├── ClusterProfShinyORA.Rproj
├── README.md
├── intro.Rmd
├── server-enrichGo.R
├── server-inputData.R
├── server-plots.R
├── server.R
├── ui-tab-enrichGo.R
├── ui-tab-enrichKegg.R
├── ui-tab-goplots.R
├── ui-tab-inputdata.R
├── ui-tab-intro.R
├── ui-tab-keggplots.R
├── ui-tab-pathview.R
├── ui-tab-wordcloud.R
├── ui.R
└── www
├── barplot.png
├── cnetplot.png
├── custom.css
├── custom.js
├── dotplot.png
├── exampleData
├── SRX003935_vs_SRX003924.csv
└── drosphila_example_de.csv
├── goplot.png
├── imgModal.js
├── pathview.png
├── plotsAll.jpg
├── sampleTable.png
├── seuratWorkflow.png
└── wordcloud.png
/ClusterProfShinyORA.Rproj:
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1 | Version: 1.0
2 |
3 | RestoreWorkspace: Default
4 | SaveWorkspace: Default
5 | AlwaysSaveHistory: Default
6 |
7 | EnableCodeIndexing: Yes
8 | UseSpacesForTab: Yes
9 | NumSpacesForTab: 2
10 | Encoding: UTF-8
11 |
12 | RnwWeave: Sweave
13 | LaTeX: pdfLaTeX
14 |
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/README.md:
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1 | # ClusterProfShinyORA
2 | - clusterProfiler Over-representation analysis R shiny
3 | - This is part of the NASQAR toolbox
4 | - Pre-print: [NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization](https://doi.org/10.1101/709980)
5 |
6 | ---
7 |
8 | This is a web-based interactive application that wraps the popular clusterProfiler DESeq2 Deseq2Shiny Pathview package tutorial
41 |
42 |
43 |
44 | A .csv/.txt file that contains a table of differential gene expression (DGE) data
Eg. the output of DESeq2
The file can be either comma or tab delimited
The required columns are Gene name/id, Log2 Fold Change, p-adjusted values
You will have to select the column names that match the above required columns
For a sample file, click here
51 |
52 |
53 |
54 |
55 |
56 |
Figure 2: Eg. DGE data file
57 |
58 |
59 |
60 |
61 |
62 |
63 |
64 |
clusterProfiler DESeq2 Deseq2Shiny Pathview package tutorial closely
22 |
23 | See **Figure 1** below for example output plots (Click on image to enlarge).
24 |
25 |
28 |
Figure 1: Example plots
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97 |
98 |
× Close
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103 |
tutorial in order to get familiar with the app
119 |
120 | ### 2. Upload your own data (gene counts):
121 |
122 |
123 |
124 |
125 |
126 | A .csv/.txt file that contains a table of differential gene expression (DGE) data
Eg. the output of DESeq2
The file can be either comma or tab delimited
The required columns are Gene name/id, Log2 Fold Change, p-adjusted values
You will have to select the column names that match the above required columns
For a sample file, click here
133 |
134 |
135 |
136 |
137 |
138 |
Figure 2: Eg. DGE data file
139 |
140 |
141 |
142 |
143 |
144 |
145 |
146 |
',outputText[3],' ')
252 |
253 | paste("",outputText,"
")
254 | })
255 |
256 | observeEvent(input$gotoGoPlots, {
257 | GotoTab('goplotsTab')
258 | })
259 |
260 | observeEvent(input$gotoKeggPlots, {
261 | GotoTab('keggPlotsTab')
262 | })
263 |
264 | observeEvent(input$gotoPathview, {
265 | GotoTab('pathviewTab')
266 | })
267 |
268 | observeEvent(input$gotoWordcloud, {
269 | GotoTab('wordcloudTab')
270 | })
271 |
272 | observeEvent(input$gotoWordcloud1, {
273 | GotoTab('wordcloudTab')
274 | })
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/server-inputData.R:
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1 |
2 | observe({
3 |
4 | shinyjs::hide(selector = "a[data-value=\"enrichGoTab\"]")
5 | shinyjs::hide(selector = "a[data-value=\"enrichKeggTab\"]")
6 | shinyjs::hide(selector = "a[data-value=\"goplotsTab\"]")
7 | shinyjs::hide(selector = "a[data-value=\"keggPlotsTab\"]")
8 | shinyjs::hide(selector = "a[data-value=\"pathviewTab\"]")
9 | shinyjs::hide(selector = "a[data-value=\"wordcloudTab\"]")
10 |
11 | inputDataReactive()
12 |
13 |
14 | })
15 |
16 | inputDataReactive <- reactive({
17 |
18 | print("inputting data")
19 |
20 | query <- parseQueryString(session$clientData$url_search)
21 |
22 | # Check if example selected, or if not then ask to upload a file.
23 | shiny:: validate(
24 | need( identical(input$data_file_type,"examplecounts")|(!is.null(input$datafile)),
25 | message = "Please select a file")
26 | )
27 |
28 | if (!is.null(query[['countsdata']]) ) {
29 | inFile = decryptUrlParam(query[['countsdata']])
30 |
31 | shinyjs::show(selector = "a[data-value=\"datainput\"]")
32 | shinyjs::disable("data_file_type")
33 | shinyjs::disable("datafile")
34 | #js$collapse("uploadbox")
35 |
36 | }
37 | else
38 | {
39 | inFile <- input$datafile
40 | # if (is.null(inFile))
41 | # return(NULL)
42 | #
43 | # inFile = inFile$datapath
44 | }
45 |
46 | #inFile <- input$datafile
47 | js$addStatusIcon("datainput","loading")
48 |
49 | if (!is.null(inFile)) {
50 | seqdata <- read.csv(inFile$datapath, header=TRUE, sep=",")
51 | print('uploaded seqdata')
52 | if(ncol(seqdata)==1) { # if file appears not to work as csv try tsv
53 | seqdata <- read.tsv(inFile$datapath, header=TRUE)
54 | print('changed to tsv, uploaded seqdata')
55 | }
56 | shiny::validate(need(ncol(seqdata)>1,
57 | message="File appears to be one column. Check that it is a comma or tab delimited (.csv) file."))
58 |
59 | js$addStatusIcon("datainput","done")
60 | js$collapse("uploadbox")
61 |
62 | return(list('data'=seqdata))
63 | }
64 | else{
65 | if(input$data_file_type=="examplecounts")
66 | {
67 | js$addStatusIcon("datainput","loading")
68 | #pbmc.data <- Read10X(data.dir = "www/hg19/")
69 |
70 | #data = read.csv("www/exampleData/SRX003935_vs_SRX003924.csv")
71 |
72 | data = read.csv("www/exampleData/drosphila_example_de.csv")
73 |
74 |
75 |
76 | js$addStatusIcon("datainput","done")
77 | js$collapse("uploadbox")
78 | return(list('data'=data))
79 | }
80 | return(NULL)
81 | }
82 | })
83 |
84 |
85 | output$countdataDT <- renderDataTable({
86 | tmp <- inputDataReactive()
87 |
88 | if(!is.null(tmp))
89 | {
90 | tmp$data
91 | }
92 |
93 | },
94 | options = list(scrollX = TRUE))
95 |
96 | # check if a file has been uploaded and create output variable to report this
97 | output$fileUploaded <- reactive({
98 |
99 |
100 | if(!is.null(inputDataReactive()))
101 | {
102 | updateSelectInput(session, "geneColumn", choices = names(inputDataReactive()$data))
103 | updateSelectInput(session, "log2fcColumn", choices = names(inputDataReactive()$data))
104 | updateSelectInput(session, "padjColumn", choices = names(inputDataReactive()$data))
105 |
106 | if(input$data_file_type=="examplecounts")
107 | {
108 | updateSelectInput(session, "geneColumn", selected = "X")
109 | updateSelectInput(session, "log2fcColumn", selected = "log2FoldChange")
110 | updateSelectInput(session, "padjColumn", selected = "padj")
111 | }
112 |
113 | return(T)
114 | }
115 |
116 | return(F)
117 |
118 | })
119 | outputOptions(output, 'fileUploaded', suspendWhenHidden=FALSE)
120 |
121 |
122 | observeEvent(input$nextInitParams,{
123 |
124 | js$collapse("iParamsbox")
125 |
126 | organismsDbChoices = c("Human (org.Hs.eg.db)"="org.Hs.eg.db","Mouse (org.Mm.eg.db)"="org.Mm.eg.db","Rat (org.Rn.eg.db)"="org.Rn.eg.db",
127 | "Yeast (org.Sc.sgd.db)"="org.Sc.sgd.db","Fly (org.Dm.eg.db)"="org.Dm.eg.db","Arabidopsis (org.At.tair.db)"="org.At.tair.db",
128 | "Zebrafish (org.Dr.eg.db)"="org.Dr.eg.db","Bovine (org.Bt.eg.db)"="org.Bt.eg.db","Worm (org.Ce.eg.db)"="org.Ce.eg.db",
129 | "Chicken (org.Gg.eg.db)"="org.Gg.eg.db","Canine (org.Cf.eg.db)"="org.Cf.eg.db","Pig (org.Ss.eg.db)"="org.Ss.eg.db",
130 | "Rhesus (org.Mmu.eg.db)"="org.Mmu.eg.db","E coli strain K12 (org.EcK12.eg.db)"="org.EcK12.eg.db","Xenopus (org.Xl.eg.db)"="org.Xl.eg.db",
131 | "Chimp (org.Pt.eg.db)"="org.Pt.eg.db","Anopheles (org.Ag.eg.db)"="org.Ag.eg.db","Malaria (org.Pf.plasmo.db)"="org.Pf.plasmo.db",
132 | "E coli strain Sakai (org.EcSakai.eg.db)"="org.EcSakai.eg.db")
133 |
134 | updateSelectInput(session, "organismDb", choices = organismsDbChoices)
135 |
136 | if(input$data_file_type=="examplecounts")
137 | updateSelectInput(session, "organismDb", selected = "org.Dm.eg.db")
138 |
139 |
140 | js$collapse("createGoBox")
141 |
142 | })
143 |
144 |
145 | observeEvent(input$organismDb,{
146 | if(input$organismDb == "")
147 | return(NULL)
148 |
149 | library(input$organismDb, character.only = T)
150 |
151 | annDb = eval(parse(text = input$organismDb))
152 | keytypes = keytypes(annDb)
153 | updateSelectInput(session, "keytype", choices = keytypes, selected = "ENSEMBL")
154 |
155 | })
156 |
157 |
158 |
159 |
160 |
161 |
162 |
163 |
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/server-plots.R:
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1 | output$upsetPlot = renderPlot({
2 | withProgress(message = "Plotting upsetplot ...",{
3 | go_enrich = enrichGoReactive()$go_enrich
4 |
5 | upsetplot(go_enrich,
6 | n = input$showCategory_upset)
7 | })
8 |
9 | })
10 |
11 | output$barPlot = renderPlot({
12 | withProgress(message = "Plotting barplot ...",{
13 | go_enrich = enrichGoReactive()$go_enrich
14 |
15 | barplot(go_enrich,
16 | drop = TRUE,
17 | showCategory = input$showCategory_bar,
18 | title = "GO Biological Pathways",
19 | font.size = 8)
20 | })
21 |
22 | })
23 |
24 |
25 | output$dotPlot = renderPlot({
26 | withProgress(message = "Plotting dotplot ...",{
27 | go_enrich = enrichGoReactive()$go_enrich
28 |
29 | dotplot(go_enrich,
30 | #drop = TRUE,
31 | showCategory = input$showCategory_dot,
32 | #title = "GO Biological Pathways",
33 | font.size = 8)
34 | })
35 |
36 | })
37 |
38 | output$enrichPlotMap = renderPlot({
39 | withProgress(message = "Plotting enrichment map ...",{
40 | go_enrich = enrichGoReactive()$go_enrich
41 |
42 | emapplot(go_enrich, showCategory = input$showCategory_enrichmap)
43 | })
44 |
45 | })
46 |
47 |
48 | output$goInducedGraph = renderPlot({
49 | withProgress(message = "Plotting induced GO DAG ...",{
50 |
51 | go_enrich = enrichGoReactive()$go_enrich
52 |
53 | goplot(go_enrich, showCategory = input$showCategory_goplot)
54 |
55 | })
56 |
57 | })
58 |
59 |
60 | output$cnetplot = renderPlot({
61 |
62 | withProgress(message = "Plotting Gene-Concept Network ...",{
63 | go_enrich = enrichGoReactive()$go_enrich
64 |
65 | cnetplot(go_enrich, categorySize="pvalue", foldChange=myValues$gene_list, showCategory = input$showCategory_cnet)
66 | })
67 |
68 | })
69 |
70 | output$wordcloud = renderWordcloud2({
71 | withProgress(message = "Plotting Wordcloud ...",{
72 |
73 | if(input$plotWordcloud)
74 | {
75 | isolate({
76 | if(input$wordcloudGoOrKegg == "enrichGo")
77 | {
78 | go_enrich = enrichGoReactive()$go_enrich
79 | }
80 | else
81 | {
82 | go_enrich = enrichGoReactive()$kegg_enrich
83 | }
84 |
85 | wcdf<-read.table(text=go_enrich$GeneRatio, sep = "/")[1]
86 | wcdf$term<-go_enrich[,2]
87 | # wc = wordcloud(words = wcdf$term, freq = wcdf$V1, scale=(c(2, .5)), colors=brewer.pal(8, "Dark2"), max.words = input$maxWords)
88 |
89 | wordsDF = data.frame(word=go_enrich[,2], freq=wcdf$V1)
90 |
91 | wordsDF = wordsDF[order(-wordsDF$freq),]
92 |
93 | wordsDF = head(wordsDF, input$maxWords)
94 |
95 | wordcloud2(wordsDF, color = input$wordsColor, shape = input$wordShape, size = 0.1)
96 | })
97 |
98 | }
99 |
100 |
101 | })
102 |
103 | })
104 |
105 |
106 | ### KEGG
107 |
108 | output$barPlot_kegg = renderPlot({
109 | withProgress(message = "Plotting barplot ...",{
110 | kegg_enrich = enrichGoReactive()$kegg_enrich
111 |
112 | barplot(kegg_enrich,
113 | drop = TRUE,
114 | showCategory = input$showCategory_bar_kegg,
115 | title = "Enriched Pathways",
116 | font.size = 8)
117 | })
118 |
119 | })
120 |
121 |
122 | output$dotPlot_kegg = renderPlot({
123 | withProgress(message = "Plotting dotplot ...",{
124 | kegg_enrich = enrichGoReactive()$kegg_enrich
125 |
126 | dotplot(kegg_enrich,
127 | #drop = TRUE,
128 | showCategory = input$showCategory_dot_kegg,
129 | title = "Enriched Pathways",
130 | font.size = 8)
131 | })
132 |
133 | })
134 |
135 | output$enrichPlotMap_kegg = renderPlot({
136 | withProgress(message = "Plotting Enrichment Map ...",{
137 | kegg_enrich = enrichGoReactive()$kegg_enrich
138 |
139 | emapplot(kegg_enrich, showCategory = input$showCategory_enrichmap_kegg)
140 |
141 | })
142 |
143 | })
144 |
145 |
146 | output$cnetplot_kegg = renderPlot({
147 |
148 | withProgress(message = "Plotting Gene-Concept Network ...",{
149 | kegg_enrich = enrichGoReactive()$kegg_enrich
150 |
151 | cnetplot(kegg_enrich, categorySize="pvalue", foldChange=myValues$kegg_gene_list, showCategory = input$showCategory_cnet_kegg)
152 | })
153 |
154 | })
155 |
156 |
157 | pathviewReactive = eventReactive(input$generatePathview,{
158 | withProgress(message = 'Plotting Pathview ...', {
159 |
160 | isolate({
161 | kegg_enrich = enrichGoReactive()$kegg_enrich
162 |
163 | setProgress(value = 0.3, detail = paste0("Pathview ID ",input$pathwayIds," ..."))
164 | dme <- pathview(gene.data=myValues$gene_list, pathway.id=input$pathwayIds, species = myValues$organismKegg, gene.idtype=input$geneid_type)
165 | file.copy(paste0(input$pathwayIds,".pathview.png"),paste0("testimage"))
166 |
167 | setProgress(value = 0.7, detail = paste0("Pathview ID ",input$pathwayIds," generating pdf ..."))
168 | dmePdf <- pathview(gene.data=myValues$gene_list, pathway.id=input$pathwayIds, species = myValues$organismKegg, gene.idtype=input$geneid_type,kegg.native = F)
169 |
170 | myValues$imagePath = paste0(input$pathwayIds,".pathview.")
171 | return(list(
172 | src = paste0("testimage"),
173 | filetype = "image/png",
174 | alt = "pathview image"
175 | ))
176 | })
177 |
178 | })
179 | })
180 |
181 | output$pathview_plot = renderImage({
182 |
183 | return(pathviewReactive())
184 |
185 | })
186 |
187 | output$pathviewPlotsAvailable <-
188 | reactive({
189 | return(!is.null(pathviewReactive()))
190 | })
191 | outputOptions(output, 'pathviewPlotsAvailable', suspendWhenHidden=FALSE)
192 |
193 | output$downloadPathviewPng <- downloadHandler(
194 | filename = function() {paste0(myValues$imagePath,"png")},
195 | content = function(file) {
196 | file.copy(paste0(getwd(),'/',myValues$imagePath,"png"), file)
197 | }
198 | )
199 |
200 | output$downloadPathviewPdf <- downloadHandler(
201 | filename = function() {paste0(myValues$imagePath,"pdf")},
202 | content = function(file) {
203 | file.copy(paste0(getwd(),'/',myValues$imagePath,"pdf"), file)
204 | }
205 | )
206 |
207 | output$wordcloud_kegg = renderWordcloud2({
208 | withProgress(message = "Plotting Wordcloud ...",{
209 | kegg_enrich = enrichGoReactive()$kegg_enrich
210 |
211 | wcdf<-read.table(text=kegg_enrich$GeneRatio, sep = "/")[1]
212 | wcdf$term<-kegg_enrich[,2]
213 | # wc = wordcloud(words = wcdf$term, freq = wcdf$V1, scale=(c(2, .5)), colors=brewer.pal(8, "Dark2"), max.words = input$maxWords)
214 |
215 | wordsDF = data.frame(word=kegg_enrich[,2], freq=wcdf$V1)
216 |
217 | wordsDF = wordsDF[order(-wordsDF$freq),]
218 |
219 | wordsDF = head(wordsDF, input$maxWords_kegg)
220 | #browser()
221 | wordcloud2(wordsDF, color = input$wordsColor_kegg, shape = input$wordShape_kegg, size = 0.1)
222 | })
223 |
224 | })
225 |
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/server.R:
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1 |
2 | # Max upload size
3 | options(shiny.maxRequestSize = 60*1024^2)
4 |
5 | # Define server
6 | server <- function(input, output, session) {
7 |
8 | source("server-inputData.R",local = TRUE)
9 | #
10 | source("server-enrichGo.R",local = TRUE)
11 | #
12 | source("server-plots.R",local = TRUE)
13 |
14 |
15 | GotoTab <- function(name){
16 | #updateTabItems(session, "tabs", name)
17 |
18 | shinyjs::show(selector = paste0("a[data-value=\"",name,"\"]"))
19 |
20 | shinyjs::runjs("window.scrollTo(0, 0)")
21 | }
22 | }
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/ui-tab-enrichGo.R:
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1 | tabItem(tabName = "enrichGoTab",
2 |
3 | conditionalPanel("output.enrichGoAvailable",
4 |
5 | column(2,
6 | h3(strong("enrichGo Results")),
7 | hr(),
8 | checkboxInput("showGeneidGo","Show geneID column", value = F),
9 | downloadButton('downloadEnrichGoCSV','Save Results as CSV File', class = "btn btn-info", style="margin: 7px;"),
10 | actionButton("gotoGoPlots","enrichGo Plots",class = "btn btn-warning",icon = icon("chart-area"), style="margin: 7px;"),
11 | actionButton("gotoWordcloud","Word Cloud",class = "btn btn-warning",icon = icon("chart-area"), style="margin: 7px;")
12 | ),
13 | column(10,
14 | tags$div(class = "BoxArea2",
15 | withSpinner(dataTableOutput('enrichGoTable'))
16 | ),
17 | tags$div(class = "clearBoth")
18 | ),
19 | tags$div(class = "clearBoth")
20 |
21 | )
22 | )
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/ui-tab-enrichKegg.R:
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1 | tabItem(tabName = "enrichKeggTab",
2 |
3 | conditionalPanel("output.enrichKEGGAvailable",
4 |
5 | column(2,
6 | h3(strong("enrichKEGG Results")),
7 | hr(),
8 | checkboxInput("showGeneidKegg","Show geneID column", value = F),
9 | downloadButton('downloadEnrichKEGGCSV','Save Results as CSV File', class = "btn btn-info", style="margin: 7px;"),
10 | actionButton("gotoKeggPlots","enrichKEGG Plots",class = "btn btn-warning",icon = icon("chart-area"), style="margin: 7px;"),
11 | actionButton("gotoPathview","Generate Pathview Plot",class = "btn btn-warning",icon = icon("chart-area"), style="margin: 7px;"),
12 | actionButton("gotoWordcloud1","Word Cloud",class = "btn btn-warning",icon = icon("chart-area"), style="margin: 7px;"),
13 |
14 | wellPanel(h4(strong("Output warning:"), tags$a(href = "#", bubbletooltip = "Description ...",icon("info-circle"))),
15 | htmlOutput("warningText"), style = "background-color: #f9d8d3;")
16 |
17 | ),
18 | column(10,
19 | tags$div(class = "BoxArea2",
20 | withSpinner(dataTableOutput('enrichKEGGTable'))
21 | ),
22 | tags$div(class = "clearBoth")
23 | ),
24 | tags$div(class = "clearBoth")
25 |
26 | )
27 | )
--------------------------------------------------------------------------------
/ui-tab-goplots.R:
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1 | tabItem(tabName = "goplotsTab",
2 | h2(strong("GO Plots")),
3 | tags$div(
4 | box(title = "Upset Plot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "barplot",
5 | fluidRow(
6 | column(3,
7 | wellPanel(
8 | numericInput("showCategory_upset", "number of categories to show", value = 10)
9 | )
10 | ),
11 | column(9,
12 | wellPanel(
13 | withSpinner(plotOutput(outputId = "upsetPlot"),type = 8)
14 | )
15 | )
16 | )
17 | ),
18 | box(title = "Bar Plot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "barplot",
19 | fluidRow(
20 | column(3,
21 | wellPanel(
22 | numericInput("showCategory_bar", "number of categories to show", value = 10)
23 | )
24 | ),
25 | column(9,
26 | wellPanel(
27 | withSpinner(plotOutput(outputId = "barPlot"),type = 8)
28 | )
29 | )
30 | )
31 | ),
32 | box(title = "Dot Plot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "dotplot",
33 | fluidRow(
34 | column(3,
35 | wellPanel(
36 | numericInput("showCategory_dot", "number of categories to show", value = 10)
37 | )
38 | ),
39 | column(9,
40 | wellPanel(
41 | withSpinner(plotOutput(outputId = "dotPlot"),type = 8)
42 | )
43 |
44 | )
45 | )
46 | ),
47 | box(title = "Encrichment plot map", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "enrichPlotMap",
48 | fluidRow(
49 | column(3,
50 | wellPanel(
51 | numericInput("showCategory_enrichmap", "number of categories to show", value = 5)
52 | )
53 | )
54 | ,
55 | column(9,
56 | wellPanel(
57 | plotOutput(outputId = "enrichPlotMap")
58 | )
59 | )
60 | )
61 | ),
62 | box(title = "Category Netplot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "goInducedGraph",
63 | fluidRow(
64 | column(12,
65 | wellPanel(
66 | numericInput("showCategory_goplot", "number of categories to show", value = 5)
67 | )
68 | )
69 | ,
70 | column(12,
71 | wellPanel(
72 | plotOutput(outputId = "goInducedGraph")
73 | )
74 | )
75 | )
76 | ),
77 | box(title = "Enriched GO induced graph (cnetplot)", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "cnetplot",
78 | fluidRow(
79 | column(12,
80 | wellPanel(
81 | numericInput("showCategory_cnet", "number of categories to show", value = 5)
82 | )
83 | ),
84 | column(12,
85 | wellPanel(
86 | plotOutput(outputId = "cnetplot",width = "100%", height = "400px")
87 | )
88 | )
89 | )
90 | )
91 |
92 | , style = "display:table;")
93 | )
--------------------------------------------------------------------------------
/ui-tab-inputdata.R:
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1 | tabItem(tabName = "datainput",
2 | hr(),
3 | fluidRow(column(6,
4 | box(title = "Upload Data", solidHeader = T, status = "success", width = 12, collapsible = T,id = "uploadbox",
5 |
6 | #downloadLink("instructionspdf",label="Download Instructions (pdf)"),
7 | radioButtons('data_file_type','Use example file or upload your own data',
8 | c(
9 | 'Upload .CSV'="csvfile",
10 | 'Example Data'="examplecounts"
11 | ),selected = "csvfile"),
12 |
13 | conditionalPanel(condition="input.data_file_type=='csvfile'",
14 | p("CSV counts file")
15 |
16 | ),
17 | conditionalPanel(condition = "input.data_file_type=='csvfile'",
18 | fileInput('datafile', 'Choose File(s) Containing Data', multiple = TRUE)
19 | )
20 |
21 | ),
22 | conditionalPanel("output.fileUploaded",
23 | box(title = "Initialize Parameters", solidHeader = T, status = "primary", width = 12, collapsible = T,id = "iParamsbox",
24 |
25 | wellPanel(
26 | column(
27 | 4,
28 | selectInput("geneColumn","Select Genes column:", choices = c("sdfs","dfs"))
29 | ),
30 | column(4,
31 | selectInput("log2fcColumn","Select Log2FC column:", choices = c("sdfs","dfs"))
32 | ),
33 | column(4,
34 | selectInput("padjColumn","Select padj column:", choices = c("sdfs","dfs"))
35 | ),
36 | column(6,
37 | numericInput("padjCutoff","padj cutoff:", value = 0.05)
38 | ),
39 | column(6,
40 | numericInput("logfcCuttoff","min log2 fold change :", value = 2)
41 | ),
42 | tags$div(class = "clearBoth")
43 | ),
44 | actionButton("nextInitParams","Next", class = "btn-info", style = "width: 100%")
45 |
46 | ),
47 |
48 |
49 | box(title = "EnrichGO object Parameters", solidHeader = T, status = "primary", width = 12, collapsible = T,id = "createGoBox", collapsed = T,
50 | wellPanel(
51 | column(6,
52 | selectInput("organismDb","Organism:", choices = NULL, selected = NULL)
53 | ),
54 | column(6,
55 | selectInput("keytype","Keytype:", choices = c(""), selected = NULL)
56 | ),
57 | column(6,
58 | selectInput("ontology","Ontology:", choices = c("MF", "BP", "CC"), selected = "BP")
59 | ),
60 | column(4,
61 | numericInput("minGSSize","minGSSize:", value = 5)
62 | ),
63 | column(4,
64 | numericInput("maxGSSize","maxGSSize:", value = 500)
65 | ),
66 | column(6,
67 | numericInput("pvalCuttoff","P-Value Cutoff:", value = 0.05)
68 | ),
69 | column(6,
70 | numericInput("qvalCuttoff","Q-Value Cutoff:", value = 0.1)
71 | ),
72 | column(6,
73 | selectInput("pAdjustMethod","pAdjustMethod:", choices = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), selected = "none")
74 | ),
75 | tags$div(class = "clearBoth")
76 | ),
77 | actionButton("initGo","Create EnrichGO Object", class = "btn-info", style = "width: 100%")
78 | )
79 | )
80 | ),#column
81 | column(6,
82 | bsCollapse(id="input_collapse_panel",open="data_panel",multiple = FALSE,
83 | bsCollapsePanel(title="Data Contents Table:",value="data_panel",
84 | p("Note: if there are more than 20 columns, only the first 20 will show here"),
85 | textOutput("inputInfo"),
86 | withSpinner(dataTableOutput('countdataDT'))
87 | )
88 | )#bscollapse
89 | )#column
90 | )#fluidrow
91 | )#tabpanel
92 |
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/ui-tab-intro.R:
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1 | tabItem(tabName = "introTab",
2 | fluidRow(
3 |
4 | box(title = "User Guide", width = 11, solidHeader = T, status = "primary",
5 | column(12,
6 | includeMarkdown("intro.Rmd")
7 | )
8 | )
9 | )
10 | )
11 |
--------------------------------------------------------------------------------
/ui-tab-keggplots.R:
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1 | tabItem(tabName = "keggPlotsTab",
2 | h2(strong("KEGG Plots")),
3 | tags$div(
4 | box(title = "Bar Plot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "barplot",
5 | fluidRow(
6 | column(3,
7 | wellPanel(
8 | numericInput("showCategory_bar_kegg", "number of categories to show", value = 10)
9 | )
10 | ),
11 | column(9,
12 | wellPanel(
13 | withSpinner(plotOutput(outputId = "barPlot_kegg"),type = 8)
14 | )
15 | )
16 | )
17 | ),
18 | box(title = "Dot Plot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "dotplot",
19 | fluidRow(
20 | column(3,
21 | wellPanel(
22 | numericInput("showCategory_dot_kegg", "number of categories to show", value = 10)
23 | )
24 | ),
25 | column(9,
26 | wellPanel(
27 | withSpinner(plotOutput(outputId = "dotPlot_kegg"),type = 8)
28 | )
29 | )
30 | )
31 | ),
32 | box(title = "Encrichment plot map", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "enrichPlotMap_kegg",
33 | fluidRow(
34 | column(3,
35 | wellPanel(
36 | numericInput("showCategory_enrichmap_kegg", "number of categories to show", value = 5)
37 | )
38 | )
39 | ,
40 | column(9,
41 | wellPanel(
42 | plotOutput(outputId = "enrichPlotMap_kegg")
43 | )
44 | )
45 | )
46 | ),
47 | box(title = "Category Netplot", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "cnetplot",
48 | fluidRow(
49 | column(12,
50 | wellPanel(
51 | numericInput("showCategory_cnet_kegg", "number of categories to show", value = 5)
52 | )
53 | ),
54 | column(12,
55 | wellPanel(
56 | plotOutput(outputId = "cnetplot_kegg",width = "100%", height = "400px")
57 | )
58 | )
59 | )
60 | )
61 |
62 | , style = "display:table;")
63 | )
--------------------------------------------------------------------------------
/ui-tab-pathview.R:
--------------------------------------------------------------------------------
1 | tabItem(tabName = "pathviewTab",
2 | h2(strong("Pathview Plot")),
3 | wellPanel(
4 | column(6,
5 |
6 | selectizeInput("pathwayIds", label="Select Pathway ID",
7 | choices=NULL,
8 | multiple=F,
9 | options = list(
10 | placeholder =
11 | 'Start typing pathway id'
12 | )
13 | )
14 |
15 | )
16 | ,
17 | column(6,
18 | selectInput("geneid_type","Gene ID type:", choices = c(""), selected = NULL)
19 | ),
20 | column(6,
21 | actionButton("generatePathview", "Generate Pathview", class = "btn btn-info")
22 | ),
23 | conditionalPanel("output.pathviewPlotsAvailable",
24 | column(3,
25 | downloadButton('downloadPathviewPng','Download .png', class = "btn btn-warning", style="margin: 7px;")
26 | ),
27 | column(3,
28 | downloadButton('downloadPathviewPdf','Download .pdf', class = "btn btn-warning", style="margin: 7px;")
29 | )
30 | )
31 | ,
32 | tags$div(class = "clearBoth")
33 |
34 | ),
35 | withSpinner(imageOutput(outputId = "pathview_plot", inline = T),type = 8)
36 |
37 |
38 | )
--------------------------------------------------------------------------------
/ui-tab-wordcloud.R:
--------------------------------------------------------------------------------
1 | tabItem(tabName = "wordcloudTab",
2 | h2(strong("GO Plots")),
3 | box(title = "Word Cloud", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "wordcloud",
4 | fluidRow(
5 | column(3,
6 | wellPanel(
7 | numericInput("maxWords", "Max. Words", value = 25),
8 | radioButtons("wordsColor","Color theme:", c("Light"="random-light", "Dark"="random-dark")),
9 | selectizeInput("wordShape","Shape:", c("circle","cardioid","diamond","triangle-forward","triangle","triangle","star")),
10 | radioButtons("wordcloudGoOrKegg","Type:", choices = c("enrichGo","enrichKEGG")),
11 | actionButton("plotWordcloud","Plot Word Cloud", class = "btn btn-info")
12 | )
13 | ),
14 | column(9,
15 | wellPanel(
16 | wordcloud2Output(outputId = "wordcloud")
17 | )
18 |
19 | )
20 | )
21 | )
22 | # ,
23 |
24 | # box(title = "Word Cloud", solidHeader = T, status = "danger", width = 12, collapsible = T,id = "wordcloud_kegg",
25 | # fluidRow(
26 | # column(3,
27 | # wellPanel(
28 | # numericInput("maxWords_kegg", "Max. Words", value = 25),
29 | # radioButtons("wordsColor_kegg","Color theme:", c("Light"="random-light", "Dark"="random-dark")),
30 | # selectizeInput("wordShape_kegg","Shape:", c("circle","cardioid","diamond","triangle-forward","triangle","triangle","star"))
31 | # )
32 | # ),
33 | # column(9,
34 | # wellPanel(
35 | # wordcloud2Output(outputId = "wordcloud_kegg")
36 | # )
37 | #
38 | # )
39 | # )
40 | # )
41 |
42 | )
--------------------------------------------------------------------------------
/ui.R:
--------------------------------------------------------------------------------
1 | require(shinydashboard)
2 | require(shinyjs)
3 | require(shinyBS)
4 | require(shinycssloaders)
5 | require(DT)
6 | require(shiny)
7 |
8 |
9 | library(clusterProfiler)
10 | library(DOSE)
11 | library(GOplot)
12 | library(enrichplot)
13 | library(pathview)
14 | library(wordcloud2)
15 |
16 | # BiocInstaller::biocLite(c("org.Hs.eg.db","org.Mm.eg.db","org.Rn.eg.db","org.Sc.sgd.db","org.Dm.eg.db","org.At.tair.db","org.Dr.eg.db","org.Bt.eg.db","org.Ce.eg.db","org.Gg.eg.db","org.Cf.eg.db","org.Ss.eg.db","org.Mmu.eg.db","org.EcK12.eg.db","org.Xl.eg.db","org.Pt.eg.db","org.Ag.eg.db","org.Pf.plasmo.db","org.EcSakai.eg.db"))
17 |
18 |
19 | ui <- tagList(
20 | dashboardPage(
21 | skin = "purple",
22 | dashboardHeader(title = "ClusterProfShiny (ORA)"),
23 | dashboardSidebar(
24 | sidebarMenu(
25 | id = "tabs",
26 | menuItem("User Guide", tabName = "introTab", icon = icon("info-circle")),
27 | menuItem("Input Data", tabName = "datainput", icon = icon("upload")),
28 | menuItem("enrichGo", tabName = "enrichGoTab", icon = icon("th")),
29 | menuItem("enrichKegg", tabName = "enrichKeggTab", icon = icon("th")),
30 | menuItem("Go Plots", tabName = "goplotsTab", icon = icon("bar-chart")),
31 | menuItem("KEGG Plots", tabName = "keggPlotsTab", icon = icon("bar-chart")),
32 | menuItem("Pathview Plots", tabName = "pathviewTab", icon = icon("bar-chart")),
33 | menuItem("Word Clouds", tabName = "wordcloudTab", icon = icon("bar-chart"))
34 | )
35 | ),
36 | dashboardBody(
37 | shinyjs::useShinyjs(),
38 | extendShinyjs(script = "www/custom.js"),
39 | tags$head(
40 | tags$style(HTML(
41 | " .shiny-output-error-validation {color: darkred; }"
42 | )),
43 | tags$style(
44 | type="text/css",
45 | "#pathview_plot img {max-width: 100%; width: 100%; height: auto}"),
46 | tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
47 | ),
48 | tabItems(
49 | source("ui-tab-intro.R", local = TRUE)$value,
50 | source("ui-tab-inputdata.R", local = TRUE)$value,
51 | source("ui-tab-enrichGo.R", local = TRUE)$value,
52 | source("ui-tab-enrichKegg.R", local = TRUE)$value,
53 | source("ui-tab-goplots.R", local = TRUE)$value,
54 | source("ui-tab-keggplots.R", local = TRUE)$value,
55 | source("ui-tab-pathview.R", local = TRUE)$value,
56 | source("ui-tab-wordcloud.R", local = TRUE)$value
57 | )
58 |
59 | )
60 |
61 | ),
62 | tags$footer(
63 | wellPanel(
64 | HTML(
65 | '
66 | Core Bioinformatics, Center for Genomics and Systems Biology, NYU Abu Dhabi
67 | Github: https://github.com/nasqar/ClusterProfShiny/
68 | Maintained by: Ayman Yousif
69 | Using ClusterProfiler
70 | Acknowledgements:
71 | 1) GuangchuangYu/clusterProfiler
72 | 2) Mohammed Khalfan - Over Representation Analysis Tutorial
73 | Copyright (C) 2019, code licensed under GPLv3
'
74 | )
75 | ),
76 | tags$script(src = "imgModal.js")
77 | )
78 | )
--------------------------------------------------------------------------------
/www/barplot.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/nasqar/ClusterProfShinyORA/756a9fc317fa36419d05601f72c9e62001fbbfa5/www/barplot.png
--------------------------------------------------------------------------------
/www/cnetplot.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/nasqar/ClusterProfShinyORA/756a9fc317fa36419d05601f72c9e62001fbbfa5/www/cnetplot.png
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/www/custom.css:
--------------------------------------------------------------------------------
1 | #loading-bar-spinner.spinner {
2 | left: 50%;
3 | margin-left: -20px;
4 | top: 50%;
5 | z-index: 19 !important;
6 | animation: loading-bar-spinner 1000ms linear infinite;
7 | float: right;
8 | }
9 |
10 | #loading-bar-spinner.spinner .spinner-icon {
11 | width: 20px;
12 | height: 20px;
13 | border: solid 4px transparent;
14 | border-top-color: #00C8B1 !important;
15 | border-left-color: #00C8B1 !important;
16 | border-radius: 50%;
17 | }
18 |
19 | @keyframes loading-bar-spinner {
20 | 0% { transform: rotate(0deg); transform: rotate(0deg); }
21 | 100% { transform: rotate(360deg); transform: rotate(360deg); }
22 | }
23 |
24 |
25 |
26 | hr {
27 | border-top: 1px solid #bbb8b8;
28 | }
29 |
30 | body {
31 | font-size: 16px;
32 | }
33 |
34 |
35 | .checkmark__circle {
36 | stroke-dasharray: 166;
37 | stroke-dashoffset: 166;
38 | stroke-width: 2;
39 | stroke-miterlimit: 10;
40 | stroke: #7ac142;
41 | fill: none;
42 | animation: stroke 0.6s cubic-bezier(0.65, 0, 0.45, 1) forwards;
43 | }
44 |
45 | .checkmark {
46 | width: 20px;
47 | height: 20px;
48 | border-radius: 50%;
49 | display: block;
50 | stroke-width: 6;
51 | stroke: #fff;
52 | stroke-miterlimit: 10;
53 | box-shadow: inset 0px 0px 0px #7ac142;
54 | animation: fill .4s ease-in-out .4s forwards, scale .3s ease-in-out .9s both;
55 | }
56 |
57 | .checkmark__check {
58 | transform-origin: 50% 50%;
59 | stroke-dasharray: 48;
60 | stroke-dashoffset: 48;
61 | animation: stroke 0.3s cubic-bezier(0.65, 0, 0.45, 1) 0.8s forwards;
62 | }
63 |
64 | @keyframes stroke {
65 | 100% {
66 | stroke-dashoffset: 0;
67 | }
68 | }
69 | @keyframes scale {
70 | 0%, 100% {
71 | transform: none;
72 | }
73 | 50% {
74 | transform: scale3d(1.1, 1.1, 1);
75 | }
76 | }
77 | @keyframes fill {
78 | 100% {
79 | box-shadow: inset 0px 0px 0px 30px #7ac142;
80 | }
81 | }
82 |
83 |
84 |
85 |
86 | /* Fix indent icon on side bar*/
87 | .sidebar-menu>li .badge,.sidebar-menu>li .label {
88 | margin-right: 0;
89 | }
90 |
91 |
92 |
93 |
94 | .mybuttonclass{background-color:#CD0000;} .mybuttonclass{color: #fff;} .mybuttonclass{border-color: #9E0000;}
95 |
96 | .BoxArea2 { padding:19px; margin: 5px; border-radius:10px; background-color: #e8e6f5;}
97 |
98 | .BoxArea { padding:19px; margin: 5px; border: 3px solid; border-color:rgba(24, 188, 156, 1); border-radius:10px; background-color:#fdfdfd; opacity: 0.90;}
99 |
100 | .BoxArea4 { padding:14px; margin: 5px; border: 3px solid; border-color:rgb(214, 226, 232); border-radius:5px; background-color:white;}
101 |
102 | .clearBoth{ clear:both; }
103 |
104 | a > .highlight { background-color:#fdfdfd;}
105 |
106 | .modal-dialog { width: 50%;}
107 |
108 | .dangerColor {
109 | background-color: #f5705f!important;
110 | color:white;
111 | }
112 |
113 | .content-wrapper, .right-side {
114 | background-color: #f3faff !important
115 | }
116 |
117 |
118 | .well {
119 | word-wrap: break-word;
120 | }
121 |
122 | a[bubbletooltip]:link, a[bubbletooltip]:visited
123 | {
124 | text-decoration: none;
125 | position: relative;
126 | }
127 |
128 | a[bubbletooltip]:before
129 | {
130 | content: "";
131 | position: absolute;
132 | border-top: 26px solid #292f45;
133 | border-left: 26px solid transparent;
134 | border-right: 26px solid transparent;
135 | visibility: hidden;
136 | top: -20px;
137 | left: -12px;
138 | }
139 |
140 | a[bubbletooltip]:after
141 | {
142 | position: absolute;
143 | content: attr(bubbletooltip);
144 | top: -35px;
145 | left: -26px;
146 | background: #292f45;
147 | color: #FFFFFF;
148 | padding: 5px 10px;
149 | -moz-border-radius: 6px;
150 | -webkit-border-radius:6px;
151 | -khtml-border-radius:6px;
152 | border-radius: 6px;
153 | white-space: nowrap;
154 | visibility: hidden;
155 | z-index:999;
156 | }
157 |
158 | a[bubbletooltip]:hover:before, a[bubbletooltip]:hover:after
159 | {
160 | visibility: visible;
161 | -moz-transition: visibility 0s linear .3s;
162 | }
163 |
--------------------------------------------------------------------------------
/www/custom.js:
--------------------------------------------------------------------------------
1 | shinyjs.addStatusIcon = function(params)
2 | {
3 | var tabname = params[0];
4 | var status = params[1];
5 |
6 | var menuitem = $('.sidebar-menu > li > a[data-value="' + tabname +'"]');
7 |
8 | menuitem.children('#loading-bar-spinner').remove();
9 | menuitem.children('#checkmarkdone').remove();
10 | menuitem.children('span.badge').remove();
11 |
12 |
13 | switch(status)
14 | {
15 | case 'loading':
16 | $("button.btn").removeClass("button-3d");
17 | $("button.btn").attr("disabled", "disabled");
18 |
19 | $("a.btn").addClass("hidden");
20 | menuitem.append('');
21 | break;
22 |
23 | case 'done':
24 | menuitem.append('\
25 | ');
27 | $("button.btn").addClass("button-3d");
28 | $("button.btn").removeAttr("disabled");
29 |
30 | $("a.btn").removeClass("hidden");
31 | break;
32 |
33 | case 'next':
34 | menuitem.append('Next ');
35 | break;
36 |
37 | case 'graph':
38 | menuitem.append(' 
23 |
24 |
25 | 
59 | 
39 | 
48 | 
57 | 
70 | 
79 | 
88 |