d3js.org= website. You can customise this variable to use a locally stored file.
284 | - ={{json-content}}=: The generated JSON file with the network definition
285 | - ={{d3-colourscheme}}=: Content of ~denote-explore-network-d3-colours~. this variable assigns a colour palette for the node file types. You can choose between any of the available categorical colour schemes in the D3 package. Colours are assigned in the graph in order of appearance in the JSON file, so file types can have different colours in different graphs.
286 | 
287 | ** GraphViz
288 | [[https://graphviz.org/][GraphViz]] is an open-source graph visualisation software toolkit, ideal for this task. The Denote-Explorer software saves the graph in the DOT language as a =.gv= file. The GraphViz software converts the DOT code to an =SVG= file.
289 | 
290 | You will need to install GraphViz to enable this functionality. Denote-Explorer will raise an error when trying to create a GraphViz graph without the required external software available.
291 | 
292 | Hover over any node to reveal its name and relevant metadata. Clicking on any node in a community or neighbourhood graph opens the relevant file in the browser, or whatever application the browser associates with the relevant file type.
293 | 
294 | For community and neighbourhood graphs, the diameter of nodes is proportional to their degree. Thus, the most linked note in your query will be the most visible. When generating a neighbourhood, the source node is marked in a contrasting colour.
295 | 
296 | For nodes with a degree greater than two, the name is displayed outside the node. In keyword graphs, the thickness of the edges indicates the number of times two keywords are associated with each other.
297 | 
298 | The diameter of nodes are sized relative to their degree. Thus, the most referenced note in your system will be the most visible. For nodes with a degree greater than two, the name is displayed outside the node (top left). 
299 | 
300 | The configurable ~denote-explore-network-graphviz-header~ variable defines the basic settings for GraphViz graphs, such as the layout method and default node and edge settings.
301 | 
302 | The ~denote-explore-network-graphviz-filetype~ variable defines the GraphViz output format. SVG (the default) or PDF provide the best results.
303 | 
304 | ** Graph Exchange XML Format
305 | The first two formats an insight into parts of your knowledge network, but there is a lot more you can do with this type of information. While GraphViz and D3 are suitable for analysing sections of your network, this third option is ideal for storing the complete Denote network for further analysis.
306 | 
307 | Graph Exchange XML Format (=GEXF=) is a language for describing complex network structures. This option saves the network as a =GEXF= file without opening it in external software. 
308 | 
309 | To save the whole network, use the Community option and enter an empty search string to include all files.
310 | 
311 | You can analyse the exported file with [[https://gephi.org/gephi-lite/][Gephi Lite]], a free online network analysis tool. The =GEXF= file only contains the IDs, names and degree of the nodes; and the edges and their weights. 
312 | 
313 | ** Analysing the Denote Network
314 | A well-trodden trope in network analysis is that all people are linked within six degrees of separation. This may also be the case for your notes, but digging more than three layers deep is not very informative as the network can become large and difficult to review.
315 | 
316 | It might seem that adding more connections between your notes improves them, but this is not necessarily the case. The extreme case is a complete network where every file links to every other file. This situation lacks any interesting structure and wouldn't be informative. So, be mindful of your approach to linking notes and attachments.
317 | 
318 | Your Denote network is unlikely to be a fully connected graph. In a connected graph, there is a path from any point to any other point. Within the context of Denote, this means that all files have at least one link or backlink. Your network will most likely have isolated nodes (files without any (back)links) and islands of connected notes.
319 | 
320 | The previously mentioned ~denote-explore-isolated-files~ command lists all files without any links and backlinks to and from the note in the minibuffer. You can select any note and add links as required to release it from isolation. Calling this function with the universal argument =C-u= includes attachments in the list of lonely files. You can configure the behaviour of this function by customising ~denote-explore-isolated-ignore-keywords~. This variable provides a list of keywords to ignore when identifying isolated notes.
321 | 
322 | The number of links and backlinks in a file (in mathematical terms, edges connected to a node) is the total degree of a node. The degree distribution of a network is the probability distribution of these degrees over the whole network. The ~denote-explore-barchart-degree~ function uses the built-in chart package to display a simple bar chart of the frequency of the total degree.
323 | 
324 | This function might take a moment to run, depending on the number of notes in your system. Evaluating this function with the universal argument =C-u= excludes attachments from the analysis.
325 | 
326 | The importance of a note is directly related to the number of backlinks. The ~denote-explore-barchart-backlinks~ function visualises the number of backlinks in the top-n notes in a horizontal bar chart, ordered by the number of backlinks. This function asks for the number of nodes to visualise and then analyses the complete network of Denote notes (attachments are excluded because they don't have links from them), which can take a brief moment.
327 | 
328 | * Installation and Package Configuration
329 | This package is available from GitHub or through MELPA.
330 | 
331 | The configuration below customises all available variables and binds all available commands to the =C-c e= prefix. To get started you don't need to configure anything. You should modify this configuration to suit your needs, as one person's sensible defaults are another person's nightmare.
332 | 
333 | #+begin_src elisp
334 |   (use-package denote-explore
335 |     :custom
336 |     ;; Where to store network data and in which format
337 |     (denote-explore-network-directory "<folder>")
338 |     (denote-explore-network-filename "denote-network")
339 |     (denote-explore-network-keywords-ignore "<keywords list>")
340 |     (denote-explore-network-regex-ignore "<regex>")
341 |     (denote-explore-network-format 'd3.js)
342 |     (denote-explore-network-d3-colours 'SchemeObservable10)
343 |     (denote-explore-network-d3-js "https://d3js.org/d3.v7.min.js")
344 |     (denote-explore-network-d3-template "<file path>")
345 |     (denote-explore-network-graphviz-header "<header strings>")
346 |     (denote-explore-network-graphviz-filetype 'svg)
347 |     :bind
348 |     (;; Statistics
349 |      ("C-c e s n" . denote-explore-count-notes)
350 |      ("C-c e s k" . denote-explore-count-keywords)
351 |      ("C-c e s e" . denote-explore-barchart-filetypes)
352 |      ("C-c e s w" . denote-explore-barchart-keywords)
353 |      ("C-c e s t" . denote-explore-barchart-timeline)
354 |      ;; Random walks
355 |      ("C-c e w n" . denote-explore-random-note)
356 |      ("C-c e w r" . denote-explore-random-regex)
357 |      ("C-c e w l" . denote-explore-random-link)
358 |      ("C-c e w k" . denote-explore-random-keyword)
359 |      ;; Denote Janitor
360 |      ("C-c e j d" . denote-explore-duplicate-notes)
361 |      ("C-c e j D" . denote-explore-duplicate-notes-dired)
362 |      ("C-c e j l" . denote-explore-dead-links)
363 |      ("C-c e j z" . denote-explore-zero-keywords)
364 |      ("C-c e j s" . denote-explore-single-keywords)
365 |      ("C-c e j r" . denote-explore-rename-keywords)
366 |      ("C-c e j y" . denote-explore-sync-metadata)
367 |      ("C-c e j i" . denote-explore-isolated-files)
368 |      ;; Visualise denote
369 |      ("C-c e n" . denote-explore-network)
370 |      ("C-c e r" . denote-explore-network-regenerate)
371 |      ("C-c e d" . denote-explore-barchart-degree)
372 |      ("C-c e b" . denote-explore-barchart-backlinks)))
373 | #+end_src
374 | 
375 | You can use the most recent development version directly from GitHub (Emacs 29.1 or higher):
376 | 
377 | #+begin_src elisp
378 |   (unless (package-installed-p 'denote-explore)
379 |     (package-vc-install
380 |      '(denote-explore
381 |        :url "https://github.com/pprevos/denote-explore/")))
382 | #+end_src
383 | 
384 | * Acknowledgements
385 | This code would only have existed with the help of Protesilaos Stavrou, developer of Denote.
386 | 
387 | In addition, Jakub Szczerbowski, Samuel W. Flint, Ad (skissue), Vedang Manerikar, Jousimies, Alexis Praga, Dav1d23 and Quijote Libre made significant contributions and suggestions.
388 | 
389 | Noor Us Sabah on Fiverr wrote the first version of the D3.JS template file. All enhancements were generated with the assistance of ChatGPT.
390 | 
391 | Feel free to raise an issue here on GitHub if you have any questions or find bugs or suggestions for enhanced functionality.
392 | 
393 | * License
394 | This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License or (at your option) any later version.
395 | 
396 | This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY, INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
397 | 
398 | For a full copy of the GNU General Public License, see <https://www.gnu.org/licenses/>.
399 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
  1 |                     GNU GENERAL PUBLIC LICENSE
  2 |                        Version 3, 29 June 2007
  3 | 
  4 |  Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  5 |  Everyone is permitted to copy and distribute verbatim copies
  6 |  of this license document, but changing it is not allowed.
  7 | 
  8 |                             Preamble
  9 | 
 10 |   The GNU General Public License is a free, copyleft license for
 11 | software and other kinds of works.
 12 | 
 13 |   The licenses for most software and other practical works are designed
 14 | to take away your freedom to share and change the works.  By contrast,
 15 | the GNU General Public License is intended to guarantee your freedom to
 16 | share and change all versions of a program--to make sure it remains free
 17 | software for all its users.  We, the Free Software Foundation, use the
 18 | GNU General Public License for most of our software; it applies also to
 19 | any other work released this way by its authors.  You can apply it to
 20 | your programs, too.
 21 | 
 22 |   When we speak of free software, we are referring to freedom, not
 23 | price.  Our General Public Licenses are designed to make sure that you
 24 | have the freedom to distribute copies of free software (and charge for
 25 | them if you wish), that you receive source code or can get it if you
 26 | want it, that you can change the software or use pieces of it in new
 27 | free programs, and that you know you can do these things.
 28 | 
 29 |   To protect your rights, we need to prevent others from denying you
 30 | these rights or asking you to surrender the rights.  Therefore, you have
 31 | certain responsibilities if you distribute copies of the software, or if
 32 | you modify it: responsibilities to respect the freedom of others.
 33 | 
 34 |   For example, if you distribute copies of such a program, whether
 35 | gratis or for a fee, you must pass on to the recipients the same
 36 | freedoms that you received.  You must make sure that they, too, receive
 37 | or can get the source code.  And you must show them these terms so they
 38 | know their rights.
 39 | 
 40 |   Developers that use the GNU GPL protect your rights with two steps:
 41 | (1) assert copyright on the software, and (2) offer you this License
 42 | giving you legal permission to copy, distribute and/or modify it.
 43 | 
 44 |   For the developers' and authors' protection, the GPL clearly explains
 45 | that there is no warranty for this free software.  For both users' and
 46 | authors' sake, the GPL requires that modified versions be marked as
 47 | changed, so that their problems will not be attributed erroneously to
 48 | authors of previous versions.
 49 | 
 50 |   Some devices are designed to deny users access to install or run
 51 | modified versions of the software inside them, although the manufacturer
 52 | can do so.  This is fundamentally incompatible with the aim of
 53 | protecting users' freedom to change the software.  The systematic
 54 | pattern of such abuse occurs in the area of products for individuals to
 55 | use, which is precisely where it is most unacceptable.  Therefore, we
 56 | have designed this version of the GPL to prohibit the practice for those
 57 | products.  If such problems arise substantially in other domains, we
 58 | stand ready to extend this provision to those domains in future versions
 59 | of the GPL, as needed to protect the freedom of users.
 60 | 
 61 |   Finally, every program is threatened constantly by software patents.
 62 | States should not allow patents to restrict development and use of
 63 | software on general-purpose computers, but in those that do, we wish to
 64 | avoid the special danger that patents applied to a free program could
 65 | make it effectively proprietary.  To prevent this, the GPL assures that
 66 | patents cannot be used to render the program non-free.
 67 | 
 68 |   The precise terms and conditions for copying, distribution and
 69 | modification follow.
 70 | 
 71 |                        TERMS AND CONDITIONS
 72 | 
 73 |   0. Definitions.
 74 | 
 75 |   "This License" refers to version 3 of the GNU General Public License.
 76 | 
 77 |   "Copyright" also means copyright-like laws that apply to other kinds of
 78 | works, such as semiconductor masks.
 79 | 
 80 |   "The Program" refers to any copyrightable work licensed under this
 81 | License.  Each licensee is addressed as "you".  "Licensees" and
 82 | "recipients" may be individuals or organizations.
 83 | 
 84 |   To "modify" a work means to copy from or adapt all or part of the work
 85 | in a fashion requiring copyright permission, other than the making of an
 86 | exact copy.  The resulting work is called a "modified version" of the
 87 | earlier work or a work "based on" the earlier work.
 88 | 
 89 |   A "covered work" means either the unmodified Program or a work based
 90 | on the Program.
 91 | 
 92 |   To "propagate" a work means to do anything with it that, without
 93 | permission, would make you directly or secondarily liable for
 94 | infringement under applicable copyright law, except executing it on a
 95 | computer or modifying a private copy.  Propagation includes copying,
 96 | distribution (with or without modification), making available to the
 97 | public, and in some countries other activities as well.
 98 | 
 99 |   To "convey" a work means any kind of propagation that enables other
100 | parties to make or receive copies.  Mere interaction with a user through
101 | a computer network, with no transfer of a copy, is not conveying.
102 | 
103 |   An interactive user interface displays "Appropriate Legal Notices"
104 | to the extent that it includes a convenient and prominently visible
105 | feature that (1) displays an appropriate copyright notice, and (2)
106 | tells the user that there is no warranty for the work (except to the
107 | extent that warranties are provided), that licensees may convey the
108 | work under this License, and how to view a copy of this License.  If
109 | the interface presents a list of user commands or options, such as a
110 | menu, a prominent item in the list meets this criterion.
111 | 
112 |   1. Source Code.
113 | 
114 |   The "source code" for a work means the preferred form of the work
115 | for making modifications to it.  "Object code" means any non-source
116 | form of a work.
117 | 
118 |   A "Standard Interface" means an interface that either is an official
119 | standard defined by a recognized standards body, or, in the case of
120 | interfaces specified for a particular programming language, one that
121 | is widely used among developers working in that language.
122 | 
123 |   The "System Libraries" of an executable work include anything, other
124 | than the work as a whole, that (a) is included in the normal form of
125 | packaging a Major Component, but which is not part of that Major
126 | Component, and (b) serves only to enable use of the work with that
127 | Major Component, or to implement a Standard Interface for which an
128 | implementation is available to the public in source code form.  A
129 | "Major Component", in this context, means a major essential component
130 | (kernel, window system, and so on) of the specific operating system
131 | (if any) on which the executable work runs, or a compiler used to
132 | produce the work, or an object code interpreter used to run it.
133 | 
134 |   The "Corresponding Source" for a work in object code form means all
135 | the source code needed to generate, install, and (for an executable
136 | work) run the object code and to modify the work, including scripts to
137 | control those activities.  However, it does not include the work's
138 | System Libraries, or general-purpose tools or generally available free
139 | programs which are used unmodified in performing those activities but
140 | which are not part of the work.  For example, Corresponding Source
141 | includes interface definition files associated with source files for
142 | the work, and the source code for shared libraries and dynamically
143 | linked subprograms that the work is specifically designed to require,
144 | such as by intimate data communication or control flow between those
145 | subprograms and other parts of the work.
146 | 
147 |   The Corresponding Source need not include anything that users
148 | can regenerate automatically from other parts of the Corresponding
149 | Source.
150 | 
151 |   The Corresponding Source for a work in source code form is that
152 | same work.
153 | 
154 |   2. Basic Permissions.
155 | 
156 |   All rights granted under this License are granted for the term of
157 | copyright on the Program, and are irrevocable provided the stated
158 | conditions are met.  This License explicitly affirms your unlimited
159 | permission to run the unmodified Program.  The output from running a
160 | covered work is covered by this License only if the output, given its
161 | content, constitutes a covered work.  This License acknowledges your
162 | rights of fair use or other equivalent, as provided by copyright law.
163 | 
164 |   You may make, run and propagate covered works that you do not
165 | convey, without conditions so long as your license otherwise remains
166 | in force.  You may convey covered works to others for the sole purpose
167 | of having them make modifications exclusively for you, or provide you
168 | with facilities for running those works, provided that you comply with
169 | the terms of this License in conveying all material for which you do
170 | not control copyright.  Those thus making or running the covered works
171 | for you must do so exclusively on your behalf, under your direction
172 | and control, on terms that prohibit them from making any copies of
173 | your copyrighted material outside their relationship with you.
174 | 
175 |   Conveying under any other circumstances is permitted solely under
176 | the conditions stated below.  Sublicensing is not allowed; section 10
177 | makes it unnecessary.
178 | 
179 |   3. Protecting Users' Legal Rights From Anti-Circumvention Law.
180 | 
181 |   No covered work shall be deemed part of an effective technological
182 | measure under any applicable law fulfilling obligations under article
183 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or
184 | similar laws prohibiting or restricting circumvention of such
185 | measures.
186 | 
187 |   When you convey a covered work, you waive any legal power to forbid
188 | circumvention of technological measures to the extent such circumvention
189 | is effected by exercising rights under this License with respect to
190 | the covered work, and you disclaim any intention to limit operation or
191 | modification of the work as a means of enforcing, against the work's
192 | users, your or third parties' legal rights to forbid circumvention of
193 | technological measures.
194 | 
195 |   4. Conveying Verbatim Copies.
196 | 
197 |   You may convey verbatim copies of the Program's source code as you
198 | receive it, in any medium, provided that you conspicuously and
199 | appropriately publish on each copy an appropriate copyright notice;
200 | keep intact all notices stating that this License and any
201 | non-permissive terms added in accord with section 7 apply to the code;
202 | keep intact all notices of the absence of any warranty; and give all
203 | recipients a copy of this License along with the Program.
204 | 
205 |   You may charge any price or no price for each copy that you convey,
206 | and you may offer support or warranty protection for a fee.
207 | 
208 |   5. Conveying Modified Source Versions.
209 | 
210 |   You may convey a work based on the Program, or the modifications to
211 | produce it from the Program, in the form of source code under the
212 | terms of section 4, provided that you also meet all of these conditions:
213 | 
214 |     a) The work must carry prominent notices stating that you modified
215 |     it, and giving a relevant date.
216 | 
217 |     b) The work must carry prominent notices stating that it is
218 |     released under this License and any conditions added under section
219 |     7.  This requirement modifies the requirement in section 4 to
220 |     "keep intact all notices".
221 | 
222 |     c) You must license the entire work, as a whole, under this
223 |     License to anyone who comes into possession of a copy.  This
224 |     License will therefore apply, along with any applicable section 7
225 |     additional terms, to the whole of the work, and all its parts,
226 |     regardless of how they are packaged.  This License gives no
227 |     permission to license the work in any other way, but it does not
228 |     invalidate such permission if you have separately received it.
229 | 
230 |     d) If the work has interactive user interfaces, each must display
231 |     Appropriate Legal Notices; however, if the Program has interactive
232 |     interfaces that do not display Appropriate Legal Notices, your
233 |     work need not make them do so.
234 | 
235 |   A compilation of a covered work with other separate and independent
236 | works, which are not by their nature extensions of the covered work,
237 | and which are not combined with it such as to form a larger program,
238 | in or on a volume of a storage or distribution medium, is called an
239 | "aggregate" if the compilation and its resulting copyright are not
240 | used to limit the access or legal rights of the compilation's users
241 | beyond what the individual works permit.  Inclusion of a covered work
242 | in an aggregate does not cause this License to apply to the other
243 | parts of the aggregate.
244 | 
245 |   6. Conveying Non-Source Forms.
246 | 
247 |   You may convey a covered work in object code form under the terms
248 | of sections 4 and 5, provided that you also convey the
249 | machine-readable Corresponding Source under the terms of this License,
250 | in one of these ways:
251 | 
252 |     a) Convey the object code in, or embodied in, a physical product
253 |     (including a physical distribution medium), accompanied by the
254 |     Corresponding Source fixed on a durable physical medium
255 |     customarily used for software interchange.
256 | 
257 |     b) Convey the object code in, or embodied in, a physical product
258 |     (including a physical distribution medium), accompanied by a
259 |     written offer, valid for at least three years and valid for as
260 |     long as you offer spare parts or customer support for that product
261 |     model, to give anyone who possesses the object code either (1) a
262 |     copy of the Corresponding Source for all the software in the
263 |     product that is covered by this License, on a durable physical
264 |     medium customarily used for software interchange, for a price no
265 |     more than your reasonable cost of physically performing this
266 |     conveying of source, or (2) access to copy the
267 |     Corresponding Source from a network server at no charge.
268 | 
269 |     c) Convey individual copies of the object code with a copy of the
270 |     written offer to provide the Corresponding Source.  This
271 |     alternative is allowed only occasionally and noncommercially, and
272 |     only if you received the object code with such an offer, in accord
273 |     with subsection 6b.
274 | 
275 |     d) Convey the object code by offering access from a designated
276 |     place (gratis or for a charge), and offer equivalent access to the
277 |     Corresponding Source in the same way through the same place at no
278 |     further charge.  You need not require recipients to copy the
279 |     Corresponding Source along with the object code.  If the place to
280 |     copy the object code is a network server, the Corresponding Source
281 |     may be on a different server (operated by you or a third party)
282 |     that supports equivalent copying facilities, provided you maintain
283 |     clear directions next to the object code saying where to find the
284 |     Corresponding Source.  Regardless of what server hosts the
285 |     Corresponding Source, you remain obligated to ensure that it is
286 |     available for as long as needed to satisfy these requirements.
287 | 
288 |     e) Convey the object code using peer-to-peer transmission, provided
289 |     you inform other peers where the object code and Corresponding
290 |     Source of the work are being offered to the general public at no
291 |     charge under subsection 6d.
292 | 
293 |   A separable portion of the object code, whose source code is excluded
294 | from the Corresponding Source as a System Library, need not be
295 | included in conveying the object code work.
296 | 
297 |   A "User Product" is either (1) a "consumer product", which means any
298 | tangible personal property which is normally used for personal, family,
299 | or household purposes, or (2) anything designed or sold for incorporation
300 | into a dwelling.  In determining whether a product is a consumer product,
301 | doubtful cases shall be resolved in favor of coverage.  For a particular
302 | product received by a particular user, "normally used" refers to a
303 | typical or common use of that class of product, regardless of the status
304 | of the particular user or of the way in which the particular user
305 | actually uses, or expects or is expected to use, the product.  A product
306 | is a consumer product regardless of whether the product has substantial
307 | commercial, industrial or non-consumer uses, unless such uses represent
308 | the only significant mode of use of the product.
309 | 
310 |   "Installation Information" for a User Product means any methods,
311 | procedures, authorization keys, or other information required to install
312 | and execute modified versions of a covered work in that User Product from
313 | a modified version of its Corresponding Source.  The information must
314 | suffice to ensure that the continued functioning of the modified object
315 | code is in no case prevented or interfered with solely because
316 | modification has been made.
317 | 
318 |   If you convey an object code work under this section in, or with, or
319 | specifically for use in, a User Product, and the conveying occurs as
320 | part of a transaction in which the right of possession and use of the
321 | User Product is transferred to the recipient in perpetuity or for a
322 | fixed term (regardless of how the transaction is characterized), the
323 | Corresponding Source conveyed under this section must be accompanied
324 | by the Installation Information.  But this requirement does not apply
325 | if neither you nor any third party retains the ability to install
326 | modified object code on the User Product (for example, the work has
327 | been installed in ROM).
328 | 
329 |   The requirement to provide Installation Information does not include a
330 | requirement to continue to provide support service, warranty, or updates
331 | for a work that has been modified or installed by the recipient, or for
332 | the User Product in which it has been modified or installed.  Access to a
333 | network may be denied when the modification itself materially and
334 | adversely affects the operation of the network or violates the rules and
335 | protocols for communication across the network.
336 | 
337 |   Corresponding Source conveyed, and Installation Information provided,
338 | in accord with this section must be in a format that is publicly
339 | documented (and with an implementation available to the public in
340 | source code form), and must require no special password or key for
341 | unpacking, reading or copying.
342 | 
343 |   7. Additional Terms.
344 | 
345 |   "Additional permissions" are terms that supplement the terms of this
346 | License by making exceptions from one or more of its conditions.
347 | Additional permissions that are applicable to the entire Program shall
348 | be treated as though they were included in this License, to the extent
349 | that they are valid under applicable law.  If additional permissions
350 | apply only to part of the Program, that part may be used separately
351 | under those permissions, but the entire Program remains governed by
352 | this License without regard to the additional permissions.
353 | 
354 |   When you convey a copy of a covered work, you may at your option
355 | remove any additional permissions from that copy, or from any part of
356 | it.  (Additional permissions may be written to require their own
357 | removal in certain cases when you modify the work.)  You may place
358 | additional permissions on material, added by you to a covered work,
359 | for which you have or can give appropriate copyright permission.
360 | 
361 |   Notwithstanding any other provision of this License, for material you
362 | add to a covered work, you may (if authorized by the copyright holders of
363 | that material) supplement the terms of this License with terms:
364 | 
365 |     a) Disclaiming warranty or limiting liability differently from the
366 |     terms of sections 15 and 16 of this License; or
367 | 
368 |     b) Requiring preservation of specified reasonable legal notices or
369 |     author attributions in that material or in the Appropriate Legal
370 |     Notices displayed by works containing it; or
371 | 
372 |     c) Prohibiting misrepresentation of the origin of that material, or
373 |     requiring that modified versions of such material be marked in
374 |     reasonable ways as different from the original version; or
375 | 
376 |     d) Limiting the use for publicity purposes of names of licensors or
377 |     authors of the material; or
378 | 
379 |     e) Declining to grant rights under trademark law for use of some
380 |     trade names, trademarks, or service marks; or
381 | 
382 |     f) Requiring indemnification of licensors and authors of that
383 |     material by anyone who conveys the material (or modified versions of
384 |     it) with contractual assumptions of liability to the recipient, for
385 |     any liability that these contractual assumptions directly impose on
386 |     those licensors and authors.
387 | 
388 |   All other non-permissive additional terms are considered "further
389 | restrictions" within the meaning of section 10.  If the Program as you
390 | received it, or any part of it, contains a notice stating that it is
391 | governed by this License along with a term that is a further
392 | restriction, you may remove that term.  If a license document contains
393 | a further restriction but permits relicensing or conveying under this
394 | License, you may add to a covered work material governed by the terms
395 | of that license document, provided that the further restriction does
396 | not survive such relicensing or conveying.
397 | 
398 |   If you add terms to a covered work in accord with this section, you
399 | must place, in the relevant source files, a statement of the
400 | additional terms that apply to those files, or a notice indicating
401 | where to find the applicable terms.
402 | 
403 |   Additional terms, permissive or non-permissive, may be stated in the
404 | form of a separately written license, or stated as exceptions;
405 | the above requirements apply either way.
406 | 
407 |   8. Termination.
408 | 
409 |   You may not propagate or modify a covered work except as expressly
410 | provided under this License.  Any attempt otherwise to propagate or
411 | modify it is void, and will automatically terminate your rights under
412 | this License (including any patent licenses granted under the third
413 | paragraph of section 11).
414 | 
415 |   However, if you cease all violation of this License, then your
416 | license from a particular copyright holder is reinstated (a)
417 | provisionally, unless and until the copyright holder explicitly and
418 | finally terminates your license, and (b) permanently, if the copyright
419 | holder fails to notify you of the violation by some reasonable means
420 | prior to 60 days after the cessation.
421 | 
422 |   Moreover, your license from a particular copyright holder is
423 | reinstated permanently if the copyright holder notifies you of the
424 | violation by some reasonable means, this is the first time you have
425 | received notice of violation of this License (for any work) from that
426 | copyright holder, and you cure the violation prior to 30 days after
427 | your receipt of the notice.
428 | 
429 |   Termination of your rights under this section does not terminate the
430 | licenses of parties who have received copies or rights from you under
431 | this License.  If your rights have been terminated and not permanently
432 | reinstated, you do not qualify to receive new licenses for the same
433 | material under section 10.
434 | 
435 |   9. Acceptance Not Required for Having Copies.
436 | 
437 |   You are not required to accept this License in order to receive or
438 | run a copy of the Program.  Ancillary propagation of a covered work
439 | occurring solely as a consequence of using peer-to-peer transmission
440 | to receive a copy likewise does not require acceptance.  However,
441 | nothing other than this License grants you permission to propagate or
442 | modify any covered work.  These actions infringe copyright if you do
443 | not accept this License.  Therefore, by modifying or propagating a
444 | covered work, you indicate your acceptance of this License to do so.
445 | 
446 |   10. Automatic Licensing of Downstream Recipients.
447 | 
448 |   Each time you convey a covered work, the recipient automatically
449 | receives a license from the original licensors, to run, modify and
450 | propagate that work, subject to this License.  You are not responsible
451 | for enforcing compliance by third parties with this License.
452 | 
453 |   An "entity transaction" is a transaction transferring control of an
454 | organization, or substantially all assets of one, or subdividing an
455 | organization, or merging organizations.  If propagation of a covered
456 | work results from an entity transaction, each party to that
457 | transaction who receives a copy of the work also receives whatever
458 | licenses to the work the party's predecessor in interest had or could
459 | give under the previous paragraph, plus a right to possession of the
460 | Corresponding Source of the work from the predecessor in interest, if
461 | the predecessor has it or can get it with reasonable efforts.
462 | 
463 |   You may not impose any further restrictions on the exercise of the
464 | rights granted or affirmed under this License.  For example, you may
465 | not impose a license fee, royalty, or other charge for exercise of
466 | rights granted under this License, and you may not initiate litigation
467 | (including a cross-claim or counterclaim in a lawsuit) alleging that
468 | any patent claim is infringed by making, using, selling, offering for
469 | sale, or importing the Program or any portion of it.
470 | 
471 |   11. Patents.
472 | 
473 |   A "contributor" is a copyright holder who authorizes use under this
474 | License of the Program or a work on which the Program is based.  The
475 | work thus licensed is called the contributor's "contributor version".
476 | 
477 |   A contributor's "essential patent claims" are all patent claims
478 | owned or controlled by the contributor, whether already acquired or
479 | hereafter acquired, that would be infringed by some manner, permitted
480 | by this License, of making, using, or selling its contributor version,
481 | but do not include claims that would be infringed only as a
482 | consequence of further modification of the contributor version.  For
483 | purposes of this definition, "control" includes the right to grant
484 | patent sublicenses in a manner consistent with the requirements of
485 | this License.
486 | 
487 |   Each contributor grants you a non-exclusive, worldwide, royalty-free
488 | patent license under the contributor's essential patent claims, to
489 | make, use, sell, offer for sale, import and otherwise run, modify and
490 | propagate the contents of its contributor version.
491 | 
492 |   In the following three paragraphs, a "patent license" is any express
493 | agreement or commitment, however denominated, not to enforce a patent
494 | (such as an express permission to practice a patent or covenant not to
495 | sue for patent infringement).  To "grant" such a patent license to a
496 | party means to make such an agreement or commitment not to enforce a
497 | patent against the party.
498 | 
499 |   If you convey a covered work, knowingly relying on a patent license,
500 | and the Corresponding Source of the work is not available for anyone
501 | to copy, free of charge and under the terms of this License, through a
502 | publicly available network server or other readily accessible means,
503 | then you must either (1) cause the Corresponding Source to be so
504 | available, or (2) arrange to deprive yourself of the benefit of the
505 | patent license for this particular work, or (3) arrange, in a manner
506 | consistent with the requirements of this License, to extend the patent
507 | license to downstream recipients.  "Knowingly relying" means you have
508 | actual knowledge that, but for the patent license, your conveying the
509 | covered work in a country, or your recipient's use of the covered work
510 | in a country, would infringe one or more identifiable patents in that
511 | country that you have reason to believe are valid.
512 | 
513 |   If, pursuant to or in connection with a single transaction or
514 | arrangement, you convey, or propagate by procuring conveyance of, a
515 | covered work, and grant a patent license to some of the parties
516 | receiving the covered work authorizing them to use, propagate, modify
517 | or convey a specific copy of the covered work, then the patent license
518 | you grant is automatically extended to all recipients of the covered
519 | work and works based on it.
520 | 
521 |   A patent license is "discriminatory" if it does not include within
522 | the scope of its coverage, prohibits the exercise of, or is
523 | conditioned on the non-exercise of one or more of the rights that are
524 | specifically granted under this License.  You may not convey a covered
525 | work if you are a party to an arrangement with a third party that is
526 | in the business of distributing software, under which you make payment
527 | to the third party based on the extent of your activity of conveying
528 | the work, and under which the third party grants, to any of the
529 | parties who would receive the covered work from you, a discriminatory
530 | patent license (a) in connection with copies of the covered work
531 | conveyed by you (or copies made from those copies), or (b) primarily
532 | for and in connection with specific products or compilations that
533 | contain the covered work, unless you entered into that arrangement,
534 | or that patent license was granted, prior to 28 March 2007.
535 | 
536 |   Nothing in this License shall be construed as excluding or limiting
537 | any implied license or other defenses to infringement that may
538 | otherwise be available to you under applicable patent law.
539 | 
540 |   12. No Surrender of Others' Freedom.
541 | 
542 |   If conditions are imposed on you (whether by court order, agreement or
543 | otherwise) that contradict the conditions of this License, they do not
544 | excuse you from the conditions of this License.  If you cannot convey a
545 | covered work so as to satisfy simultaneously your obligations under this
546 | License and any other pertinent obligations, then as a consequence you may
547 | not convey it at all.  For example, if you agree to terms that obligate you
548 | to collect a royalty for further conveying from those to whom you convey
549 | the Program, the only way you could satisfy both those terms and this
550 | License would be to refrain entirely from conveying the Program.
551 | 
552 |   13. Use with the GNU Affero General Public License.
553 | 
554 |   Notwithstanding any other provision of this License, you have
555 | permission to link or combine any covered work with a work licensed
556 | under version 3 of the GNU Affero General Public License into a single
557 | combined work, and to convey the resulting work.  The terms of this
558 | License will continue to apply to the part which is the covered work,
559 | but the special requirements of the GNU Affero General Public License,
560 | section 13, concerning interaction through a network will apply to the
561 | combination as such.
562 | 
563 |   14. Revised Versions of this License.
564 | 
565 |   The Free Software Foundation may publish revised and/or new versions of
566 | the GNU General Public License from time to time.  Such new versions will
567 | be similar in spirit to the present version, but may differ in detail to
568 | address new problems or concerns.
569 | 
570 |   Each version is given a distinguishing version number.  If the
571 | Program specifies that a certain numbered version of the GNU General
572 | Public License "or any later version" applies to it, you have the
573 | option of following the terms and conditions either of that numbered
574 | version or of any later version published by the Free Software
575 | Foundation.  If the Program does not specify a version number of the
576 | GNU General Public License, you may choose any version ever published
577 | by the Free Software Foundation.
578 | 
579 |   If the Program specifies that a proxy can decide which future
580 | versions of the GNU General Public License can be used, that proxy's
581 | public statement of acceptance of a version permanently authorizes you
582 | to choose that version for the Program.
583 | 
584 |   Later license versions may give you additional or different
585 | permissions.  However, no additional obligations are imposed on any
586 | author or copyright holder as a result of your choosing to follow a
587 | later version.
588 | 
589 |   15. Disclaimer of Warranty.
590 | 
591 |   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592 | APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
596 | PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
597 | IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599 | 
600 |   16. Limitation of Liability.
601 | 
602 |   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610 | SUCH DAMAGES.
611 | 
612 |   17. Interpretation of Sections 15 and 16.
613 | 
614 |   If the disclaimer of warranty and limitation of liability provided
615 | above cannot be given local legal effect according to their terms,
616 | reviewing courts shall apply local law that most closely approximates
617 | an absolute waiver of all civil liability in connection with the
618 | Program, unless a warranty or assumption of liability accompanies a
619 | copy of the Program in return for a fee.
620 | 
621 |                      END OF TERMS AND CONDITIONS
622 | 
623 |             How to Apply These Terms to Your New Programs
624 | 
625 |   If you develop a new program, and you want it to be of the greatest
626 | possible use to the public, the best way to achieve this is to make it
627 | free software which everyone can redistribute and change under these terms.
628 | 
629 |   To do so, attach the following notices to the program.  It is safest
630 | to attach them to the start of each source file to most effectively
631 | state the exclusion of warranty; and each file should have at least
632 | the "copyright" line and a pointer to where the full notice is found.
633 | 
634 |     <one line to give the program's name and a brief idea of what it does.>
635 |     Copyright (C) <year>  <name of author>
636 | 
637 |     This program is free software: you can redistribute it and/or modify
638 |     it under the terms of the GNU General Public License as published by
639 |     the Free Software Foundation, either version 3 of the License, or
640 |     (at your option) any later version.
641 | 
642 |     This program is distributed in the hope that it will be useful,
643 |     but WITHOUT ANY WARRANTY; without even the implied warranty of
644 |     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
645 |     GNU General Public License for more details.
646 | 
647 |     You should have received a copy of the GNU General Public License
648 |     along with this program.  If not, see <https://www.gnu.org/licenses/>.
649 | 
650 | Also add information on how to contact you by electronic and paper mail.
651 | 
652 |   If the program does terminal interaction, make it output a short
653 | notice like this when it starts in an interactive mode:
654 | 
655 |     <program>  Copyright (C) <year>  <name of author>
656 |     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657 |     This is free software, and you are welcome to redistribute it
658 |     under certain conditions; type `show c' for details.
659 | 
660 | The hypothetical commands `show w' and `show c' should show the appropriate
661 | parts of the General Public License.  Of course, your program's commands
662 | might be different; for a GUI interface, you would use an "about box".
663 | 
664 |   You should also get your employer (if you work as a programmer) or school,
665 | if any, to sign a "copyright disclaimer" for the program, if necessary.
666 | For more information on this, and how to apply and follow the GNU GPL, see
667 | <https://www.gnu.org/licenses/>.
668 | 
669 |   The GNU General Public License does not permit incorporating your program
670 | into proprietary programs.  If your program is a subroutine library, you
671 | may consider it more useful to permit linking proprietary applications with
672 | the library.  If this is what you want to do, use the GNU Lesser General
673 | Public License instead of this License.  But first, please read
674 | <https://www.gnu.org/licenses/why-not-lgpl.html>.
675 | 


--------------------------------------------------------------------------------
/denote-explore.texi:
--------------------------------------------------------------------------------
  1 | \input texinfo    @c -*- texinfo -*-
  2 | @c %**start of header
  3 | @setfilename denote-explore.info
  4 | @settitle Denote Explorer: Explore your Denote digital garden
  5 | @documentencoding UTF-8
  6 | @documentlanguage en
  7 | @set MAINTAINERSITE @uref{https://lucidmanager.org/tags/emacs,maintainer webpage}
  8 | @set MAINTAINER Peter Prevos
  9 | @set MAINTAINEREMAIL @email{peter@prevos.net}
 10 | @set MAINTAINERCONTACT @uref{mailto:peter@prevos.net,contact the maintainer}
 11 | @c %**end of header
 12 | 
 13 | @dircategory Emacs misc features
 14 | @direntry
 15 | * Denote Explorer: (denote-explore). Explore, visualise and analyse Denote files.
 16 | @end direntry
 17 | 
 18 | @finalout
 19 | @titlepage
 20 | @title Denote Explorer: Explore your Denote digital garden
 21 | @author Peter Prevos
 22 | @end titlepage
 23 | 
 24 | @ifnottex
 25 | @node Top
 26 | @top Denote Explorer: Explore your Denote digital garden
 27 | 
 28 | The Denote package by Protesilaos (Prot) Stavrou provides extensive functionality for creating, retrieving, managing, and linking files in plain text, Markdown, and Org Mode. The most redeeming qualities of this package are its filename convention and modular simplicity.
 29 | 
 30 | Due to its reliance on file names, you can also use the package to access other file types, such as PDFs or multimedia files (which we call Denote attachments). In this way, Denote becomes a fully-featured personal knowledge management system. 
 31 | 
 32 | The Denote-Explorer package came into existence as my collection of Denote files grew. I created some auxiliary functions to manage and explore my burgeoning Denote files, resulting in four types of commands:
 33 | 
 34 | @enumerate
 35 | @item
 36 | Descriptive statistics: Count notes, attachments and keywords.
 37 | @item
 38 | Random walks: Generate new ideas using serendipity.
 39 | @item
 40 | Janitor: Maintain your denote collection.
 41 | @item
 42 | Knowledge Graphs: Visualise and analyse your Denote files as a network.
 43 | @end enumerate
 44 | 
 45 | @end ifnottex
 46 | 
 47 | @menu
 48 | * Descriptive Statistics::
 49 | * Random Walks::
 50 | * Janitor::
 51 | * Knowledge Graphs::
 52 | * Installation and Package Configuration::
 53 | * Acknowledgements::
 54 | * License::
 55 | 
 56 | @detailmenu
 57 | --- The Detailed Node Listing ---
 58 | 
 59 | Janitor
 60 | 
 61 | * Duplicate notes::
 62 | * Missing Links::
 63 | * Managing Keywords::
 64 | * Synchronising Meta Data::
 65 | 
 66 | Knowledge Graphs
 67 | 
 68 | * Principles of Knowledge Graphs::
 69 | * Community of Notes::
 70 | * Note Neighbourhood::
 71 | * Sequences Network::
 72 | * Keyword Network::
 73 | * Network Layout and Presentation::
 74 | * D3.js: D3js. 
 75 | * GraphViz::
 76 | * Graph Exchange XML Format::
 77 | * Analysing the Denote Network::
 78 | 
 79 | @end detailmenu
 80 | @end menu
 81 | 
 82 | @node Descriptive Statistics
 83 | @chapter Descriptive Statistics
 84 | 
 85 | The Denote-Explorer package distinguishes between Denote files (notes) and attachments. Denote files are either Org Mode, Markdown, or Plain Text. All other files, such as photographs, PDFs, media files, @LaTeX{}, and HTML, are attachments.
 86 | 
 87 | After a day of working hard on your digital knowledge garden, you can count the notes and attachments in your collection. Two functions provide some basic statistics of your Denote files:
 88 | 
 89 | @enumerate
 90 | @item
 91 | @code{denote-explore-count-notes}: Count the number of notes and attachments. With universal argument, only count notes.
 92 | @item
 93 | @code{denote-explore-count-keywords}: Count the number of distinct Denote keywords. 
 94 | @end enumerate
 95 | 
 96 | These functions are informative, but a graph says more than a thousand numbers. The built-in @samp{chart.el} package by Eric M@. Ludlam is a quaint tool for creating bar charts in a plain text buffer. Two commands are available in Denote-Explorer to visualise basic statistics: 
 97 | 
 98 | @enumerate
 99 | @item
100 | @code{denote-explore-barchart-filetypes}: Visualise used file extensions. With universal argument @samp{C-u} visualises only attachments.
101 | @item
102 | @code{denote-explore-barchart-keywords}: Visualise the top-n keywords
103 | @item
104 | @code{denote-explore-barchart-timeline}: Visualise notes created by year
105 | @end enumerate
106 | 
107 | The @code{denote-excluded-files-regexp} variable can contain a regular expression of files excluded from these statistical functions.
108 | 
109 | @node Random Walks
110 | @chapter Random Walks
111 | 
112 | Creativity springs from a medley of experiences, emotions, subconscious musings, and connecting random ideas. Introducing random elements into the creative process generates avenues of thought you might not have travelled otherwise. Random walks through your notes can be beneficial when you're stuck in a rut or just like to walk through your files randomly.
113 | 
114 | A random walk is an arbitrary sequence without a defined relationship between the steps. You take a random walk by jumping to a random note, connected or unconnected to the current buffer.
115 | 
116 | The Denote-Explorer package provides three commands to inject some randomness into your explorations:
117 | 
118 | @enumerate
119 | @item
120 | @code{denote-explore-random-note}: Jump to a random Denote file.
121 | @item
122 | @code{denote-explore-random-regex}: Jump to a random Denote file that matches a regular expression.
123 | @item
124 | @code{denote-explore-random-link}: Jump to a random linked note (either forward or backward) or attachments (forward only).
125 | @item
126 | @code{denote-explore-random-keyword}: Jump to a random Denote file with the same selected keyword(s).
127 | @item
128 | @code{denote-explore-random-signature}: Jump to a random Denote file with the same (partial) signature.
129 | @end enumerate
130 | 
131 | The default state is that these functions jump to any Denote text file (plain text, Markdown or Org-mode). Prefixing the universal argument (@samp{C-u}) includes attachments in the sample for a random jump, otherwise the walk remains within the collection of notes. The @code{denote-explore-random-regex-ignore} variable can contain a regular expression of files excluded from the sample of files to jump to.
132 | 
133 | Jumping to a note that matches a regular expression lets you find random notes matching a search string. For example, to find a note you wrote in May 2022, use @samp{^202205} and using @samp{202305.*_journal} jumps to a random journal entry in May 2023.
134 | 
135 | Jumping to a randomly linked file naturally only works when the current buffer is a Denote file. A warning appears when the current buffer is an isolated note (no links or backlinks available).
136 | 
137 | When jumping to a random file with one or more matching keywords, you can choose one or more keywords from the current buffer, or override the completion options with free text. The asterisk symbol @samp{*} selects all keywords in the completion list. This section process is skipped when the current buffer only has one keyword. When the current buffer is not a Denote file, you can choose any available keyword(s) in your Denote collection.
138 | 
139 | Jumping to a random note and matching multiple keywords only works when @code{denote-sort-keywords} is enabled, or when the selected keywords are in the same order as in the target file. You can alphabetise keywords in your Denote files with @code{denote-explore-sort-keywords}, explained in the next section.
140 | 
141 | @node Janitor
142 | @chapter Janitor
143 | 
144 | After hoarding Denote files for a while, you may need a janitor to organise your collection. A janitor ensures cleanliness, orderliness, and sanitation in a building, so this role is also perfect for managing to your Denote files. The Denote-Explorer package provides a series of commands to assist with cleaning, organising, and sanitising your files.
145 | 
146 | @menu
147 | * Duplicate notes::
148 | * Missing Links::
149 | * Managing Keywords::
150 | * Synchronising Meta Data::
151 | @end menu
152 | 
153 | @node Duplicate notes
154 | @section Duplicate notes
155 | 
156 | The Denote package prevents duplicate identifiers when creating a new note, but when assigning filenames manually, or when exporting org files, duplicates might appear.
157 | 
158 | The Denote identifier is a unique string constructed of the note's creation date and time in ISO 8601 format (e.g., @samp{2024035T203312}). Denote either uses the current date and time when generating a new note or the date and time the file was created on the file system.
159 | 
160 | The file's creation date and time are not always relevant for attachments. For example, when adding scanned historical records, the identifier might be centuries ago, so it must be added manually.
161 | 
162 | The @code{denote-explore-identify-duplicate-notes} command lists all duplicate Denote files in a popup org buffer, which includes links to the suspected duplicate notes and attachments.
163 | 
164 | Additionally, the @code{denote-explore-identify-duplicate-notes-dired} command displays files with duplicate identifiers in a Dired buffer. You can directly change filenames in the Dired buffer with @code{dired-toggle-read-only} (@samp{C-x C-q}) or remove individual duplicates with @samp{D} (@code{dired-do-delete}). Note that this function only shows files in the denote directory and not its subdirectories or symbolic links.
165 | 
166 | With the universal argument (@samp{C-u}), these commands ignore any duplicated identifiers created when exporting Denote Org mode files.
167 | 
168 | The @code{denote-excluded-files-regexp} variable can contain a regular expression of files excluded from duplicate detection. 
169 | 
170 | Be careful when manually changing the identifier of a Denote file, as it can destroy the integrity of your links. Please ensure that the file you rename does not have any links pointing to it. You can use the @code{denote-find-link} and @code{denote-find-backlink} commands to check a file for links, or use the Denote Explorer link checker.
171 | 
172 | @node Missing Links
173 | @section Missing Links
174 | 
175 | The Denote identifier keeps links active even when you change the file name, tags or signature. But missing or dead links might still appear in your network of notes when you delete redundant information or you manually change an identifier.
176 | 
177 | Using @code{denote-explore-missing-links} lists all links to non-existing notes, attachments and links to other files (such as images) in your Denote directory.
178 | 
179 | This function creates a read-only Org mode file with two tables of source documents and the missing linked Denote file or other linked files. You can click on the links to jump to the source file at the missing link location and either remove or edit it. Links will appear in their literal form, i.e. @samp{[[<link>][<description>]]}. You can toggle this behaviour with @code{org-toggle-link-display} to show the formatted links.
180 | 
181 | The link contains an Elisp function to open the linked document and find the relevant link. Emacs will ask for confirmation every time you follow such a link. You can disable these warnings by setting @code{org-link-elisp-confirm-function} to @samp{nil}.
182 | 
183 | When the missing link is found because perhaps you already removed it, an error message pops up in the echo area.
184 | 
185 | The @code{denote-excluded-files-regexp} variable can contain a regular expression of files that are excluded from the search for missing Denote links.
186 | 
187 | @node Managing Keywords
188 | @section Managing Keywords
189 | 
190 | Denote keywords connect notes with similar content. Denote explore provides a few commands to assist with managing your menagerie of keywords.
191 | 
192 | First step is to explore the keywords already being used in your collection of notes. The @code{denote-explore-list-keywords} command lists all used Denote keywords in a table, sorted by usage counts. Calling this function with the universal argument (@samp{C-u}), sorts the list alphabetically. This command provides similar functionality to @code{denote-explore-barchart-keywords}, but can show all keywords in one buffer. 
193 | 
194 | Keywords should not exist in solitude because a category with only one member is not informative. Single keywords can arise because topics need to be fully developed or due to a typo. The @code{denote-explore-single-keywords} command provides a list of file tags that are only used once. The list of single keywords is presented in the minibuffer, from where you can open the relevant note or attachment.
195 | 
196 | You can also find notes or attachments without keywords with the @code{denote-explore-zero-keywords} command. This command lists all notes and attachments without keywords in the minibuffer, so you can open them and consider adding keywords or leaving them as is.
197 | 
198 | You can rename or remove keywords with @code{denote-explore-rename-keyword}. Select one or more existing keywords from the completion list and enter the new keyword. This function renames all chosen keywords or removes the original keyword from all existing notes when you enter an empty string as new keyword. This function cycles through all notes and attachments containing one or more selected keywords and asks for confirmation before making any changes. The new keyword list is stored alphabetically. This function uses the front matter as the source of truth for notes and the file name for attachments.
199 | 
200 | The @code{denote-excluded-files-regexp} variable can contain a regular expression of files that are excluded from the purview of these functions.
201 | 
202 | You can also visualise keywords using knowledge graphs described below.
203 | 
204 | @node Synchronising Meta Data
205 | @section Synchronising Meta Data
206 | 
207 | Denote stores the metadata for each note in the filename using its ingenious format. Some of this metadata is copied to the front matter of a note, which can lead to discrepancies between the two metadata sources.
208 | 
209 | The @code{denote-explore-sync-metadata} function checks all notes and asks the user to rename any file where the front matter data differs from the file name. The front matter data is the source of truth for the title and keywords. This function also enforces the alphabetisation of keywords, which assists with finding notes.
210 | 
211 | The @code{denote-excluded-files-regexp} variable can contain a regular expression of files that are excluded from this synchronisation.
212 | 
213 | @node Knowledge Graphs
214 | @chapter Knowledge Graphs
215 | 
216 | Emacs is a text processor with limited graphical capabilities. However, committing your ideas to text requires a linear way of thinking since you can only process one word at a time. Visual thinking through tools such as mind maps or network diagrams is another way to approach your ideas. One of the most common methods to visualise interlinked documents is in a network or a personal knowledge graph, or in more general terms, a network diagram.
217 | 
218 | @menu
219 | * Principles of Knowledge Graphs::
220 | * Community of Notes::
221 | * Note Neighbourhood::
222 | * Sequences Network::
223 | * Keyword Network::
224 | * Network Layout and Presentation::
225 | * D3.js: D3js. 
226 | * GraphViz::
227 | * Graph Exchange XML Format::
228 | * Analysing the Denote Network::
229 | @end menu
230 | 
231 | @node Principles of Knowledge Graphs
232 | @section Principles of Knowledge Graphs
233 | 
234 | Denote implements a linking mechanism that connects notes (either Org, Markdown, or plain text files) to other notes or attachments. This mechanism allows the user to visualise all notes as a network diagram.
235 | 
236 | Network visualisation in Denote is not just a feature but a powerful tool that visualises how notes are linked, helping you discover previously unseen connections between your thoughts and enhancing your creative process.
237 | 
238 | It's important to note that Denote-Explorer does not offer live previews of your note collection. This deliberate choice prevents the 'dopamine traps' of seeing your thoughts develop in real-time. Instead, Denote-Explorer provides a focused tool for the surgical dissection of your second brain, while the main user interface remains text-based.
239 | 
240 | A network diagram has nodes (vertices) and edges. Each node represents a note or an attachment, and each edge represents a link between them. A link between file is directed and the arrow indicates the source and target of the link. The diagram below shows the basic principle of a knowledge graph. In the actual output, nodes are circles.
241 | 
242 | @example
243 | ┌──────────────┐        ┌──────────────┐
244 | │     node     │  edge  │     node     │
245 | │    (note)    ├───────►│    (note)    │
246 | │ (attachment) │ (link) │ (attachment) │
247 | └──────────────┘        └──────────────┘
248 | @end example
249 | 
250 | Denote-Explorer provides three types of network diagrams to explore the relationships between your thoughts:
251 | 
252 | @enumerate
253 | @item
254 | Community: Notes matching a regular expression
255 | @item
256 | Neighbourhood: Search n-deep in a selected note
257 | @item
258 | Sequence: Visualise a hierarchical sequence
259 | @item
260 | Keywords: Relationships between keywords
261 | @end enumerate
262 | 
263 | The package exports and displays these in one of three formats, with JSON displayed in HTML / D3.js files as the default. Other options are GraphViz and GEXF@.
264 | 
265 | You create a network with the @code{denote-explore-network} command. This command will ask the user to select the type of network to create. Each network type requires additional inputs to analyse to a defined part of your Denote files.
266 | 
267 | The @code{denote-explore-network-regenerate} command recreates the previous graph with the same parameters, which is useful when changing the structure of your notes and you like to see the result visualised without having to re-enter the parameters.
268 | 
269 | Using the universal argument @samp{C-u} before issuing these two command (re)generates a network excluding attachments. The @code{denote-excluded-files-regexp} variable can contain a regular expression of files that are excluded from visualisation.
270 | 
271 | @node Community of Notes
272 | @section Community of Notes
273 | 
274 | A community graph displays all notes matching a regular expression and their connections. The example below indicates the community that contains the @samp{_emacs} regular expression, within the dashed line. The algorithm prunes any links to non-matching notes, which in the example below is the note with the @samp{_vim} keyword.
275 | 
276 | @example
277 | ┌ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┐        
278 |    _emacs community        
279 | │ ┌──────┐  ┌──────┐ │  ┌────┐        
280 |   │_emacs│  │_emacs│───►│_vim│       
281 | │ └──┬───┘  └──────┘ │  └────┘        
282 |      │                       
283 | │    ▼               │        
284 |   ┌──────┐              
285 | │ │_emacs│           │
286 |   └──────┘            
287 | └ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┘        
288 | @end example
289 | 
290 | To generate a community graph, use @code{denote-explore-network}, choose 'Community' and enter a regular expression. When no matching files are found or there are only solitary nodes, then the network is not generated and you will see this warning: @samp{No Denote files or (back)links found for regex}.
291 | 
292 | The @code{denote-explore-network-regex-ignore} variable defines a regular expression to exclude certain notes from community networks. For example, if you create meta notes with long lists of dynamic links and they have the @samp{_meta} keyword, then you could exclude these nodes by customising this variable to the relevant regular expression.
293 | 
294 | @node Note Neighbourhood
295 | @section Note Neighbourhood
296 | 
297 | The neighbourhood of a note consists of all files linked to it at one or more steps deep. The algorithm selects members of the graph from linked and back-linked notes. This visualisation effectively creates the possible paths you can follow with the @code{denote-explore-random-link} function discussed in the Random Walks section above.
298 | 
299 | The illustration below shows the principle of the linking depth. Notes B and C are at linking depth 1 from A and notes D and E are at depth 2 from A@.
300 | 
301 | @example
302 | Depth 1      2
303 |      ┌─┐    ┌─┐ 
304 |   ┌─►│B│◄───┤D│ 
305 |   │  └─┘    └─┘ 
306 |  ┌┴┐            
307 |  │A│            
308 |  └─┘            
309 |   ▲  ┌─┐    ┌─┐ 
310 |   └──┤C├───►│E│ 
311 |      └─┘    └─┘
312 | @end example
313 | 
314 | To generate a neighbourhood graph from the current Denote note buffer, use @code{denote-explore-network} and enter the graph's depth. The user enters the required depth, and the software searches all notes linked to the current buffer at that depth. When building this graph from a buffer that is not a Denote file, the system also asks to select a source file (A in the diagram). The system issues a warning when you select a note without links or backlinks. You can identify Denote files without any links with the @code{denote-explore-isolated-notes} function describe above.
315 | 
316 | The complete set of your Denote files is most likely a disconnected Graph, meaning that there is no one path that connects all nodes. Firstly, there will be isolated notes. There will also exist isolated neighbourhoods of notes that connect to each other but not to other files.
317 | 
318 | A depth of more than three links is usually not informative because the network can become to large to read, or you hit the edges of your island of connected notes.
319 | 
320 | The @code{denote-explore-network-regex-ignore} variable lets you define a regular expression of notes exclude from neighbourhood networks.
321 | 
322 | @node Sequences Network
323 | @section Sequences Network
324 | 
325 | Denote signatures can define a hierarchical sequence of notes, using a family analogy. For example a note with signature @samp{1=a} is the child of a note with signature @samp{1} and a note with signature @samp{1=b} is its sibling. The note with signature @samp{1=a=1} is the child of @samp{1=a} and the grandchild of @samp{1}, and so forth. In a sequence network, links exist independent of any Denote links inside a note, the relationship is only based on the hierarchy of the signatures.
326 | 
327 | @example
328 | ┌─────┐    ┌─────┐    ┌─────┐  
329 | |  1  ├───►│ 1=a ├───►│1=a=1│ 
330 | └──┬──┘    └─────┘    └─────┘
331 |    │       ┌─────┐ 
332 |    └──────►│ 1=b │ 
333 |            └─────┘
334 | @end example
335 | 
336 | The content of the signatures can be either numbers or letters as the order of children is not taken into consideration. These sequences can go on to many generations, building a family tree of your notes. These sequences are the basic building block of the popular Zettelkasten methodology.
337 | 
338 | The Denote-Sequence package provides specialised functions to manage hierarchical connections between files, @ref{Top,info denote-sequence,,denote-sequence,}. 
339 | 
340 | To generate a sequence graph, use @code{denote-explore-network} and select the signature of the root node (note @samp{1} in the diagram). When not selecting any signature, all Denote files with a signature are included in the visualisation.
341 | 
342 | The @code{denote-explore-network-regex-ignore} variable lets you define a regular expression of notes exclude from neighbourhood networks.
343 | 
344 | @node Keyword Network
345 | @section Keyword Network
346 | 
347 | The last available method to visualise your Denote collection is to develop a network of keywords. Two keywords are connected when used in the same note.
348 | 
349 | All keywords in a note form a complete network. The union of all complete networks from all files in your Denote collection defines the keywords network. The relationship between two keywords can exist in multiple notes, so the links between keywords are weighted. The line thickness between two keywords indicates the frequency (weight) of their relationship.
350 | 
351 | While the first two graph types are directed (arrows indicate the direction of links), the keyword network is undirected. These links are bidirectional associations between keywords. The diagram below shows three notes, two with two keywords and one with three keywords. Each notes forms a small complete network that links all keywords.
352 | 
353 | @example
354 | ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐
355 | │_kwd1├─┤_kwd2│   │_kwd1├─┤_kwd2│   │_kwd3├─┤_kwd4│
356 | └─────┘ └─────┘   └─┬───┘ └───┬─┘   └─────┘ └─────┘
357 |                     │ ┌─────┐ │  
358 |                     └─┤_kwd3├─┘  
359 |                       └─────┘    
360 | @end example
361 | 
362 | The union of these three networks forms the keyword network for this collection of notes. The example generates the following keyword network.
363 | 
364 | @example
365 | ┌─────┐ ┌─────┐                                
366 | │_kwd1├─┤_kwd2│                                
367 | └─┬───┘ └───┬─┘                                
368 |   │         │                                  
369 |   │ ┌─────┐ │  ┌─────┐                         
370 |   └─┤_kwd3├─┴──┤_kwd4│                         
371 |     └─────┘    └─────┘                         
372 | @end example
373 | 
374 | When generating this graph type, you will need to enter a minimum edge weight (n). The graph then will only show those keywords that are at least n times associated with each other. The default is one.
375 | 
376 | Some keywords might have to be excluded from this graph because they skew the results. For example, when using the Citar-Denote package, you might like to exclude the @samp{bib} keyword from the diagram because it is only used to minimise the search space for bibliographic notes and has no further semantic value. The @code{denote-explore-network-keywords-ignore} variable lists keywords ignored in this visualisation.
377 | 
378 | @node Network Layout and Presentation
379 | @section Network Layout and Presentation
380 | 
381 | Emacs cannot independently generate graphics and thus relies on external software. This package can use three external mechanisms to create graphs (configurable with @code{denote-explore-network-format}), set to D3.js / JSON output by default. Other available formats are GraphViz SVG and GEXF, discussed in detail below.
382 | 
383 | The Denote-Explorer network algorithm consists of four steps:
384 | 
385 | @enumerate
386 | @item
387 | The @code{denote-explore-network} function determines the relevant functions based on user input.
388 | @item
389 | The code generates a nested association list for the selected graph:
390 | @itemize
391 | @item
392 | Metadata e.g.: @samp{(meta (directed . t) (type . "Neighbourhood") (parameters "20210104T194405" 2))}
393 | @item
394 | Association list of nodes, e.g., @samp{(((id . "20210104T194405") (name . "Platonic Solids") (keywords "geometry" "esotericism") (type . "org") (degree . 4)) ...)}. In the context of Denote, the degree of a network node is the unweighted sum of links and backlinks in a note. 
395 | @item
396 | Association list of edges and their weights: @samp{(((source . "20220529T190246") (target . "20201229T143000") (weight . 1)) ...)}. The weight of an edge indicates the number of time the two files are linked, or the number of times two keywords appear in the same note in case of a keyword graph.
397 | @end itemize
398 | @item
399 | The package encodes the association list to a either a JSON, GraphViz DOT, or GEXF file. The location and name of this file is configurable with the  @code{denote-explore-network-directory} and @code{denote-explore-network-filename} variables.
400 | @item
401 | Relevant external software displays the result (in most cases a web browser).
402 | @end enumerate
403 | 
404 | @node D3js
405 | @section D3.js
406 | 
407 | @uref{https://d3js.org/, D3.js} is a JavaScript library for visualising data. This method provides an aesthetically pleasing and interactive view of the structure of your notes. Denote-Explorer stores the desired network as a JSON file. This JSON file is merged with a HTML / JavaScript template to visualise the network. Emacs invokes your default internet browser to view the network. 
408 | 
409 | Hover over any node to reveal its name and relevant metadata. For neighbourhood and community graphs, when the note is an image or PDF file, a preview appears in the tooltip. Clicking on a node opens the relevant file in the browser, or whatever application the browser associates with the relevant file type.
410 | 
411 | For community and neighbourhood graphs, the diameter of nodes is proportional to their degree. Thus, the most linked note in your query will be the most visible. The colours indicate the file type of each node. The size of nodes in a network graph is the same for all.
412 | 
413 | For nodes with a degree greater than two, the name is displayed outside the node.
414 | 
415 | In keyword graphs, the thickness of the edges indicates the number of times two keywords are associated with each other.
416 | 
417 | The info button shows the type of network and provides some basic statistics, such as the number of nodes (files) and edges (links) and the network density. The density of a network is the ratio between the number of edges and the potential number of edges. A density of zero, as such means that no nodes are connected. In a network with a density of one all nodes are connected to each other.
418 | 
419 | For community graphs the panel also provides the option to show or hide isolated nodes to increase clarity. Neighbourhood and keyword graphs by their definition do not have isolated nodes.
420 | 
421 | For community and neighbourhood graphs, the info panel also shows the distribution of keywords for the visualised network.
422 | 
423 | You can customise the output of the network files by modifying the template. The @code{denote-explore-network-d3-template} variable contains the location of the HTML/JavaScript template file so you can craft your own versions. This file contains several shortcodes:
424 | 
425 | @itemize
426 | @item
427 | @samp{@{@{graph-type@}@}}: Type of graph, community, neighbourhood or network
428 | @item
429 | @samp{@{@{d3-js@}@}}: Content of the @code{denote-explore-network-d3-js} variable, which contains the URL of the D3 source code, which has to be version 7 or above. The default template fetches the JavaScript code from the @samp{d3js.org} website. You can customise this variable to use a locally stored file.
430 | @item
431 | @samp{@{@{json-content@}@}}: The generated JSON file with the network definition
432 | @item
433 | @samp{@{@{d3-colourscheme@}@}}: Content of @code{denote-explore-network-d3-colours}. this variable assigns a colour palette for the node file types. You can choose between any of the available categorical colour schemes in the D3 package. Colours are assigned in the graph in order of appearance in the JSON file, so file types can have different colours in different graphs.
434 | @end itemize
435 | 
436 | @node GraphViz
437 | @section GraphViz
438 | 
439 | @uref{https://graphviz.org/, GraphViz} is an open-source graph visualisation software toolkit, ideal for this task. The Denote-Explorer software saves the graph in the DOT language as a @samp{.gv} file. The GraphViz software converts the DOT code to an @samp{SVG} file.
440 | 
441 | You will need to install GraphViz to enable this functionality. Denote-Explorer will raise an error when trying to create a GraphViz graph without the required external software available.
442 | 
443 | Hover over any node to reveal its name and relevant metadata. Clicking on any node in a community or neighbourhood graph opens the relevant file in the browser, or whatever application the browser associates with the relevant file type.
444 | 
445 | For community and neighbourhood graphs, the diameter of nodes is proportional to their degree. Thus, the most linked note in your query will be the most visible. When generating a neighbourhood, the source node is marked in a contrasting colour.
446 | 
447 | For nodes with a degree greater than two, the name is displayed outside the node. In keyword graphs, the thickness of the edges indicates the number of times two keywords are associated with each other.
448 | 
449 | The diameter of nodes are sized relative to their degree. Thus, the most referenced note in your system will be the most visible. For nodes with a degree greater than two, the name is displayed outside the node (top left). 
450 | 
451 | The configurable @code{denote-explore-network-graphviz-header} variable defines the basic settings for GraphViz graphs, such as the layout method and default node and edge settings.
452 | 
453 | The @code{denote-explore-network-graphviz-filetype} variable defines the GraphViz output format. SVG (the default) or PDF provide the best results.
454 | 
455 | @node Graph Exchange XML Format
456 | @section Graph Exchange XML Format
457 | 
458 | The first two formats an insight into parts of your knowledge network, but there is a lot more you can do with this type of information. While GraphViz and D3 are suitable for analysing sections of your network, this third option is ideal for storing the complete Denote network for further analysis.
459 | 
460 | Graph Exchange XML Format (@samp{GEXF}) is a language for describing complex network structures. This option saves the network as a @samp{GEXF} file without opening it in external software. 
461 | 
462 | To save the whole network, use the Community option and enter an empty search string to include all files.
463 | 
464 | You can analyse the exported file with @uref{https://gephi.org/gephi-lite/, Gephi Lite}, a free online network analysis tool. The @samp{GEXF} file only contains the IDs, names and degree of the nodes; and the edges and their weights.
465 | 
466 | @node Analysing the Denote Network
467 | @section Analysing the Denote Network
468 | 
469 | A well-trodden trope in network analysis is that all people are linked within six degrees of separation. This may also be the case for your notes, but digging more than three layers deep is not very informative as the network can become large and difficult to review.
470 | 
471 | It might seem that adding more connections between your notes improves them, but this is not necessarily the case. The extreme case is a complete network where every file links to every other file. This situation lacks any interesting structure and wouldn't be informative. So, be mindful of your approach to linking notes and attachments.
472 | 
473 | Your Denote network is unlikely to be a fully connected graph. In a connected graph, there is a path from any point to any other point. Within the context of Denote, this means that all files have at least one link or backlink. Your network will most likely have isolated nodes (files without any (back)links) and islands of connected notes.
474 | 
475 | The previously mentioned @code{denote-explore-isolated-files} command lists all files without any links and backlinks to and from the note in the minibuffer. You can select any note and add links as required to release it from isolation. Calling this function with the universal argument @samp{C-u} includes attachments in the list of lonely files. You can configure the behaviour of this function by customising @code{denote-explore-isolated-ignore-keywords}. This variable provides a list of keywords to ignore when identifying isolated notes.
476 | 
477 | The number of links and backlinks in a file (in mathematical terms, edges connected to a node) is the total degree of a node. The degree distribution of a network is the probability distribution of these degrees over the whole network. The @code{denote-explore-barchart-degree} function uses the built-in chart package to display a simple bar chart of the frequency of the total degree.
478 | 
479 | This function might take a moment to run, depending on the number of notes in your system. Evaluating this function with the universal argument @samp{C-u} excludes attachments from the analysis.
480 | 
481 | The importance of a note is directly related to the number of backlinks. The @code{denote-explore-barchart-backlinks} function visualises the number of backlinks in the top-n notes in a horizontal bar chart, ordered by the number of backlinks. This function asks for the number of nodes to visualise and then analyses the complete network of Denote notes (attachments are excluded because they don't have links from them), which can take a brief moment.
482 | 
483 | @node Installation and Package Configuration
484 | @chapter Installation and Package Configuration
485 | 
486 | This package is available from GitHub or through MELPA@.
487 | 
488 | The configuration below customises all available variables and binds all available commands to the @samp{C-c e} prefix. To get started you don't need to configure anything. You should modify this configuration to suit your needs, as one person's sensible defaults are another person's nightmare.
489 | 
490 | @lisp
491 | (use-package denote-explore
492 |   :custom
493 |   ;; Where to store network data and in which format
494 |   (denote-explore-network-directory "<folder>")
495 |   (denote-explore-network-filename "denote-network")
496 |   (denote-explore-network-keywords-ignore "<keywords list>")
497 |   (denote-explore-network-regex-ignore "<regex>")
498 |   (denote-explore-network-format 'd3.js)
499 |   (denote-explore-network-d3-colours 'SchemeObservable10)
500 |   (denote-explore-network-d3-js "https://d3js.org/d3.v7.min.js")
501 |   (denote-explore-network-d3-template "<file path>")
502 |   (denote-explore-network-graphviz-header "<header strings>")
503 |   (denote-explore-network-graphviz-filetype 'svg)
504 |   :bind
505 |   (;; Statistics
506 |    ("C-c e s n" . denote-explore-count-notes)
507 |    ("C-c e s k" . denote-explore-count-keywords)
508 |    ("C-c e s e" . denote-explore-barchart-filetypes)
509 |    ("C-c e s w" . denote-explore-barchart-keywords)
510 |    ("C-c e s t" . denote-explore-barchart-timeline)
511 |    ;; Random walks
512 |    ("C-c e w n" . denote-explore-random-note)
513 |    ("C-c e w r" . denote-explore-random-regex)
514 |    ("C-c e w l" . denote-explore-random-link)
515 |    ("C-c e w k" . denote-explore-random-keyword)
516 |    ;; Denote Janitor
517 |    ("C-c e j d" . denote-explore-duplicate-notes)
518 |    ("C-c e j D" . denote-explore-duplicate-notes-dired)
519 |    ("C-c e j l" . denote-explore-dead-links)
520 |    ("C-c e j z" . denote-explore-zero-keywords)
521 |    ("C-c e j s" . denote-explore-single-keywords)
522 |    ("C-c e j r" . denote-explore-rename-keywords)
523 |    ("C-c e j y" . denote-explore-sync-metadata)
524 |    ("C-c e j i" . denote-explore-isolated-files)
525 |    ;; Visualise denote
526 |    ("C-c e n" . denote-explore-network)
527 |    ("C-c e r" . denote-explore-network-regenerate)
528 |    ("C-c e d" . denote-explore-barchart-degree)
529 |    ("C-c e b" . denote-explore-barchart-backlinks)))
530 | @end lisp
531 | 
532 | You can use the most recent development version directly from GitHub (Emacs 29.1 or higher):
533 | 
534 | @lisp
535 | (unless (package-installed-p 'denote-explore)
536 |   (package-vc-install
537 |    '(denote-explore
538 |      :url "https://github.com/pprevos/denote-explore/")))
539 | @end lisp
540 | 
541 | @node Acknowledgements
542 | @chapter Acknowledgements
543 | 
544 | This code would only have existed with the help of Protesilaos Stavrou, developer of Denote.
545 | 
546 | In addition, Jakub Szczerbowski, Samuel W@. Flint, Ad (skissue), Vedang Manerikar, Jousimies, Alexis Praga, Dav1d23 and Quijote Libre made significant contributions and suggestions.
547 | 
548 | Noor Us Sabah on Fiverr wrote the first version of the D3.JS template file. All enhancements were generated with the assistance of ChatGPT@.
549 | 
550 | Feel free to raise an issue here on GitHub if you have any questions or find bugs or suggestions for enhanced functionality.
551 | 
552 | @node License
553 | @chapter License
554 | 
555 | This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License or (at your option) any later version.
556 | 
557 | This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY, INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE@. See the GNU General Public License for more details.
558 | 
559 | For a full copy of the GNU General Public License, see @uref{https://www.gnu.org/licenses/}.
560 | 
561 | @bye
562 | 


--------------------------------------------------------------------------------
/denote-explore.info:
--------------------------------------------------------------------------------
  1 | This is denote-explore.info, produced by makeinfo version 7.2 from
  2 | denote-explore.texi.
  3 | 
  4 | INFO-DIR-SECTION Emacs misc features
  5 | START-INFO-DIR-ENTRY
  6 | * Denote Explorer: (denote-explore). Explore, visualise and analyse Denote files.
  7 | END-INFO-DIR-ENTRY
  8 | 
  9 | 
 10 | File: denote-explore.info,  Node: Top,  Next: Descriptive Statistics,  Up: (dir)
 11 | 
 12 | Denote Explorer: Explore your Denote digital garden
 13 | ***************************************************
 14 | 
 15 | The Denote package by Protesilaos (Prot) Stavrou provides extensive
 16 | functionality for creating, retrieving, managing, and linking files in
 17 | plain text, Markdown, and Org Mode.  The most redeeming qualities of
 18 | this package are its filename convention and modular simplicity.
 19 | 
 20 |    Due to its reliance on file names, you can also use the package to
 21 | access other file types, such as PDFs or multimedia files (which we call
 22 | Denote attachments).  In this way, Denote becomes a fully-featured
 23 | personal knowledge management system.
 24 | 
 25 |    The Denote-Explorer package came into existence as my collection of
 26 | Denote files grew.  I created some auxiliary functions to manage and
 27 | explore my burgeoning Denote files, resulting in four types of commands:
 28 | 
 29 |   1. Descriptive statistics: Count notes, attachments and keywords.
 30 |   2. Random walks: Generate new ideas using serendipity.
 31 |   3. Janitor: Maintain your denote collection.
 32 |   4. Knowledge Graphs: Visualise and analyse your Denote files as a
 33 |      network.
 34 | 
 35 | * Menu:
 36 | 
 37 | * Descriptive Statistics::
 38 | * Random Walks::
 39 | * Janitor::
 40 | * Knowledge Graphs::
 41 | * Installation and Package Configuration::
 42 | * Acknowledgements::
 43 | * License::
 44 | 
 45 | -- The Detailed Node Listing --
 46 | 
 47 | Janitor
 48 | 
 49 | * Duplicate notes::
 50 | * Missing Links::
 51 | * Managing Keywords::
 52 | * Synchronising Meta Data::
 53 | 
 54 | Knowledge Graphs
 55 | 
 56 | * Principles of Knowledge Graphs::
 57 | * Community of Notes::
 58 | * Note Neighbourhood::
 59 | * Sequences Network::
 60 | * Keyword Network::
 61 | * Network Layout and Presentation::
 62 | * D3.js: D3js.
 63 | * GraphViz::
 64 | * Graph Exchange XML Format::
 65 | * Analysing the Denote Network::
 66 | 
 67 | 
 68 | File: denote-explore.info,  Node: Descriptive Statistics,  Next: Random Walks,  Prev: Top,  Up: Top
 69 | 
 70 | 1 Descriptive Statistics
 71 | ************************
 72 | 
 73 | The Denote-Explorer package distinguishes between Denote files (notes)
 74 | and attachments.  Denote files are either Org Mode, Markdown, or Plain
 75 | Text.  All other files, such as photographs, PDFs, media files, LaTeX,
 76 | and HTML, are attachments.
 77 | 
 78 |    After a day of working hard on your digital knowledge garden, you can
 79 | count the notes and attachments in your collection.  Two functions
 80 | provide some basic statistics of your Denote files:
 81 | 
 82 |   1. ‘denote-explore-count-notes’: Count the number of notes and
 83 |      attachments.  With universal argument, only count notes.
 84 |   2. ‘denote-explore-count-keywords’: Count the number of distinct
 85 |      Denote keywords.
 86 | 
 87 |    These functions are informative, but a graph says more than a
 88 | thousand numbers.  The built-in ‘chart.el’ package by Eric M.  Ludlam is
 89 | a quaint tool for creating bar charts in a plain text buffer.  Two
 90 | commands are available in Denote-Explorer to visualise basic statistics:
 91 | 
 92 |   1. ‘denote-explore-barchart-filetypes’: Visualise used file
 93 |      extensions.  With universal argument ‘C-u’ visualises only
 94 |      attachments.
 95 |   2. ‘denote-explore-barchart-keywords’: Visualise the top-n keywords
 96 |   3. ‘denote-explore-barchart-timeline’: Visualise notes created by year
 97 | 
 98 |    The ‘denote-excluded-files-regexp’ variable can contain a regular
 99 | expression of files excluded from these statistical functions.
100 | 
101 | 
102 | File: denote-explore.info,  Node: Random Walks,  Next: Janitor,  Prev: Descriptive Statistics,  Up: Top
103 | 
104 | 2 Random Walks
105 | **************
106 | 
107 | Creativity springs from a medley of experiences, emotions, subconscious
108 | musings, and connecting random ideas.  Introducing random elements into
109 | the creative process generates avenues of thought you might not have
110 | travelled otherwise.  Random walks through your notes can be beneficial
111 | when you're stuck in a rut or just like to walk through your files
112 | randomly.
113 | 
114 |    A random walk is an arbitrary sequence without a defined relationship
115 | between the steps.  You take a random walk by jumping to a random note,
116 | connected or unconnected to the current buffer.
117 | 
118 |    The Denote-Explorer package provides three commands to inject some
119 | randomness into your explorations:
120 | 
121 |   1. ‘denote-explore-random-note’: Jump to a random Denote file.
122 |   2. ‘denote-explore-random-regex’: Jump to a random Denote file that
123 |      matches a regular expression.
124 |   3. ‘denote-explore-random-link’: Jump to a random linked note (either
125 |      forward or backward) or attachments (forward only).
126 |   4. ‘denote-explore-random-keyword’: Jump to a random Denote file with
127 |      the same selected keyword(s).
128 |   5. ‘denote-explore-random-signature’: Jump to a random Denote file
129 |      with the same (partial) signature.
130 | 
131 |    The default state is that these functions jump to any Denote text
132 | file (plain text, Markdown or Org-mode).  Prefixing the universal
133 | argument (‘C-u’) includes attachments in the sample for a random jump,
134 | otherwise the walk remains within the collection of notes.  The
135 | ‘denote-explore-random-regex-ignore’ variable can contain a regular
136 | expression of files excluded from the sample of files to jump to.
137 | 
138 |    Jumping to a note that matches a regular expression lets you find
139 | random notes matching a search string.  For example, to find a note you
140 | wrote in May 2022, use ‘^202205’ and using ‘202305.*_journal’ jumps to a
141 | random journal entry in May 2023.
142 | 
143 |    Jumping to a randomly linked file naturally only works when the
144 | current buffer is a Denote file.  A warning appears when the current
145 | buffer is an isolated note (no links or backlinks available).
146 | 
147 |    When jumping to a random file with one or more matching keywords, you
148 | can choose one or more keywords from the current buffer, or override the
149 | completion options with free text.  The asterisk symbol ‘*’ selects all
150 | keywords in the completion list.  This section process is skipped when
151 | the current buffer only has one keyword.  When the current buffer is not
152 | a Denote file, you can choose any available keyword(s) in your Denote
153 | collection.
154 | 
155 |    Jumping to a random note and matching multiple keywords only works
156 | when ‘denote-sort-keywords’ is enabled, or when the selected keywords
157 | are in the same order as in the target file.  You can alphabetise
158 | keywords in your Denote files with ‘denote-explore-sort-keywords’,
159 | explained in the next section.
160 | 
161 | 
162 | File: denote-explore.info,  Node: Janitor,  Next: Knowledge Graphs,  Prev: Random Walks,  Up: Top
163 | 
164 | 3 Janitor
165 | *********
166 | 
167 | After hoarding Denote files for a while, you may need a janitor to
168 | organise your collection.  A janitor ensures cleanliness, orderliness,
169 | and sanitation in a building, so this role is also perfect for managing
170 | to your Denote files.  The Denote-Explorer package provides a series of
171 | commands to assist with cleaning, organising, and sanitising your files.
172 | 
173 | * Menu:
174 | 
175 | * Duplicate notes::
176 | * Missing Links::
177 | * Managing Keywords::
178 | * Synchronising Meta Data::
179 | 
180 | 
181 | File: denote-explore.info,  Node: Duplicate notes,  Next: Missing Links,  Up: Janitor
182 | 
183 | 3.1 Duplicate notes
184 | ===================
185 | 
186 | The Denote package prevents duplicate identifiers when creating a new
187 | note, but when assigning filenames manually, or when exporting org
188 | files, duplicates might appear.
189 | 
190 |    The Denote identifier is a unique string constructed of the note's
191 | creation date and time in ISO 8601 format (e.g., ‘2024035T203312’).
192 | Denote either uses the current date and time when generating a new note
193 | or the date and time the file was created on the file system.
194 | 
195 |    The file's creation date and time are not always relevant for
196 | attachments.  For example, when adding scanned historical records, the
197 | identifier might be centuries ago, so it must be added manually.
198 | 
199 |    The ‘denote-explore-identify-duplicate-notes’ command lists all
200 | duplicate Denote files in a popup org buffer, which includes links to
201 | the suspected duplicate notes and attachments.
202 | 
203 |    Additionally, the ‘denote-explore-identify-duplicate-notes-dired’
204 | command displays files with duplicate identifiers in a Dired buffer.
205 | You can directly change filenames in the Dired buffer with
206 | ‘dired-toggle-read-only’ (‘C-x C-q’) or remove individual duplicates
207 | with ‘D’ (‘dired-do-delete’).  Note that this function only shows files
208 | in the denote directory and not its subdirectories or symbolic links.
209 | 
210 |    With the universal argument (‘C-u’), these commands ignore any
211 | duplicated identifiers created when exporting Denote Org mode files.
212 | 
213 |    The ‘denote-excluded-files-regexp’ variable can contain a regular
214 | expression of files excluded from duplicate detection.
215 | 
216 |    Be careful when manually changing the identifier of a Denote file, as
217 | it can destroy the integrity of your links.  Please ensure that the file
218 | you rename does not have any links pointing to it.  You can use the
219 | ‘denote-find-link’ and ‘denote-find-backlink’ commands to check a file
220 | for links, or use the Denote Explorer link checker.
221 | 
222 | 
223 | File: denote-explore.info,  Node: Missing Links,  Next: Managing Keywords,  Prev: Duplicate notes,  Up: Janitor
224 | 
225 | 3.2 Missing Links
226 | =================
227 | 
228 | The Denote identifier keeps links active even when you change the file
229 | name, tags or signature.  But missing or dead links might still appear
230 | in your network of notes when you delete redundant information or you
231 | manually change an identifier.
232 | 
233 |    Using ‘denote-explore-missing-links’ lists all links to non-existing
234 | notes, attachments and links to other files (such as images) in your
235 | Denote directory.
236 | 
237 |    This function creates a read-only Org mode file with two tables of
238 | source documents and the missing linked Denote file or other linked
239 | files.  You can click on the links to jump to the source file at the
240 | missing link location and either remove or edit it.  Links will appear
241 | in their literal form, i.e.  ‘[[<link>][<description>]]’.  You can
242 | toggle this behaviour with ‘org-toggle-link-display’ to show the
243 | formatted links.
244 | 
245 |    The link contains an Elisp function to open the linked document and
246 | find the relevant link.  Emacs will ask for confirmation every time you
247 | follow such a link.  You can disable these warnings by setting
248 | ‘org-link-elisp-confirm-function’ to ‘nil’.
249 | 
250 |    When the missing link is found because perhaps you already removed
251 | it, an error message pops up in the echo area.
252 | 
253 |    The ‘denote-excluded-files-regexp’ variable can contain a regular
254 | expression of files that are excluded from the search for missing Denote
255 | links.
256 | 
257 | 
258 | File: denote-explore.info,  Node: Managing Keywords,  Next: Synchronising Meta Data,  Prev: Missing Links,  Up: Janitor
259 | 
260 | 3.3 Managing Keywords
261 | =====================
262 | 
263 | Denote keywords connect notes with similar content.  Denote explore
264 | provides a few commands to assist with managing your menagerie of
265 | keywords.
266 | 
267 |    First step is to explore the keywords already being used in your
268 | collection of notes.  The ‘denote-explore-list-keywords’ command lists
269 | all used Denote keywords in a table, sorted by usage counts.  Calling
270 | this function with the universal argument (‘C-u’), sorts the list
271 | alphabetically.  This command provides similar functionality to
272 | ‘denote-explore-barchart-keywords’, but can show all keywords in one
273 | buffer.
274 | 
275 |    Keywords should not exist in solitude because a category with only
276 | one member is not informative.  Single keywords can arise because topics
277 | need to be fully developed or due to a typo.  The
278 | ‘denote-explore-single-keywords’ command provides a list of file tags
279 | that are only used once.  The list of single keywords is presented in
280 | the minibuffer, from where you can open the relevant note or attachment.
281 | 
282 |    You can also find notes or attachments without keywords with the
283 | ‘denote-explore-zero-keywords’ command.  This command lists all notes
284 | and attachments without keywords in the minibuffer, so you can open them
285 | and consider adding keywords or leaving them as is.
286 | 
287 |    You can rename or remove keywords with
288 | ‘denote-explore-rename-keyword’.  Select one or more existing keywords
289 | from the completion list and enter the new keyword.  This function
290 | renames all chosen keywords or removes the original keyword from all
291 | existing notes when you enter an empty string as new keyword.  This
292 | function cycles through all notes and attachments containing one or more
293 | selected keywords and asks for confirmation before making any changes.
294 | The new keyword list is stored alphabetically.  This function uses the
295 | front matter as the source of truth for notes and the file name for
296 | attachments.
297 | 
298 |    The ‘denote-excluded-files-regexp’ variable can contain a regular
299 | expression of files that are excluded from the purview of these
300 | functions.
301 | 
302 |    You can also visualise keywords using knowledge graphs described
303 | below.
304 | 
305 | 
306 | File: denote-explore.info,  Node: Synchronising Meta Data,  Prev: Managing Keywords,  Up: Janitor
307 | 
308 | 3.4 Synchronising Meta Data
309 | ===========================
310 | 
311 | Denote stores the metadata for each note in the filename using its
312 | ingenious format.  Some of this metadata is copied to the front matter
313 | of a note, which can lead to discrepancies between the two metadata
314 | sources.
315 | 
316 |    The ‘denote-explore-sync-metadata’ function checks all notes and asks
317 | the user to rename any file where the front matter data differs from the
318 | file name.  The front matter data is the source of truth for the title
319 | and keywords.  This function also enforces the alphabetisation of
320 | keywords, which assists with finding notes.
321 | 
322 |    The ‘denote-excluded-files-regexp’ variable can contain a regular
323 | expression of files that are excluded from this synchronisation.
324 | 
325 | 
326 | File: denote-explore.info,  Node: Knowledge Graphs,  Next: Installation and Package Configuration,  Prev: Janitor,  Up: Top
327 | 
328 | 4 Knowledge Graphs
329 | ******************
330 | 
331 | Emacs is a text processor with limited graphical capabilities.  However,
332 | committing your ideas to text requires a linear way of thinking since
333 | you can only process one word at a time.  Visual thinking through tools
334 | such as mind maps or network diagrams is another way to approach your
335 | ideas.  One of the most common methods to visualise interlinked
336 | documents is in a network or a personal knowledge graph, or in more
337 | general terms, a network diagram.
338 | 
339 | * Menu:
340 | 
341 | * Principles of Knowledge Graphs::
342 | * Community of Notes::
343 | * Note Neighbourhood::
344 | * Sequences Network::
345 | * Keyword Network::
346 | * Network Layout and Presentation::
347 | * D3.js: D3js.
348 | * GraphViz::
349 | * Graph Exchange XML Format::
350 | * Analysing the Denote Network::
351 | 
352 | 
353 | File: denote-explore.info,  Node: Principles of Knowledge Graphs,  Next: Community of Notes,  Up: Knowledge Graphs
354 | 
355 | 4.1 Principles of Knowledge Graphs
356 | ==================================
357 | 
358 | Denote implements a linking mechanism that connects notes (either Org,
359 | Markdown, or plain text files) to other notes or attachments.  This
360 | mechanism allows the user to visualise all notes as a network diagram.
361 | 
362 |    Network visualisation in Denote is not just a feature but a powerful
363 | tool that visualises how notes are linked, helping you discover
364 | previously unseen connections between your thoughts and enhancing your
365 | creative process.
366 | 
367 |    It's important to note that Denote-Explorer does not offer live
368 | previews of your note collection.  This deliberate choice prevents the
369 | 'dopamine traps' of seeing your thoughts develop in real-time.  Instead,
370 | Denote-Explorer provides a focused tool for the surgical dissection of
371 | your second brain, while the main user interface remains text-based.
372 | 
373 |    A network diagram has nodes (vertices) and edges.  Each node
374 | represents a note or an attachment, and each edge represents a link
375 | between them.  A link between file is directed and the arrow indicates
376 | the source and target of the link.  The diagram below shows the basic
377 | principle of a knowledge graph.  In the actual output, nodes are
378 | circles.
379 | 
380 |      ┌──────────────┐        ┌──────────────┐
381 |      │     node     │  edge  │     node     │
382 |      │    (note)    ├───────►│    (note)    │
383 |      │ (attachment) │ (link) │ (attachment) │
384 |      └──────────────┘        └──────────────┘
385 | 
386 |    Denote-Explorer provides three types of network diagrams to explore
387 | the relationships between your thoughts:
388 | 
389 |   1. Community: Notes matching a regular expression
390 |   2. Neighbourhood: Search n-deep in a selected note
391 |   3. Sequence: Visualise a hierarchical sequence
392 |   4. Keywords: Relationships between keywords
393 | 
394 |    The package exports and displays these in one of three formats, with
395 | JSON displayed in HTML / D3.js files as the default.  Other options are
396 | GraphViz and GEXF.
397 | 
398 |    You create a network with the ‘denote-explore-network’ command.  This
399 | command will ask the user to select the type of network to create.  Each
400 | network type requires additional inputs to analyse to a defined part of
401 | your Denote files.
402 | 
403 |    The ‘denote-explore-network-regenerate’ command recreates the
404 | previous graph with the same parameters, which is useful when changing
405 | the structure of your notes and you like to see the result visualised
406 | without having to re-enter the parameters.
407 | 
408 |    Using the universal argument ‘C-u’ before issuing these two command
409 | (re)generates a network excluding attachments.  The
410 | ‘denote-excluded-files-regexp’ variable can contain a regular expression
411 | of files that are excluded from visualisation.
412 | 
413 | 
414 | File: denote-explore.info,  Node: Community of Notes,  Next: Note Neighbourhood,  Prev: Principles of Knowledge Graphs,  Up: Knowledge Graphs
415 | 
416 | 4.2 Community of Notes
417 | ======================
418 | 
419 | A community graph displays all notes matching a regular expression and
420 | their connections.  The example below indicates the community that
421 | contains the ‘_emacs’ regular expression, within the dashed line.  The
422 | algorithm prunes any links to non-matching notes, which in the example
423 | below is the note with the ‘_vim’ keyword.
424 | 
425 |      ┌ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┐
426 |         _emacs community
427 |      │ ┌──────┐  ┌──────┐ │  ┌────┐
428 |        │_emacs│  │_emacs│───►│_vim│
429 |      │ └──┬───┘  └──────┘ │  └────┘
430 |           │
431 |      │    ▼               │
432 |        ┌──────┐
433 |      │ │_emacs│           │
434 |        └──────┘
435 |      └ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┘
436 | 
437 |    To generate a community graph, use ‘denote-explore-network’, choose
438 | 'Community' and enter a regular expression.  When no matching files are
439 | found or there are only solitary nodes, then the network is not
440 | generated and you will see this warning: ‘No Denote files or (back)links
441 | found for regex’.
442 | 
443 |    The ‘denote-explore-network-regex-ignore’ variable defines a regular
444 | expression to exclude certain notes from community networks.  For
445 | example, if you create meta notes with long lists of dynamic links and
446 | they have the ‘_meta’ keyword, then you could exclude these nodes by
447 | customising this variable to the relevant regular expression.
448 | 
449 | 
450 | File: denote-explore.info,  Node: Note Neighbourhood,  Next: Sequences Network,  Prev: Community of Notes,  Up: Knowledge Graphs
451 | 
452 | 4.3 Note Neighbourhood
453 | ======================
454 | 
455 | The neighbourhood of a note consists of all files linked to it at one or
456 | more steps deep.  The algorithm selects members of the graph from linked
457 | and back-linked notes.  This visualisation effectively creates the
458 | possible paths you can follow with the ‘denote-explore-random-link’
459 | function discussed in the Random Walks section above.
460 | 
461 |    The illustration below shows the principle of the linking depth.
462 | Notes B and C are at linking depth 1 from A and notes D and E are at
463 | depth 2 from A.
464 | 
465 |      Depth 1      2
466 |           ┌─┐    ┌─┐
467 |        ┌─►│B│◄───┤D│
468 |        │  └─┘    └─┘
469 |       ┌┴┐
470 |       │A│
471 |       └─┘
472 |        ▲  ┌─┐    ┌─┐
473 |        └──┤C├───►│E│
474 |           └─┘    └─┘
475 | 
476 |    To generate a neighbourhood graph from the current Denote note
477 | buffer, use ‘denote-explore-network’ and enter the graph's depth.  The
478 | user enters the required depth, and the software searches all notes
479 | linked to the current buffer at that depth.  When building this graph
480 | from a buffer that is not a Denote file, the system also asks to select
481 | a source file (A in the diagram).  The system issues a warning when you
482 | select a note without links or backlinks.  You can identify Denote files
483 | without any links with the ‘denote-explore-isolated-notes’ function
484 | describe above.
485 | 
486 |    The complete set of your Denote files is most likely a disconnected
487 | Graph, meaning that there is no one path that connects all nodes.
488 | Firstly, there will be isolated notes.  There will also exist isolated
489 | neighbourhoods of notes that connect to each other but not to other
490 | files.
491 | 
492 |    A depth of more than three links is usually not informative because
493 | the network can become to large to read, or you hit the edges of your
494 | island of connected notes.
495 | 
496 |    The ‘denote-explore-network-regex-ignore’ variable lets you define a
497 | regular expression of notes exclude from neighbourhood networks.
498 | 
499 | 
500 | File: denote-explore.info,  Node: Sequences Network,  Next: Keyword Network,  Prev: Note Neighbourhood,  Up: Knowledge Graphs
501 | 
502 | 4.4 Sequences Network
503 | =====================
504 | 
505 | Denote signatures can define a hierarchical sequence of notes, using a
506 | family analogy.  For example a note with signature ‘1=a’ is the child of
507 | a note with signature ‘1’ and a note with signature ‘1=b’ is its
508 | sibling.  The note with signature ‘1=a=1’ is the child of ‘1=a’ and the
509 | grandchild of ‘1’, and so forth.  In a sequence network, links exist
510 | independent of any Denote links inside a note, the relationship is only
511 | based on the hierarchy of the signatures.
512 | 
513 |      ┌─────┐    ┌─────┐    ┌─────┐
514 |      |  1  ├───►│ 1=a ├───►│1=a=1│
515 |      └──┬──┘    └─────┘    └─────┘
516 |         │       ┌─────┐
517 |         └──────►│ 1=b │
518 |                 └─────┘
519 | 
520 |    The content of the signatures can be either numbers or letters as the
521 | order of children is not taken into consideration.  These sequences can
522 | go on to many generations, building a family tree of your notes.  These
523 | sequences are the basic building block of the popular Zettelkasten
524 | methodology.
525 | 
526 |    The Denote-Sequence package provides specialised functions to manage
527 | hierarchical connections between files, *note info denote-sequence:
528 | (denote-sequence)Top.
529 | 
530 |    To generate a sequence graph, use ‘denote-explore-network’ and select
531 | the signature of the root node (note ‘1’ in the diagram).  When not
532 | selecting any signature, all Denote files with a signature are included
533 | in the visualisation.
534 | 
535 |    The ‘denote-explore-network-regex-ignore’ variable lets you define a
536 | regular expression of notes exclude from neighbourhood networks.
537 | 
538 | 
539 | File: denote-explore.info,  Node: Keyword Network,  Next: Network Layout and Presentation,  Prev: Sequences Network,  Up: Knowledge Graphs
540 | 
541 | 4.5 Keyword Network
542 | ===================
543 | 
544 | The last available method to visualise your Denote collection is to
545 | develop a network of keywords.  Two keywords are connected when used in
546 | the same note.
547 | 
548 |    All keywords in a note form a complete network.  The union of all
549 | complete networks from all files in your Denote collection defines the
550 | keywords network.  The relationship between two keywords can exist in
551 | multiple notes, so the links between keywords are weighted.  The line
552 | thickness between two keywords indicates the frequency (weight) of their
553 | relationship.
554 | 
555 |    While the first two graph types are directed (arrows indicate the
556 | direction of links), the keyword network is undirected.  These links are
557 | bidirectional associations between keywords.  The diagram below shows
558 | three notes, two with two keywords and one with three keywords.  Each
559 | notes forms a small complete network that links all keywords.
560 | 
561 |      ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐   ┌─────┐ ┌─────┐
562 |      │_kwd1├─┤_kwd2│   │_kwd1├─┤_kwd2│   │_kwd3├─┤_kwd4│
563 |      └─────┘ └─────┘   └─┬───┘ └───┬─┘   └─────┘ └─────┘
564 |                          │ ┌─────┐ │
565 |                          └─┤_kwd3├─┘
566 |                            └─────┘
567 | 
568 |    The union of these three networks forms the keyword network for this
569 | collection of notes.  The example generates the following keyword
570 | network.
571 | 
572 |      ┌─────┐ ┌─────┐
573 |      │_kwd1├─┤_kwd2│
574 |      └─┬───┘ └───┬─┘
575 |        │         │
576 |        │ ┌─────┐ │  ┌─────┐
577 |        └─┤_kwd3├─┴──┤_kwd4│
578 |          └─────┘    └─────┘
579 | 
580 |    When generating this graph type, you will need to enter a minimum
581 | edge weight (n).  The graph then will only show those keywords that are
582 | at least n times associated with each other.  The default is one.
583 | 
584 |    Some keywords might have to be excluded from this graph because they
585 | skew the results.  For example, when using the Citar-Denote package, you
586 | might like to exclude the ‘bib’ keyword from the diagram because it is
587 | only used to minimise the search space for bibliographic notes and has
588 | no further semantic value.  The ‘denote-explore-network-keywords-ignore’
589 | variable lists keywords ignored in this visualisation.
590 | 
591 | 
592 | File: denote-explore.info,  Node: Network Layout and Presentation,  Next: D3js,  Prev: Keyword Network,  Up: Knowledge Graphs
593 | 
594 | 4.6 Network Layout and Presentation
595 | ===================================
596 | 
597 | Emacs cannot independently generate graphics and thus relies on external
598 | software.  This package can use three external mechanisms to create
599 | graphs (configurable with ‘denote-explore-network-format’), set to D3.js
600 | / JSON output by default.  Other available formats are GraphViz SVG and
601 | GEXF, discussed in detail below.
602 | 
603 |    The Denote-Explorer network algorithm consists of four steps:
604 | 
605 |   1. The ‘denote-explore-network’ function determines the relevant
606 |      functions based on user input.
607 |   2. The code generates a nested association list for the selected
608 |      graph:
609 |         • Metadata e.g.: ‘(meta (directed . t) (type . "Neighbourhood")
610 |           (parameters "20210104T194405" 2))’
611 |         • Association list of nodes, e.g., ‘(((id . "20210104T194405")
612 |           (name . "Platonic Solids") (keywords "geometry" "esotericism")
613 |           (type . "org") (degree . 4)) ...)’.  In the context of Denote,
614 |           the degree of a network node is the unweighted sum of links
615 |           and backlinks in a note.
616 |         • Association list of edges and their weights: ‘(((source .
617 |           "20220529T190246") (target . "20201229T143000") (weight . 1))
618 |           ...)’.  The weight of an edge indicates the number of time the
619 |           two files are linked, or the number of times two keywords
620 |           appear in the same note in case of a keyword graph.
621 |   3. The package encodes the association list to a either a JSON,
622 |      GraphViz DOT, or GEXF file.  The location and name of this file is
623 |      configurable with the ‘denote-explore-network-directory’ and
624 |      ‘denote-explore-network-filename’ variables.
625 |   4. Relevant external software displays the result (in most cases a web
626 |      browser).
627 | 
628 | 
629 | File: denote-explore.info,  Node: D3js,  Next: GraphViz,  Prev: Network Layout and Presentation,  Up: Knowledge Graphs
630 | 
631 | 4.7 D3.js
632 | =========
633 | 
634 | D3.js (https://d3js.org/) is a JavaScript library for visualising data.
635 | This method provides an aesthetically pleasing and interactive view of
636 | the structure of your notes.  Denote-Explorer stores the desired network
637 | as a JSON file.  This JSON file is merged with a HTML / JavaScript
638 | template to visualise the network.  Emacs invokes your default internet
639 | browser to view the network.
640 | 
641 |    Hover over any node to reveal its name and relevant metadata.  For
642 | neighbourhood and community graphs, when the note is an image or PDF
643 | file, a preview appears in the tooltip.  Clicking on a node opens the
644 | relevant file in the browser, or whatever application the browser
645 | associates with the relevant file type.
646 | 
647 |    For community and neighbourhood graphs, the diameter of nodes is
648 | proportional to their degree.  Thus, the most linked note in your query
649 | will be the most visible.  The colours indicate the file type of each
650 | node.  The size of nodes in a network graph is the same for all.
651 | 
652 |    For nodes with a degree greater than two, the name is displayed
653 | outside the node.
654 | 
655 |    In keyword graphs, the thickness of the edges indicates the number of
656 | times two keywords are associated with each other.
657 | 
658 |    The info button shows the type of network and provides some basic
659 | statistics, such as the number of nodes (files) and edges (links) and
660 | the network density.  The density of a network is the ratio between the
661 | number of edges and the potential number of edges.  A density of zero,
662 | as such means that no nodes are connected.  In a network with a density
663 | of one all nodes are connected to each other.
664 | 
665 |    For community graphs the panel also provides the option to show or
666 | hide isolated nodes to increase clarity.  Neighbourhood and keyword
667 | graphs by their definition do not have isolated nodes.
668 | 
669 |    For community and neighbourhood graphs, the info panel also shows the
670 | distribution of keywords for the visualised network.
671 | 
672 |    You can customise the output of the network files by modifying the
673 | template.  The ‘denote-explore-network-d3-template’ variable contains
674 | the location of the HTML/JavaScript template file so you can craft your
675 | own versions.  This file contains several shortcodes:
676 | 
677 |    • ‘{{graph-type}}’: Type of graph, community, neighbourhood or
678 |      network
679 |    • ‘{{d3-js}}’: Content of the ‘denote-explore-network-d3-js’
680 |      variable, which contains the URL of the D3 source code, which has
681 |      to be version 7 or above.  The default template fetches the
682 |      JavaScript code from the ‘d3js.org’ website.  You can customise
683 |      this variable to use a locally stored file.
684 |    • ‘{{json-content}}’: The generated JSON file with the network
685 |      definition
686 |    • ‘{{d3-colourscheme}}’: Content of
687 |      ‘denote-explore-network-d3-colours’.  this variable assigns a
688 |      colour palette for the node file types.  You can choose between any
689 |      of the available categorical colour schemes in the D3 package.
690 |      Colours are assigned in the graph in order of appearance in the
691 |      JSON file, so file types can have different colours in different
692 |      graphs.
693 | 
694 | 
695 | File: denote-explore.info,  Node: GraphViz,  Next: Graph Exchange XML Format,  Prev: D3js,  Up: Knowledge Graphs
696 | 
697 | 4.8 GraphViz
698 | ============
699 | 
700 | GraphViz (https://graphviz.org/) is an open-source graph visualisation
701 | software toolkit, ideal for this task.  The Denote-Explorer software
702 | saves the graph in the DOT language as a ‘.gv’ file.  The GraphViz
703 | software converts the DOT code to an ‘SVG’ file.
704 | 
705 |    You will need to install GraphViz to enable this functionality.
706 | Denote-Explorer will raise an error when trying to create a GraphViz
707 | graph without the required external software available.
708 | 
709 |    Hover over any node to reveal its name and relevant metadata.
710 | Clicking on any node in a community or neighbourhood graph opens the
711 | relevant file in the browser, or whatever application the browser
712 | associates with the relevant file type.
713 | 
714 |    For community and neighbourhood graphs, the diameter of nodes is
715 | proportional to their degree.  Thus, the most linked note in your query
716 | will be the most visible.  When generating a neighbourhood, the source
717 | node is marked in a contrasting colour.
718 | 
719 |    For nodes with a degree greater than two, the name is displayed
720 | outside the node.  In keyword graphs, the thickness of the edges
721 | indicates the number of times two keywords are associated with each
722 | other.
723 | 
724 |    The diameter of nodes are sized relative to their degree.  Thus, the
725 | most referenced note in your system will be the most visible.  For nodes
726 | with a degree greater than two, the name is displayed outside the node
727 | (top left).
728 | 
729 |    The configurable ‘denote-explore-network-graphviz-header’ variable
730 | defines the basic settings for GraphViz graphs, such as the layout
731 | method and default node and edge settings.
732 | 
733 |    The ‘denote-explore-network-graphviz-filetype’ variable defines the
734 | GraphViz output format.  SVG (the default) or PDF provide the best
735 | results.
736 | 
737 | 
738 | File: denote-explore.info,  Node: Graph Exchange XML Format,  Next: Analysing the Denote Network,  Prev: GraphViz,  Up: Knowledge Graphs
739 | 
740 | 4.9 Graph Exchange XML Format
741 | =============================
742 | 
743 | The first two formats an insight into parts of your knowledge network,
744 | but there is a lot more you can do with this type of information.  While
745 | GraphViz and D3 are suitable for analysing sections of your network,
746 | this third option is ideal for storing the complete Denote network for
747 | further analysis.
748 | 
749 |    Graph Exchange XML Format (‘GEXF’) is a language for describing
750 | complex network structures.  This option saves the network as a ‘GEXF’
751 | file without opening it in external software.
752 | 
753 |    To save the whole network, use the Community option and enter an
754 | empty search string to include all files.
755 | 
756 |    You can analyse the exported file with Gephi Lite
757 | (https://gephi.org/gephi-lite/), a free online network analysis tool.
758 | The ‘GEXF’ file only contains the IDs, names and degree of the nodes;
759 | and the edges and their weights.
760 | 
761 | 
762 | File: denote-explore.info,  Node: Analysing the Denote Network,  Prev: Graph Exchange XML Format,  Up: Knowledge Graphs
763 | 
764 | 4.10 Analysing the Denote Network
765 | =================================
766 | 
767 | A well-trodden trope in network analysis is that all people are linked
768 | within six degrees of separation.  This may also be the case for your
769 | notes, but digging more than three layers deep is not very informative
770 | as the network can become large and difficult to review.
771 | 
772 |    It might seem that adding more connections between your notes
773 | improves them, but this is not necessarily the case.  The extreme case
774 | is a complete network where every file links to every other file.  This
775 | situation lacks any interesting structure and wouldn't be informative.
776 | So, be mindful of your approach to linking notes and attachments.
777 | 
778 |    Your Denote network is unlikely to be a fully connected graph.  In a
779 | connected graph, there is a path from any point to any other point.
780 | Within the context of Denote, this means that all files have at least
781 | one link or backlink.  Your network will most likely have isolated nodes
782 | (files without any (back)links) and islands of connected notes.
783 | 
784 |    The previously mentioned ‘denote-explore-isolated-files’ command
785 | lists all files without any links and backlinks to and from the note in
786 | the minibuffer.  You can select any note and add links as required to
787 | release it from isolation.  Calling this function with the universal
788 | argument ‘C-u’ includes attachments in the list of lonely files.  You
789 | can configure the behaviour of this function by customising
790 | ‘denote-explore-isolated-ignore-keywords’.  This variable provides a
791 | list of keywords to ignore when identifying isolated notes.
792 | 
793 |    The number of links and backlinks in a file (in mathematical terms,
794 | edges connected to a node) is the total degree of a node.  The degree
795 | distribution of a network is the probability distribution of these
796 | degrees over the whole network.  The ‘denote-explore-barchart-degree’
797 | function uses the built-in chart package to display a simple bar chart
798 | of the frequency of the total degree.
799 | 
800 |    This function might take a moment to run, depending on the number of
801 | notes in your system.  Evaluating this function with the universal
802 | argument ‘C-u’ excludes attachments from the analysis.
803 | 
804 |    The importance of a note is directly related to the number of
805 | backlinks.  The ‘denote-explore-barchart-backlinks’ function visualises
806 | the number of backlinks in the top-n notes in a horizontal bar chart,
807 | ordered by the number of backlinks.  This function asks for the number
808 | of nodes to visualise and then analyses the complete network of Denote
809 | notes (attachments are excluded because they don't have links from
810 | them), which can take a brief moment.
811 | 
812 | 
813 | File: denote-explore.info,  Node: Installation and Package Configuration,  Next: Acknowledgements,  Prev: Knowledge Graphs,  Up: Top
814 | 
815 | 5 Installation and Package Configuration
816 | ****************************************
817 | 
818 | This package is available from GitHub or through MELPA.
819 | 
820 |    The configuration below customises all available variables and binds
821 | all available commands to the ‘C-c e’ prefix.  To get started you don't
822 | need to configure anything.  You should modify this configuration to
823 | suit your needs, as one person's sensible defaults are another person's
824 | nightmare.
825 | 
826 |      (use-package denote-explore
827 |        :custom
828 |        ;; Where to store network data and in which format
829 |        (denote-explore-network-directory "<folder>")
830 |        (denote-explore-network-filename "denote-network")
831 |        (denote-explore-network-keywords-ignore "<keywords list>")
832 |        (denote-explore-network-regex-ignore "<regex>")
833 |        (denote-explore-network-format 'd3.js)
834 |        (denote-explore-network-d3-colours 'SchemeObservable10)
835 |        (denote-explore-network-d3-js "https://d3js.org/d3.v7.min.js")
836 |        (denote-explore-network-d3-template "<file path>")
837 |        (denote-explore-network-graphviz-header "<header strings>")
838 |        (denote-explore-network-graphviz-filetype 'svg)
839 |        :bind
840 |        (;; Statistics
841 |         ("C-c e s n" . denote-explore-count-notes)
842 |         ("C-c e s k" . denote-explore-count-keywords)
843 |         ("C-c e s e" . denote-explore-barchart-filetypes)
844 |         ("C-c e s w" . denote-explore-barchart-keywords)
845 |         ("C-c e s t" . denote-explore-barchart-timeline)
846 |         ;; Random walks
847 |         ("C-c e w n" . denote-explore-random-note)
848 |         ("C-c e w r" . denote-explore-random-regex)
849 |         ("C-c e w l" . denote-explore-random-link)
850 |         ("C-c e w k" . denote-explore-random-keyword)
851 |         ;; Denote Janitor
852 |         ("C-c e j d" . denote-explore-duplicate-notes)
853 |         ("C-c e j D" . denote-explore-duplicate-notes-dired)
854 |         ("C-c e j l" . denote-explore-dead-links)
855 |         ("C-c e j z" . denote-explore-zero-keywords)
856 |         ("C-c e j s" . denote-explore-single-keywords)
857 |         ("C-c e j r" . denote-explore-rename-keywords)
858 |         ("C-c e j y" . denote-explore-sync-metadata)
859 |         ("C-c e j i" . denote-explore-isolated-files)
860 |         ;; Visualise denote
861 |         ("C-c e n" . denote-explore-network)
862 |         ("C-c e r" . denote-explore-network-regenerate)
863 |         ("C-c e d" . denote-explore-barchart-degree)
864 |         ("C-c e b" . denote-explore-barchart-backlinks)))
865 | 
866 |    You can use the most recent development version directly from GitHub
867 | (Emacs 29.1 or higher):
868 | 
869 |      (unless (package-installed-p 'denote-explore)
870 |        (package-vc-install
871 |         '(denote-explore
872 |           :url "https://github.com/pprevos/denote-explore/")))
873 | 
874 | 
875 | File: denote-explore.info,  Node: Acknowledgements,  Next: License,  Prev: Installation and Package Configuration,  Up: Top
876 | 
877 | 6 Acknowledgements
878 | ******************
879 | 
880 | This code would only have existed with the help of Protesilaos Stavrou,
881 | developer of Denote.
882 | 
883 |    In addition, Jakub Szczerbowski, Samuel W.  Flint, Ad (skissue),
884 | Vedang Manerikar, Jousimies, Alexis Praga, Dav1d23 and Quijote Libre
885 | made significant contributions and suggestions.
886 | 
887 |    Noor Us Sabah on Fiverr wrote the first version of the D3.JS template
888 | file.  All enhancements were generated with the assistance of ChatGPT.
889 | 
890 |    Feel free to raise an issue here on GitHub if you have any questions
891 | or find bugs or suggestions for enhanced functionality.
892 | 
893 | 
894 | File: denote-explore.info,  Node: License,  Prev: Acknowledgements,  Up: Top
895 | 
896 | 7 License
897 | *********
898 | 
899 | This program is free software; you can redistribute it and/or modify it
900 | under the terms of the GNU General Public License as published by the
901 | Free Software Foundation, either version 3 of the License or (at your
902 | option) any later version.
903 | 
904 |    This program is distributed in the hope that it will be useful but
905 | WITHOUT ANY WARRANTY, INCLUDING THE IMPLIED WARRANTIES OF
906 | MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
907 | General Public License for more details.
908 | 
909 |    For a full copy of the GNU General Public License, see
910 | <https://www.gnu.org/licenses/>.
911 | 
912 | 
913 | Tag Table:
914 | Node: Top249
915 | Node: Descriptive Statistics1993
916 | Node: Random Walks3530
917 | Node: Janitor6498
918 | Node: Duplicate notes7074
919 | Node: Missing Links9086
920 | Node: Managing Keywords10613
921 | Node: Synchronising Meta Data12877
922 | Node: Knowledge Graphs13722
923 | Node: Principles of Knowledge Graphs14600
924 | Node: Community of Notes17551
925 | Node: Note Neighbourhood19233
926 | Node: Sequences Network21375
927 | Node: Keyword Network23223
928 | Node: Network Layout and Presentation25895
929 | Node: D3js27824
930 | Node: GraphViz31063
931 | Node: Graph Exchange XML Format32931
932 | Node: Analysing the Denote Network33970
933 | Node: Installation and Package Configuration36727
934 | Node: Acknowledgements39512
935 | Node: License40232
936 | 
937 | End Tag Table
938 | 
939 | 
940 | Local Variables:
941 | coding: utf-8
942 | Info-documentlanguage: en
943 | End:
944 | 


--------------------------------------------------------------------------------