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server-plots.R
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output$upsetPlot = renderPlot({
withProgress(message = "Plotting upsetplot ...",{
go_enrich = enrichGoReactive()$go_enrich
upsetplot(go_enrich,
n = input$showCategory_upset)
})
})
output$barPlot = renderPlot({
withProgress(message = "Plotting barplot ...",{
go_enrich = enrichGoReactive()$go_enrich
barplot(go_enrich,
drop = TRUE,
showCategory = input$showCategory_bar,
title = "GO Biological Pathways",
font.size = 8)
})
})
output$dotPlot = renderPlot({
withProgress(message = "Plotting dotplot ...",{
go_enrich = enrichGoReactive()$go_enrich
dotplot(go_enrich,
#drop = TRUE,
showCategory = input$showCategory_dot,
#title = "GO Biological Pathways",
font.size = 8)
})
})
output$enrichPlotMap = renderPlot({
withProgress(message = "Plotting enrichment map ...",{
go_enrich = enrichGoReactive()$go_enrich
emapplot(go_enrich, showCategory = input$showCategory_enrichmap)
})
})
output$goInducedGraph = renderPlot({
withProgress(message = "Plotting induced GO DAG ...",{
go_enrich = enrichGoReactive()$go_enrich
goplot(go_enrich, showCategory = input$showCategory_goplot)
})
})
output$cnetplot = renderPlot({
withProgress(message = "Plotting Gene-Concept Network ...",{
go_enrich = enrichGoReactive()$go_enrich
cnetplot(go_enrich, categorySize="pvalue", foldChange=myValues$gene_list, showCategory = input$showCategory_cnet)
})
})
output$wordcloud = renderWordcloud2({
withProgress(message = "Plotting Wordcloud ...",{
if(input$plotWordcloud)
{
isolate({
if(input$wordcloudGoOrKegg == "enrichGo")
{
go_enrich = enrichGoReactive()$go_enrich
}
else
{
go_enrich = enrichGoReactive()$kegg_enrich
}
wcdf<-read.table(text=go_enrich$GeneRatio, sep = "/")[1]
wcdf$term<-go_enrich[,2]
# wc = wordcloud(words = wcdf$term, freq = wcdf$V1, scale=(c(2, .5)), colors=brewer.pal(8, "Dark2"), max.words = input$maxWords)
wordsDF = data.frame(word=go_enrich[,2], freq=wcdf$V1)
wordsDF = wordsDF[order(-wordsDF$freq),]
wordsDF = head(wordsDF, input$maxWords)
wordcloud2(wordsDF, color = input$wordsColor, shape = input$wordShape, size = 0.1)
})
}
})
})
### KEGG
output$barPlot_kegg = renderPlot({
withProgress(message = "Plotting barplot ...",{
kegg_enrich = enrichGoReactive()$kegg_enrich
barplot(kegg_enrich,
drop = TRUE,
showCategory = input$showCategory_bar_kegg,
title = "Enriched Pathways",
font.size = 8)
})
})
output$dotPlot_kegg = renderPlot({
withProgress(message = "Plotting dotplot ...",{
kegg_enrich = enrichGoReactive()$kegg_enrich
dotplot(kegg_enrich,
#drop = TRUE,
showCategory = input$showCategory_dot_kegg,
title = "Enriched Pathways",
font.size = 8)
})
})
output$enrichPlotMap_kegg = renderPlot({
withProgress(message = "Plotting Enrichment Map ...",{
kegg_enrich = enrichGoReactive()$kegg_enrich
emapplot(kegg_enrich, showCategory = input$showCategory_enrichmap_kegg)
})
})
output$cnetplot_kegg = renderPlot({
withProgress(message = "Plotting Gene-Concept Network ...",{
kegg_enrich = enrichGoReactive()$kegg_enrich
cnetplot(kegg_enrich, categorySize="pvalue", foldChange=myValues$kegg_gene_list, showCategory = input$showCategory_cnet_kegg)
})
})
pathviewReactive = eventReactive(input$generatePathview,{
withProgress(message = 'Plotting Pathview ...', {
isolate({
kegg_enrich = enrichGoReactive()$kegg_enrich
setProgress(value = 0.3, detail = paste0("Pathview ID ",input$pathwayIds," ..."))
dme <- pathview(gene.data=myValues$gene_list, pathway.id=input$pathwayIds, species = myValues$organismKegg, gene.idtype=input$geneid_type)
file.copy(paste0(input$pathwayIds,".pathview.png"),paste0("testimage"))
setProgress(value = 0.7, detail = paste0("Pathview ID ",input$pathwayIds," generating pdf ..."))
dmePdf <- pathview(gene.data=myValues$gene_list, pathway.id=input$pathwayIds, species = myValues$organismKegg, gene.idtype=input$geneid_type,kegg.native = F)
myValues$imagePath = paste0(input$pathwayIds,".pathview.")
return(list(
src = paste0("testimage"),
filetype = "image/png",
alt = "pathview image"
))
})
})
})
output$pathview_plot = renderImage({
return(pathviewReactive())
})
output$pathviewPlotsAvailable <-
reactive({
return(!is.null(pathviewReactive()))
})
outputOptions(output, 'pathviewPlotsAvailable', suspendWhenHidden=FALSE)
output$downloadPathviewPng <- downloadHandler(
filename = function() {paste0(myValues$imagePath,"png")},
content = function(file) {
file.copy(paste0(getwd(),'/',myValues$imagePath,"png"), file)
}
)
output$downloadPathviewPdf <- downloadHandler(
filename = function() {paste0(myValues$imagePath,"pdf")},
content = function(file) {
file.copy(paste0(getwd(),'/',myValues$imagePath,"pdf"), file)
}
)
output$wordcloud_kegg = renderWordcloud2({
withProgress(message = "Plotting Wordcloud ...",{
kegg_enrich = enrichGoReactive()$kegg_enrich
wcdf<-read.table(text=kegg_enrich$GeneRatio, sep = "/")[1]
wcdf$term<-kegg_enrich[,2]
# wc = wordcloud(words = wcdf$term, freq = wcdf$V1, scale=(c(2, .5)), colors=brewer.pal(8, "Dark2"), max.words = input$maxWords)
wordsDF = data.frame(word=kegg_enrich[,2], freq=wcdf$V1)
wordsDF = wordsDF[order(-wordsDF$freq),]
wordsDF = head(wordsDF, input$maxWords_kegg)
#browser()
wordcloud2(wordsDF, color = input$wordsColor_kegg, shape = input$wordShape_kegg, size = 0.1)
})
})