├── .gitignore ├── NetworkxD3 ├── __init__.py └── NetworkxD3.py ├── docs ├── NetworkxD3.rst ├── index.rst ├── Makefile ├── make.bat └── conf.py ├── setup.py ├── README.md └── NetworkxD3example.ipynb /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc -------------------------------------------------------------------------------- /NetworkxD3/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/NetworkxD3.rst: -------------------------------------------------------------------------------- 1 | NetworkxD3 module 2 | ================= 3 | 4 | .. automodule:: NetworkxD3 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | .. NetworkxD3 documentation master file, created by 2 | sphinx-quickstart on Wed Jun 17 23:02:06 2015. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to NetworkxD3's documentation! 7 | ====================================== 8 | 9 | Contents: 10 | 11 | .. toctree:: 12 | :maxdepth: 4 13 | 14 | NetworkxD3 15 | 16 | 17 | Indices and tables 18 | ================== 19 | 20 | * :ref:`genindex` 21 | * :ref:`modindex` 22 | * :ref:`search` 23 | 24 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from setuptools import setup, find_packages 4 | import os 5 | import sys 6 | 7 | sys.path.insert(0, 'NetworkxD3') 8 | 9 | sys.path.pop(0) 10 | 11 | packages = ['NetworkxD3'] 12 | 13 | setup( 14 | name='networkxD3', 15 | version='0.20', 16 | author='Janu Verma', 17 | author_email='jv367@cornell.edu', 18 | description='D3 JavaScript networkx Graphs', 19 | url='https://github.com/Jverma/NetworkxD3', 20 | platforms=['Linux','Mac OSX', 'Windows', 'Unix'], 21 | classifiers=[ 22 | 'Development Status :: 3 - Alpha', 23 | 'Intended Audience :: Developers', 24 | 'License :: MIT License', 25 | 'Operating System :: OS Independent', 26 | 'Progamming Language :: Python', 27 | 'Topic :: Software Development :: Libraries :: Python Modules'], 28 | packages=packages, 29 | license='MIT' 30 | ) 31 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # NetworkxD3 2 | D3 JavaScript networkx Graphs 3 | 4 | This is an python high-level interface to [Christopher Gandrud](http://christophergandrud.blogspot.com/p/biocontact.html)'s R package [networkD3](https://christophergandrud.github.io/networkD3/). 5 | It renders [networkx](https://networkx.github.io/) graphs into HTML page containing a beautiful D3 visualization. Hence the name networkxD3 (shamelessly ripped from the original package networkD3), notice the x. 6 | 7 | 8 | **Requirements** 9 | - python and R both installed on the system. 10 | - rpy2 11 | - pandas 12 | - networkx 13 | 14 | 15 | 16 | **Install** 17 | 18 | python setup.py install 19 | 20 | 21 | **Usage** 22 | 23 | import networkx as nx 24 | from NetworkxD3 import simpleNetworkx 25 | 26 | G = nx.Graph() 27 | H = ["A","B","C","D","E","F","G", "H","I","J"] 28 | G.add_nodes_from(H) 29 | G.add_edges_from([("A","B"), ("A","C"), ("A","D"), ("A","J"), ("B","E"), ("B","F"), 30 | ("C","G"),("C","H"), ("D","I")]) 31 | 32 | simpleNetworkx(G) 33 | 34 | This will create an HTML page Net.html which contains the interactive plot. 35 | 36 | For a quick introduction to rpy2, check out [this post on my blog](https://januverma.wordpress.com/2015/05/17/calling-r-from-python-using-rpy2/). 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /NetworkxD3/NetworkxD3.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # D3 JavaScript networkx Graphs 3 | # Author - Janu Verma 4 | # jv367@cornell.edu 5 | # @januverma 6 | 7 | 8 | import networkx as nx 9 | from rpy2.robjects.packages import importr 10 | import rpy2.robjects as ro 11 | import pandas as p 12 | import pandas.rpy.common as com 13 | 14 | 15 | def simpleNetworkx(G): 16 | """ 17 | D3 JavaScript networkx graphs using python. 18 | 19 | This is an python interface to Christopher Gandrud's R 20 | package networkD3. 21 | 22 | Parameters 23 | ---------- 24 | G : A networkx graph. 25 | 26 | Returns 27 | ------- 28 | An HTML page containing an interactive visual of the graph. 29 | 30 | Example 31 | ------- 32 | >>> G = nx.Graph() 33 | >>> H = ["A","B","C","D","E","F","G", "H","I","J"] 34 | >>> G.add_nodes_from(H) 35 | >>> G.add_edges_from([("A","B"), ("A","C"), ("A","D"), ("A","J"), ("B","E"), ("B","F"), 36 | ("C","G"),("C","H"), ("D","I")]) 37 | >>> simpleNetworkxD3(G) 38 | >>> Net.html 39 | 40 | 41 | References 42 | ---------- 43 | [1] Christorpher Gandrud - https://github.com/christophergandrud/networkD3 44 | 45 | """ 46 | 47 | ro.r('src = c()') 48 | ro.r('target =c()') 49 | ro.r('rdf=data.frame()') 50 | 51 | df = p.DataFrame(data=G.edges()) 52 | 53 | df_r = com.convert_to_r_dataframe(df) 54 | 55 | ro.globalenv['src'] = df_r[0] 56 | ro.globalenv['target'] = df_r[1] 57 | 58 | ro.r('rdf=data.frame(src,target)') 59 | 60 | utils = importr('utils') 61 | utils.chooseCRANmirror(ind=1) 62 | 63 | 64 | try: 65 | networkD3 = importr('networkD3') 66 | except: 67 | utils.install_packages('networkD3') 68 | networkD3 = importr('networkD3') 69 | 70 | try: 71 | magrittr = importr('magrittr') 72 | except: 73 | utils.install_packages('magrittr') 74 | magrittr = importr('magrittr') 75 | 76 | 77 | ro.r('''simpleNetwork(rdf) %>% saveNetwork(file = 'Net.html')''') 78 | return None 79 | 80 | -------------------------------------------------------------------------------- /NetworkxD3example.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 3, 6 | "metadata": { 7 | "collapsed": false 8 | }, 9 | "outputs": [ 10 | { 11 | "data": { 12 | "text/html": [ 13 | "\n", 14 | " \n", 21 | " " 22 | ], 23 | "text/plain": [ 24 | "" 25 | ] 26 | }, 27 | "execution_count": 3, 28 | "metadata": {}, 29 | "output_type": "execute_result" 30 | } 31 | ], 32 | "source": [ 33 | "import networkx as nx\n", 34 | "from NetworkxD3.NetworkxD3 import simpleNetworkx\n", 35 | "from IPython.display import IFrame \n", 36 | "\n", 37 | "G = nx.Graph()\n", 38 | "H = [\"A\",\"B\",\"C\",\"D\",\"E\",\"F\",\"G\", \"H\",\"I\",\"J\"]\n", 39 | "G.add_nodes_from(H)\n", 40 | "G.add_edges_from([(\"A\",\"B\"), (\"A\",\"C\"), (\"A\",\"D\"), (\"A\",\"J\"), (\"B\",\"E\"), (\"B\",\"F\"),\n", 41 | "(\"C\",\"G\"),(\"C\",\"H\"), (\"D\",\"I\")])\n", 42 | "\n", 43 | "simpleNetworkx(G)\n", 44 | "IFrame('Net.html', width=400, height=400)" 45 | ] 46 | }, 47 | { 48 | "cell_type": "code", 49 | "execution_count": null, 50 | "metadata": { 51 | "collapsed": true 52 | }, 53 | "outputs": [], 54 | "source": [] 55 | } 56 | ], 57 | "metadata": { 58 | "kernelspec": { 59 | "display_name": "Python 2", 60 | "language": "python", 61 | "name": "python2" 62 | }, 63 | "language_info": { 64 | "codemirror_mode": { 65 | "name": "ipython", 66 | "version": 2 67 | }, 68 | "file_extension": ".py", 69 | "mimetype": "text/x-python", 70 | "name": "python", 71 | "nbconvert_exporter": "python", 72 | "pygments_lexer": "ipython2", 73 | "version": "2.7.10" 74 | } 75 | }, 76 | "nbformat": 4, 77 | "nbformat_minor": 0 78 | } 79 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # User-friendly check for sphinx-build 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) 12 | $(error The '$(SPHINXBUILD)' command was not found. 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The XML files are in %BUILDDIR%/xml. 231 | goto end 232 | ) 233 | 234 | if "%1" == "pseudoxml" ( 235 | %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml 236 | if errorlevel 1 exit /b 1 237 | echo. 238 | echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. 239 | goto end 240 | ) 241 | 242 | :end 243 | -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # NetworkxD3 documentation build configuration file, created by 4 | # sphinx-quickstart on Wed Jun 17 23:02:06 2015. 5 | # 6 | # This file is execfile()d with the current directory set to its 7 | # containing dir. 8 | # 9 | # Note that not all possible configuration values are present in this 10 | # autogenerated file. 11 | # 12 | # All configuration values have a default; values that are commented out 13 | # serve to show the default. 14 | 15 | import sys 16 | import os 17 | 18 | # If extensions (or modules to document with autodoc) are in another directory, 19 | # add these directories to sys.path here. If the directory is relative to the 20 | # documentation root, use os.path.abspath to make it absolute, like shown here. 21 | #sys.path.insert(0, os.path.abspath('.')) 22 | 23 | # -- General configuration ------------------------------------------------ 24 | 25 | # If your documentation needs a minimal Sphinx version, state it here. 26 | #needs_sphinx = '1.0' 27 | 28 | # Add any Sphinx extension module names here, as strings. They can be 29 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 30 | # ones. 31 | extensions = [ 32 | 'sphinx.ext.autodoc', 33 | 'sphinx.ext.viewcode', 34 | ] 35 | 36 | # Add any paths that contain templates here, relative to this directory. 37 | templates_path = ['_templates'] 38 | 39 | # The suffix of source filenames. 40 | source_suffix = '.rst' 41 | 42 | # The encoding of source files. 43 | #source_encoding = 'utf-8-sig' 44 | 45 | # The master toctree document. 46 | master_doc = 'index' 47 | 48 | # General information about the project. 49 | project = u'NetworkxD3' 50 | copyright = u'2015, Author' 51 | 52 | # The version info for the project you're documenting, acts as replacement for 53 | # |version| and |release|, also used in various other places throughout the 54 | # built documents. 55 | # 56 | # The short X.Y version. 57 | version = '' 58 | # The full version, including alpha/beta/rc tags. 59 | release = '' 60 | 61 | # The language for content autogenerated by Sphinx. Refer to documentation 62 | # for a list of supported languages. 63 | #language = None 64 | 65 | # There are two options for replacing |today|: either, you set today to some 66 | # non-false value, then it is used: 67 | #today = '' 68 | # Else, today_fmt is used as the format for a strftime call. 69 | #today_fmt = '%B %d, %Y' 70 | 71 | # List of patterns, relative to source directory, that match files and 72 | # directories to ignore when looking for source files. 73 | exclude_patterns = ['_build'] 74 | 75 | # The reST default role (used for this markup: `text`) to use for all 76 | # documents. 77 | #default_role = None 78 | 79 | # If true, '()' will be appended to :func: etc. cross-reference text. 80 | #add_function_parentheses = True 81 | 82 | # If true, the current module name will be prepended to all description 83 | # unit titles (such as .. function::). 84 | #add_module_names = True 85 | 86 | # If true, sectionauthor and moduleauthor directives will be shown in the 87 | # output. They are ignored by default. 88 | #show_authors = False 89 | 90 | # The name of the Pygments (syntax highlighting) style to use. 91 | pygments_style = 'sphinx' 92 | 93 | # A list of ignored prefixes for module index sorting. 94 | #modindex_common_prefix = [] 95 | 96 | # If true, keep warnings as "system message" paragraphs in the built documents. 97 | #keep_warnings = False 98 | 99 | 100 | # -- Options for HTML output ---------------------------------------------- 101 | 102 | # The theme to use for HTML and HTML Help pages. See the documentation for 103 | # a list of builtin themes. 104 | html_theme = 'default' 105 | 106 | # Theme options are theme-specific and customize the look and feel of a theme 107 | # further. For a list of options available for each theme, see the 108 | # documentation. 109 | #html_theme_options = {} 110 | 111 | # Add any paths that contain custom themes here, relative to this directory. 112 | #html_theme_path = [] 113 | 114 | # The name for this set of Sphinx documents. If None, it defaults to 115 | # " v documentation". 116 | #html_title = None 117 | 118 | # A shorter title for the navigation bar. Default is the same as html_title. 119 | #html_short_title = None 120 | 121 | # The name of an image file (relative to this directory) to place at the top 122 | # of the sidebar. 123 | #html_logo = None 124 | 125 | # The name of an image file (within the static path) to use as favicon of the 126 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 127 | # pixels large. 128 | #html_favicon = None 129 | 130 | # Add any paths that contain custom static files (such as style sheets) here, 131 | # relative to this directory. They are copied after the builtin static files, 132 | # so a file named "default.css" will overwrite the builtin "default.css". 133 | html_static_path = ['_static'] 134 | 135 | # Add any extra paths that contain custom files (such as robots.txt or 136 | # .htaccess) here, relative to this directory. These files are copied 137 | # directly to the root of the documentation. 138 | #html_extra_path = [] 139 | 140 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 141 | # using the given strftime format. 142 | #html_last_updated_fmt = '%b %d, %Y' 143 | 144 | # If true, SmartyPants will be used to convert quotes and dashes to 145 | # typographically correct entities. 146 | #html_use_smartypants = True 147 | 148 | # Custom sidebar templates, maps document names to template names. 149 | #html_sidebars = {} 150 | 151 | # Additional templates that should be rendered to pages, maps page names to 152 | # template names. 153 | #html_additional_pages = {} 154 | 155 | # If false, no module index is generated. 156 | #html_domain_indices = True 157 | 158 | # If false, no index is generated. 159 | #html_use_index = True 160 | 161 | # If true, the index is split into individual pages for each letter. 162 | #html_split_index = False 163 | 164 | # If true, links to the reST sources are added to the pages. 165 | #html_show_sourcelink = True 166 | 167 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 168 | #html_show_sphinx = True 169 | 170 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 171 | #html_show_copyright = True 172 | 173 | # If true, an OpenSearch description file will be output, and all pages will 174 | # contain a tag referring to it. The value of this option must be the 175 | # base URL from which the finished HTML is served. 176 | #html_use_opensearch = '' 177 | 178 | # This is the file name suffix for HTML files (e.g. ".xhtml"). 179 | #html_file_suffix = None 180 | 181 | # Output file base name for HTML help builder. 182 | htmlhelp_basename = 'NetworkxD3doc' 183 | 184 | 185 | # -- Options for LaTeX output --------------------------------------------- 186 | 187 | latex_elements = { 188 | # The paper size ('letterpaper' or 'a4paper'). 189 | #'papersize': 'letterpaper', 190 | 191 | # The font size ('10pt', '11pt' or '12pt'). 192 | #'pointsize': '10pt', 193 | 194 | # Additional stuff for the LaTeX preamble. 195 | #'preamble': '', 196 | } 197 | 198 | # Grouping the document tree into LaTeX files. List of tuples 199 | # (source start file, target name, title, 200 | # author, documentclass [howto, manual, or own class]). 201 | latex_documents = [ 202 | ('index', 'NetworkxD3.tex', u'NetworkxD3 Documentation', 203 | u'Author', 'manual'), 204 | ] 205 | 206 | # The name of an image file (relative to this directory) to place at the top of 207 | # the title page. 208 | #latex_logo = None 209 | 210 | # For "manual" documents, if this is true, then toplevel headings are parts, 211 | # not chapters. 212 | #latex_use_parts = False 213 | 214 | # If true, show page references after internal links. 215 | #latex_show_pagerefs = False 216 | 217 | # If true, show URL addresses after external links. 218 | #latex_show_urls = False 219 | 220 | # Documents to append as an appendix to all manuals. 221 | #latex_appendices = [] 222 | 223 | # If false, no module index is generated. 224 | #latex_domain_indices = True 225 | 226 | 227 | # -- Options for manual page output --------------------------------------- 228 | 229 | # One entry per manual page. List of tuples 230 | # (source start file, name, description, authors, manual section). 231 | man_pages = [ 232 | ('index', 'networkxd3', u'NetworkxD3 Documentation', 233 | [u'Author'], 1) 234 | ] 235 | 236 | # If true, show URL addresses after external links. 237 | #man_show_urls = False 238 | 239 | 240 | # -- Options for Texinfo output ------------------------------------------- 241 | 242 | # Grouping the document tree into Texinfo files. List of tuples 243 | # (source start file, target name, title, author, 244 | # dir menu entry, description, category) 245 | texinfo_documents = [ 246 | ('index', 'NetworkxD3', u'NetworkxD3 Documentation', 247 | u'Author', 'NetworkxD3', 'One line description of project.', 248 | 'Miscellaneous'), 249 | ] 250 | 251 | # Documents to append as an appendix to all manuals. 252 | #texinfo_appendices = [] 253 | 254 | # If false, no module index is generated. 255 | #texinfo_domain_indices = True 256 | 257 | # How to display URL addresses: 'footnote', 'no', or 'inline'. 258 | #texinfo_show_urls = 'footnote' 259 | 260 | # If true, do not generate a @detailmenu in the "Top" node's menu. 261 | #texinfo_no_detailmenu = False 262 | 263 | 264 | # -- Options for Epub output ---------------------------------------------- 265 | 266 | # Bibliographic Dublin Core info. 267 | epub_title = u'NetworkxD3' 268 | epub_author = u'Author' 269 | epub_publisher = u'Author' 270 | epub_copyright = u'2015, Author' 271 | 272 | # The basename for the epub file. It defaults to the project name. 273 | #epub_basename = u'NetworkxD3' 274 | 275 | # The HTML theme for the epub output. Since the default themes are not optimized 276 | # for small screen space, using the same theme for HTML and epub output is 277 | # usually not wise. This defaults to 'epub', a theme designed to save visual 278 | # space. 279 | #epub_theme = 'epub' 280 | 281 | # The language of the text. It defaults to the language option 282 | # or en if the language is not set. 283 | #epub_language = '' 284 | 285 | # The scheme of the identifier. Typical schemes are ISBN or URL. 286 | #epub_scheme = '' 287 | 288 | # The unique identifier of the text. This can be a ISBN number 289 | # or the project homepage. 290 | #epub_identifier = '' 291 | 292 | # A unique identification for the text. 293 | #epub_uid = '' 294 | 295 | # A tuple containing the cover image and cover page html template filenames. 296 | #epub_cover = () 297 | 298 | # A sequence of (type, uri, title) tuples for the guide element of content.opf. 299 | #epub_guide = () 300 | 301 | # HTML files that should be inserted before the pages created by sphinx. 302 | # The format is a list of tuples containing the path and title. 303 | #epub_pre_files = [] 304 | 305 | # HTML files shat should be inserted after the pages created by sphinx. 306 | # The format is a list of tuples containing the path and title. 307 | #epub_post_files = [] 308 | 309 | # A list of files that should not be packed into the epub file. 310 | epub_exclude_files = ['search.html'] 311 | 312 | # The depth of the table of contents in toc.ncx. 313 | #epub_tocdepth = 3 314 | 315 | # Allow duplicate toc entries. 316 | #epub_tocdup = True 317 | 318 | # Choose between 'default' and 'includehidden'. 319 | #epub_tocscope = 'default' 320 | 321 | # Fix unsupported image types using the PIL. 322 | #epub_fix_images = False 323 | 324 | # Scale large images. 325 | #epub_max_image_width = 0 326 | 327 | # How to display URL addresses: 'footnote', 'no', or 'inline'. 328 | #epub_show_urls = 'inline' 329 | 330 | # If false, no index is generated. 331 | #epub_use_index = True 332 | --------------------------------------------------------------------------------