inst/examples/SigNetA-app/server.R
In uc-bd2k/SigNetA:
shinyServer(function(input,output,session){
##HIDE/SHOW BASED ON WHETHER FILE UPLOADED OR EXAMPLE FILE LOADED
observe({
if ( input$load_example[1]==0 && is.null(input$file1) && session$clientData$url_search=="") {
shinyjs::disable("downloadNetworkData")
shinyjs::hide("saveImage")
shinyjs::disable("downloadEnrich")
shinyjs::hide("algorithm")
shinyjs::hide("layout")
shinyjs::hide("PPI")
shinyjs::hide("goAn")
toggle(condition = FALSE , selector = "#tabs li a[data-value=cytonet]")
toggle(condition = FALSE , selector = "#tabs li a[data-value=datTable]")
toggle(condition = FALSE , selector = "#tabs li a[data-value=irich]")
}
else{
shinyjs::enable("downloadNetworkData")
shinyjs::show("saveImage")
shinyjs::enable("downloadEnrich")
shinyjs::show("algorithm")
shinyjs::show("layout")
shinyjs::show("PPI")
shinyjs::show("goAn")
toggle(condition = TRUE , selector = "#tabs li a[data-value=cytonet]")
toggle(condition = TRUE , selector = "#tabs li a[data-value=datTable]")
toggle(condition = TRUE , selector = "#tabs li a[data-value=irich]")
# Hide the loading message when the rest of the server function has executed
hide(id = "loading-content", anim = TRUE, animType = "fade")
}
})
##END ......HIDE/SHOW BASED ON WHETHER FILE UPLOADED OR EXAMPLE FILE LOADED
##LOAD FILE BASED ON WHETHER IT'S UPLOADED,LOAD EXAMPLE OR URL##
observeEvent(session$clientData$url_search,{
if(session$clientData$url_search!=""){
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
parsedGET<-parseQueryString(session$clientData$url_search)
if (!is.null(parsedGET[["File"]])) {
#path<-paste("http://www.ilincs.org/tmp/",parsedGET[["File"]],sep="")
path<-paste("/mnt/raid/tmp/",parsedGET[["File"]],sep="")
#path<-paste("/Users/Rashid/Desktop/Rashid/Career/PhD/Research/Events/BD2KAllHandsMeeting/signatures/",parsedGET[["File"]],sep="")
loadedFile<<-read.csv(file=path,sep="\t")
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
}
}
})
observeEvent(input$load_example,{
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
loadedFile<<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[,c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
})
observeEvent(input$file1,{
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
loadedFile<<-read.csv(file=input$file1$datapath,sep="\t")
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[,c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
})
##END.........LOAD FILE BASED ON WHETHER IT'S UPLOADED,LOAD EXAMPLE OR URL##
##GENERATE NETWORK PLOT##
output$general_ui <- renderUI({
visNetworkOutput("plot")
})
output$plot<-renderVisNetwork({
datasetInput()
})
datasetInput<-reactive({
algorithm<-input$algorithm
interactionNetwork<-input$PPI
networkLayout<-input$layout
physics<-input$phyactive
input$file1
input$load_example
input$goAn
if(algorithm==1){
ret<-RWR(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==3){
ret<-dmGWAS(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==4){
ret<-modifiedBioNetwork(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==5){
ret<-topHundredNetwork(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
})
##END......GENERATE NETWORK PLOT##
##GET NETWORK DATA#
output$contents<-renderDataTable({
input$file1 # to have active reactive context everytime file changes
input$load_example
input$PPI
input$algorithm
netData<-netData[-c(1,3,4)]
colnames(netData)<-c("geneName","NCBI_Information","geneID","Diff_Exp")
netData<-netData[c("geneName","geneID","Diff_Exp","NCBI_Information")]
netData$NCBI_Information<-paste0("<a href='",netData$NCBI_Information,"' target='_blank'>",netData$NCBI_Information,"</a>")
netData # returning global variable storing network data
},escape=FALSE)
##END....GET NETWORK DATA##
##GET ENRICHMENT DATA##
output$enrichmentAnalysis<-renderDataTable({
input$file1 # to have active reactive context everytime file changes
input$load_example
input$PPI
input$algorithm
fdr<-input$enrichFDR
#geninfo<-geneInfoFromPortals(geneList=as.character(loadedFile$GeneID),symbol=T,names=F)
geninfo<- geneData[which(geneData$GeneID%in%as.character(loadedFile$GeneID)),]
geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
print("enrichment")
print(geneLabels)
subnetGenes<-netData$geneID
allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory = 10, maxGenesInCategory =1000, inBkg=TRUE, sigFDR = fdr , verbose=TRUE)
options(scipen = 999)
ID<-result$categories
Name<-result$Description
PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
NetworkGenes<-result$nGenesInCategory
AllGenes<-result$nAllGenesInCategory
logOR<-round(result$logOR,2)
tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
datatable(tableEnrichment, options=list(columnDefs=list(list(targets=4)),pageLength = 7))
})
##END...GET ENRICHMENT DATA##
##DOWNLOADS##
output$downloadNetworkData <- downloadHandler(
filename = "",
content = function(file) {
write.csv(netData, file)
})
output$downloadEnrich <- downloadHandler(
filename = "",
content = function(file) {
write.csv(tableEnrichment, file)
})
##END...DOWNLOADS##
##PHYSICS LAYOUT OPTIONS##
observe({
visNetworkProxy("plot") %>%
visOptions(highlightNearest = TRUE,nodesIdSelection=list(enabled=TRUE,values=input$nodeSelect))
})
observe({
visNetworkProxy("plot") %>%
visPhysics(enabled=input$phyactive)
})
observe({
visNetworkProxy("plot") %>%
visNodes(size=input$nodeSize)
})
observe({
visNetworkProxy("plot") %>%
visPhysics(solver=input$solve,barnesHut=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav),repulsion=list(centralGravity=input$centralGrav),forceAtlas2Based=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav))
})
##END....PHYSICS LAYOUT OPTIONS##
##ADDING GO PATHWAYS TO NETWORK##
observeEvent(input$goAn,{
if(length(input$enrichmentAnalysis_rows_selected)>0){
idSel<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,1])
nameSel<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,2])
enrichment<-list("enrichID"=idSel,"enrichName"=nameSel)
enrichIDlength<-length(enrichment$enrichID)
from<-c()
to<-c()
for(i in 1:enrichIDlength){
addGO<-genesInEnrichedCategories(enrichment$enrichID[i], netData$geneID, funcCategories = "GO", species = "Hs")
for(j in 1:ncol(addGO)){
if(addGO[,j]==TRUE){
geneConversion<-substring( colnames(addGO)[j],2)
GOnodeName<-geneConversion
from<-c(from,enrichment$enrichID[i])
to<-c(to,GOnodeName)
}
}
}
if(input$PPI==1){
GOdataframe<-data.frame(from,to,title=NA,weight=NA,X=NA,f.neighborhood=NA,f.fusion=NA,f.cooccurence=NA,f.coexpression=NA,f.experimental=NA,f.database=NA,f.textmining=NA,f.combined_score=NA,a_symbols=NA,b_symbols=NA)
}
else if (input$PPI==2){
GOdataframe<-data.frame(from,to)
}
netconGO<-rbind(netcon,GOdataframe) #add from,to edgelist from existing network to newly added GO pathway
l<-nrow(nodecon)
for(i in 1:enrichIDlength){ ##add GO node attributes
nodecon[l+i,1]<-as.character(enrichment$enrichID[i])
nodecon[l+i,2]<-as.character(enrichment$enrichID[i])
nodecon[l+i,3]<-"#ffff00 "
nodecon[l+i,4]<-2
nodecon[l+i,5]<-"black"
nodecon[l+i,6]<-paste0("<p>",enrichment$enrichName[i],"</p>")
nodecon[l+i,7]<-"square"
nodecon[l+i,8]<-20
}
nodeGO<<-nodecon
edgeGO<<-netconGO
}
else{
#Remove GO nodes when no rows are selected
nodeGO<<-NULL
edgeGO<<-NULL
}
})
##END...ADDING GO PATHWAY TO NETWORK
##DETECT CHANGES IN APP FOR REMOVING GO PATHWAYS##
observeEvent(input$algorithm,{
nodeGO<<-NULL
edgeGO<<-NULL
})
observeEvent(input$PPI,{
nodeGO<<-NULL
edgeGO<<-NULL
})
##END..DETECT CHANGES IN APP FOR REMOVING GO PATHWAYS##
##CHANGE TAB WHEN GO PATHWAYS ADDED/DELETED##
observeEvent(input$goAn,{
updateTabsetPanel(session, "tabs", selected = "cytonet")
})
})
##END SERVER FUNCTION##
#
# library(DT)
# library(shiny)
# library(shinyjs)
# library(DLBCL)
# library(BioNet)
# library(igraph)
# library(CLEAN)
# library(CLEAN.Hs)
# library(networkD3)
# library(SigNetA)
# library(visNetwork)
# library(dmGWAS)
# #library(RCurl)
#
# ##hello world!!!
# data(interactome)
# #statNet <- reactiveValues(df_data = NULL)
# #statNet<-statNet$df_data
# statNet<<-NULL
# visImg<<-NULL
# exFile<<-NULL
# en<<-NULL
# tableEnrichment<<-NULL
# shinyServer(function(input,output,session){
# observe({
# query<-parseQueryString(session$clientData$url_search)
#
# if (!is.null(query[["File"]])) {
# File<<-query[['File']]
# ##print(File)
# #print("woohoo")
# # File<<- read.delim(file=File)
# # File<<- read.csv(file=File,sep="\t")
# # #print(class(File))
# # #print(data[[GeneNames]])
# path<-paste("http://www.ilincs.org/tmp/",query[["File"]],sep="")
# # path<-paste("http://dev.ilincs.org/tmp/",query[["File"]],sep="") #get file from url look it up
# # path<-paste("/Users/Rashid/Desktop/Rashid/Career/PhD/Research/Events/BD2KAllHandsMeeting/signatures/",query[["File"]],sep="")
# File<<-path
# # File<<- read.csv(file=path,sep="\t")
# #File<<-File[complete.cases(File),]
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
# toggle(condition = File , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = File, selector = "#tabs li a[data-value=datTable]")
# toggle(condition = File, selector = "#tabs li a[data-value=irich]")
#
# Sys.sleep(2)
#
# # Hide the loading message when the rest of the server function has executed
# hide(id = "loading-content", anim = TRUE, animType = "fade")
# ##print(path)
# #File<<- read.delim(file=path)
# }
#
# else{
# File<<-""
# }
# })
# observeEvent(input$load_example,{
#
# exFile<<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=datTable]")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=irich]")
#
# })
# #shinyjs::toggle(selector = "span.logo",TRUE,condition="[data-collapsed=true]" )
#
# #shinyjs::onclick("[role=button]",shinyjs::hide(selector = "[role=button]"))
#
#
# observe({
# #shinyjs::onclick(".skin-yellow .main-header .navbar .sidebar-toggle ",shinyjs::hide(".skin-yellow .main-header .logo "))
# if (is.null(input$file1) || input$file1 == "" ) {
#
# if(!(grepl("xls",File))){
#
# shinyjs::disable("downloadNetworkImage")
# shinyjs::hide("saveImage")
# shinyjs::disable("downloadEnrich")
# shinyjs::hide("algorithm")
# shinyjs::hide("layout")
# shinyjs::hide("PPI")
# shinyjs::hide("goAn")
# }
# else{
#
# }
#
# } else {
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
#
#
# Sys.sleep(2)
#
# # Hide the loading message when the rest of the server function has executed
# hide(id = "loading-content", anim = TRUE, animType = "fade")
#
# }
#
# if(is.null(File) || File==""){
# toggle(condition = input$file1 , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = input$file1, selector = "#tabs li a[data-value=datTable]")
# toggle(condition = input$file1, selector = "#tabs li a[data-value=irich]")
# }
#
#
#
#
# })
# observeEvent(input$saveImage, {
#
# session$sendCustomMessage(type="saveImage", message="NULL")
#
# })
#
# observe({
# if(input$algorithm==3 || input$algorithm==4){
# showModal(modalDialog(
# title = "Important message",
# "Please wait.This algorithm takes time to generate the subnetwork."
# ))
# }
# })
#
# output$clickedNode = renderPrint({
# input$clickedNode
# })
#
# output$connectedNodes = renderPrint({
# input$connectedNodes
# })
#
# ##gdgsgds
# output$enrichmentAnalysis<-DT::renderDataTable({
# if (is.null(input$file1) || input$file1 == "" ) {
# if(!is.null(exFile)){
#
# enrichmentChange()
#
# }
# else if(grepl("xls",File)){
# enrichmentChange()
# }
# else{
# paste("No genes analyzed")
# }
#
#
# } else if(!is.null(input$file) || !is.null(input$PPI)){
#
#
# # if(class(err) == "try-error"){
#
# # output$input_error2=renderText("No significant enrichment analysis data generated.Please upload another signature.")
# # stopifnot(class(err) == "try-error")
# #}
# # else{
# # output$input_error2=renderText("")
#
# enrichmentChange()
#
# #this is where enrichment functionality was
#
#
# }
#
#
# # }
# }
#
#
# )
#
# #enrichmentChange<-reactive({
# enrichmentChange<-function(){
# # if((input$algorithm=="1" && input$layout=="1") || (input$algorithm=="1" && input$layout=="2"))
# if(input$algorithm=="1")
# {
# if(is.null(input$file1)){
# if(!(grepl("xls",File))){
# logic<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
# }
# else{
# logic<-read.csv(file=File,sep='\t')
# colnames(logic)<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
# }
# }
#
# else{
# logic<-read.csv(input$file1$datapath,sep="\t")
# }
#
#
# logic<-sortNetwork(logic)
#
#
# geninfo<-geneInfoFromPortals(geneList=as.character(logic$GeneID),symbol=T,names=F)
# geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
#
# if(input$PPI=="2"){
# subnetGenes<-statNet$id
# }
# else{
# ##IMPORTANT CHANGES TO BE MADE HERE
# #subnetGenes<-statNet$id ; Look into applying this
# subnetGenes<-gsub("[\\(\\)]", "", regmatches( statNet$id, gregexpr("\\(.*?\\)", statNet$id)))
# }
# allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
#
#
#
#
# result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory=10, maxGenesInCategory=1000, inBkg=TRUE, sigFDR = 0.1, verbose=TRUE)
#
#
#
#
# options(scipen = 999)
# ID<-result$categories
# Name<-result$Description
# PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
# FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
# NetworkGenes<-result$nGenesInCategory
# AllGenes<-result$nAllGenesInCategory
# logOR<-round(result$logOR,2)
# tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
# datatable(tableEnrichment, options=list(columnDefs=list(list(targets=4)),pageLength = 7))
#
#
# }
#
# # else if((input$algorithm=="2" && input$layout=="2")||(input$algorithm=="2" && input$layout=="1")){
# else if(input$algorithm=="2" || input$algorithm=="4"){
# if(is.null(input$file1)){
# if(!(grepl("xls",File))){
# logic<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
# }
# else{
# logic<-read.csv(file=File,sep='\t')
# colnames(logic)<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
# }
# }
# else{
# logic<-read.csv(input$file1$datapath,sep="\t")
# }
#
#
#
#
#
# geninfo<-geneInfoFromPortals(geneList=as.character(logic$GeneID),symbol=T,names=F)
# geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
#
# subnetGenes<-gsub("[\\(\\)]", "", regmatches( statNet$id, gregexpr("\\(.*?\\)", statNet$id)))
# allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
#
# result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory=10, maxGenesInCategory=1000, inBkg=TRUE, sigFDR = 0.1, verbose=TRUE)
#
#
#
#
# options(scipen = 999)
# ID<-result$categories
# Name<-result$Description
# PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
# FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
# NetworkGenes<-result$nGenesInCategory
# AllGenes<-result$nAllGenesInCategory
# logOR<-round(result$logOR,2)
# tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
#
#
# }
#
# }
# #})
#
# # tableChange<-reactive({
# tableChange<-function(){
#
# # if(input$algorithm=="1" ){
# if(!is.null(statNet)){
#
# statNet<-statNet[-c(1,3,4)]
#
# colnames(statNet)<-c("geneName","NCBI Information","geneID","Diff_Exp")
# statNet<-statNet[c("geneName","geneID","Diff_Exp","NCBI Information")]
#
#
# }
#
# statNet
# # }
# }
# # })
#
# output$contents <-DT::renderDataTable({
#
# if (is.null(input$file1) || input$file1 == "" ) {
# if(!is.null(exFile) || is.null(input$PPI)){
#
# tableChange()
#
# }
# else if(grepl("xls",File)){
#
# tableChange()
# }
#
# else{
# paste("No genes analyzed")
# }
# }
#
# else if(!is.null(input$file) || !is.null(input$PPI)){
#
#
#
# tableChange()
#
# }
#
#
# })
#
#
# observeEvent(input$algorithm,{
#
# tableChange()
# })
#
#
# observeEvent(input$goAn,{
#
#
# idSel<<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,1])
# nameSel<<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,2])
# en<<-data.frame(idSel,nameSel)
#
#
# if(nrow(en)>0){
#
# }
# else{
#
# en<<-NULL
#
# }
#
#
#
# # output$plot<-renderVisNetwork({
# #
# # ret<-topHundredNetwork(input$file1$datapath,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=en,package=FALSE)
# #
# # })
# #
#
#
# })
# output$genenodes <- renderText({
#
# if (is.null(input$file1) || input$file1 == "") {
# paste("No genes analyzed")
# } else {
#
#
# newlist<-c()
#
#
# for (i in 1:length(statNet$id)){
# append(statNet$id,"\n",i)
# newlist[i]<-statNet$id[i]
# }
#
# newlist
#
#
#
#
# }
#
#
#
#
# })
#
#
#
#
#
#
#
#
# output$general_ui <- renderUI({
# if(input$algorithm=="1" && input$layout=="1"){
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
# else if(input$algorithm=="2" && input$layout=="1"){
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
#
#
# #LAYOUT
# else if(input$algorithm=="1" && input$layout=="2"){
# simpleNetworkOutput("simple")
# }
# else if(input$algorithm=="2" && input$layout=="2"){
# simpleNetworkOutput("simple")
# }
#
# else{
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
#
#
#
#
# })
#
# enrichAdd<-function(){
#
# if(is.null(en)){
# retu<-NULL;
# }
# else{
# retu<-en
# }
# }
#
#
# datasetInput <- reactive({
# if(input$algorithm=="1" && (!grepl("xls",File))){
# #if(!is.null(File))
# #{ print(File)
# # ret<-topHundredNetwork(File,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
# #}
# # else{
#
# # print("algo 1")
# RWR(input$file1$datapath,upload5="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
#
# #}
#
# }
# else if(input$algorithm=="1" && (grepl("xls",File))){
# #print("algo 1 1")
# RWR(File,upload5="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
#
# }
#
#
#
# else if(input$algorithm=="2" && (!grepl("xls",File))){
# # print("algo 2")
# print(File)
# ret<-bioNetwork(input$file1$datapath,upload2="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="2" && (grepl("xls",File))){
# # print("algo 2 2")
# ret<-bioNetwork(File,upload2="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="3" && (!grepl("xls",File))){
# # print("algo 3")
# ret<-dmGWAS(input$file1$datapath,upload3="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="3" && (grepl("xls",File))){
# ret<-dmGWAS(File,upload3="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="4" && (!grepl("xls",File))){
# # print("algo4")
# modifiedBioNetwork(input$file1$datapath,upload4="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="4" && (grepl("xls",File))){
# # print("algo4 4")
# modifiedBioNetwork(File,upload4="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="5" && (!grepl("xls",File))){
# ret<-topHundredNetwork(input$file1$datapath,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
#
# }
# else if(input$algorithm=="5" && (grepl("xls",File))){
#
# ret<-topHundredNetwork(File,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
# }
#
#
#
#
#
#
#
# })
#
# layoutInput<-reactive({
#
# #if(input$layout=="2"){
# if(input$algorithm=="1"){
# #source("D3layout.R")
# ret<-D3layout(input$file1$datapath,upload3="yes")
# }
# else if(input$algorithm=="2"){
# #source("D3bioNetwork.R")
# ret<-D3bioNetwork(input$file1$datapath,upload4="yes")
# }
# }
#
#
# # }
#
# )
#
#
#
# output$plot<-renderVisNetwork({
#
# Sys.sleep(2);
#
# datasetInput()
#
#
#
#
#
#
#
#
#
#
#
# })
#
# output$simple<-renderSimpleNetwork({
#
# layoutInput()
#
# })
#
#
#
# observe({
# visNetworkProxy("plot") %>%
#
#
# visOptions(highlightNearest = TRUE,nodesIdSelection=list(enabled=TRUE,values=input$nodeSelect))
#
#
#
#
# })
# observe({
# visNetworkProxy("plot") %>%
#
# visPhysics(enabled=input$phyactive)
#
#
# })
# observe({
# visNetworkProxy("plot") %>%
#
# visNodes(size=input$nodeSize)
#
#
# })
#
#
# observe({
# visNetworkProxy("plot") %>%
#
# visPhysics(solver=input$solve,barnesHut=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav),repulsion=list(centralGravity=input$centralGrav),forceAtlas2Based=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav))
#
#
#
# })
#
#
#
#
# ##VISNETWORK INPUT END##
#
# plotInput <- function(network,nodes,edges){
#
# cyNetwork <- network
#
# rashidcytoscapejs(nodes,edges,showPanzoom=TRUE)
# }
#
#
#
# output$downloadNetworkImage <- downloadHandler(
# filename = "Shinynet.csv",
#
# content = function(file) {
# statNet<-statNet[-c(1,3,4)]
# colnames(statNet)<-c("geneName","NCBI Information","geneID","Diff_Exp","score")
# statNet<-statNet[c("geneName","geneID","Diff_Exp","score","NCBI Information")]
# write.csv(statNet, file)
#
#
# })
# output$downloadEnrich <- downloadHandler(
# filename = "Shinynet.csv",
#
# content = function(file) {
#
# write.csv(tableEnrichment, file)
#
#
# })
#
#
#
# observeEvent(input$compDataSave, {
# filename=paste("files/",input$compData)
# write.csv(statNet,file=paste(filename,".csv",sep=""),row.names=FALSE,sep = "\t")
#
# session$sendCustomMessage(type = 'testmessage',
# message = 'Thank you for clicking')
# })
#
# sig_name<-reactive({
#
# return(listfiles())
# })
# observeEvent(input$choices,{
# sigFileName<-paste("files/",input$choices,sep = "")
# sigFile<<-read.csv(file=sigFileName,sep='\t')
#
#
#
#
# })
# output$Signatures <- renderUI({
# selectInput("choices","Select Signatures",choices = as.vector(sig_name()))
# })
# output$text <- renderPrint({
# paste("you selected",input$choices,sep=" ")
# })
#
#
#
#
#
# }
# )
# ##other functions##
# #list all files
# listfiles <- function(){
#
# files <- Sys.glob("files/*.csv")
#
# l = list()
# for(i in 1:length(files)){
#
# l[[i]]=strsplit(files[i],"/")
#
# }
#
# vect = c()
# for(i in 1:length(files)){
#
# vect[i] = l[[i]][[1]][2]
# }
#
#
# return (vect)
# }
uc-bd2k/SigNetA documentation built on June 7, 2019, 7:55 a.m.
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shinyServer(function(input,output,session){
##HIDE/SHOW BASED ON WHETHER FILE UPLOADED OR EXAMPLE FILE LOADED
observe({
if ( input$load_example[1]==0 && is.null(input$file1) && session$clientData$url_search=="") {
shinyjs::disable("downloadNetworkData")
shinyjs::hide("saveImage")
shinyjs::disable("downloadEnrich")
shinyjs::hide("algorithm")
shinyjs::hide("layout")
shinyjs::hide("PPI")
shinyjs::hide("goAn")
toggle(condition = FALSE , selector = "#tabs li a[data-value=cytonet]")
toggle(condition = FALSE , selector = "#tabs li a[data-value=datTable]")
toggle(condition = FALSE , selector = "#tabs li a[data-value=irich]")
}
else{
shinyjs::enable("downloadNetworkData")
shinyjs::show("saveImage")
shinyjs::enable("downloadEnrich")
shinyjs::show("algorithm")
shinyjs::show("layout")
shinyjs::show("PPI")
shinyjs::show("goAn")
toggle(condition = TRUE , selector = "#tabs li a[data-value=cytonet]")
toggle(condition = TRUE , selector = "#tabs li a[data-value=datTable]")
toggle(condition = TRUE , selector = "#tabs li a[data-value=irich]")
# Hide the loading message when the rest of the server function has executed
hide(id = "loading-content", anim = TRUE, animType = "fade")
}
})
##END ......HIDE/SHOW BASED ON WHETHER FILE UPLOADED OR EXAMPLE FILE LOADED
##LOAD FILE BASED ON WHETHER IT'S UPLOADED,LOAD EXAMPLE OR URL##
observeEvent(session$clientData$url_search,{
if(session$clientData$url_search!=""){
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
parsedGET<-parseQueryString(session$clientData$url_search)
if (!is.null(parsedGET[["File"]])) {
#path<-paste("http://www.ilincs.org/tmp/",parsedGET[["File"]],sep="")
path<-paste("/mnt/raid/tmp/",parsedGET[["File"]],sep="")
#path<-paste("/Users/Rashid/Desktop/Rashid/Career/PhD/Research/Events/BD2KAllHandsMeeting/signatures/",parsedGET[["File"]],sep="")
loadedFile<<-read.csv(file=path,sep="\t")
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
}
}
})
observeEvent(input$load_example,{
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
loadedFile<<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[,c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
})
observeEvent(input$file1,{
nodeGO<<-NULL #To go back to default network construction and delete GO nodes
edgeGO<<-NULL
updateTabsetPanel(session, "tabs", selected = "cytonet")
loadedFile<<-read.csv(file=input$file1$datapath,sep="\t")
##UPDATED CHANGES FOR FILE COLUMN NAME CHANGE
#loadedFile<<-loadedFile[,1:5]
#colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
loadedFile<<-loadedFile[,c("ID_geneid","Name_GeneSymbol","Value_LogDiffExp","Significance_pvalue")]
loadedFile<<-cbind("signatureID"=NA,loadedFile)
colnames(loadedFile)<<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
})
##END.........LOAD FILE BASED ON WHETHER IT'S UPLOADED,LOAD EXAMPLE OR URL##
##GENERATE NETWORK PLOT##
output$general_ui <- renderUI({
visNetworkOutput("plot")
})
output$plot<-renderVisNetwork({
datasetInput()
})
datasetInput<-reactive({
algorithm<-input$algorithm
interactionNetwork<-input$PPI
networkLayout<-input$layout
physics<-input$phyactive
input$file1
input$load_example
input$goAn
if(algorithm==1){
ret<-RWR(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==3){
ret<-dmGWAS(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==4){
ret<-modifiedBioNetwork(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
else if(algorithm==5){
ret<-topHundredNetwork(loadedFile,phy=physics,layOut=networkLayout,package=FALSE,nodeGoData=nodeGO,edgeGoData=edgeGO,proteinN=interactionNetwork)
netcon<<-ret$edgeData
nodecon<<-ret$nodeData
netData<<-ret$networkData #capture network data from algorithm
ret$networkObj #return visnetwork object
}
})
##END......GENERATE NETWORK PLOT##
##GET NETWORK DATA#
output$contents<-renderDataTable({
input$file1 # to have active reactive context everytime file changes
input$load_example
input$PPI
input$algorithm
netData<-netData[-c(1,3,4)]
colnames(netData)<-c("geneName","NCBI_Information","geneID","Diff_Exp")
netData<-netData[c("geneName","geneID","Diff_Exp","NCBI_Information")]
netData$NCBI_Information<-paste0("<a href='",netData$NCBI_Information,"' target='_blank'>",netData$NCBI_Information,"</a>")
netData # returning global variable storing network data
},escape=FALSE)
##END....GET NETWORK DATA##
##GET ENRICHMENT DATA##
output$enrichmentAnalysis<-renderDataTable({
input$file1 # to have active reactive context everytime file changes
input$load_example
input$PPI
input$algorithm
fdr<-input$enrichFDR
#geninfo<-geneInfoFromPortals(geneList=as.character(loadedFile$GeneID),symbol=T,names=F)
geninfo<- geneData[which(geneData$GeneID%in%as.character(loadedFile$GeneID)),]
geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
print("enrichment")
print(geneLabels)
subnetGenes<-netData$geneID
allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory = 10, maxGenesInCategory =1000, inBkg=TRUE, sigFDR = fdr , verbose=TRUE)
options(scipen = 999)
ID<-result$categories
Name<-result$Description
PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
NetworkGenes<-result$nGenesInCategory
AllGenes<-result$nAllGenesInCategory
logOR<-round(result$logOR,2)
tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
datatable(tableEnrichment, options=list(columnDefs=list(list(targets=4)),pageLength = 7))
})
##END...GET ENRICHMENT DATA##
##DOWNLOADS##
output$downloadNetworkData <- downloadHandler(
filename = "",
content = function(file) {
write.csv(netData, file)
})
output$downloadEnrich <- downloadHandler(
filename = "",
content = function(file) {
write.csv(tableEnrichment, file)
})
##END...DOWNLOADS##
##PHYSICS LAYOUT OPTIONS##
observe({
visNetworkProxy("plot") %>%
visOptions(highlightNearest = TRUE,nodesIdSelection=list(enabled=TRUE,values=input$nodeSelect))
})
observe({
visNetworkProxy("plot") %>%
visPhysics(enabled=input$phyactive)
})
observe({
visNetworkProxy("plot") %>%
visNodes(size=input$nodeSize)
})
observe({
visNetworkProxy("plot") %>%
visPhysics(solver=input$solve,barnesHut=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav),repulsion=list(centralGravity=input$centralGrav),forceAtlas2Based=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav))
})
##END....PHYSICS LAYOUT OPTIONS##
##ADDING GO PATHWAYS TO NETWORK##
observeEvent(input$goAn,{
if(length(input$enrichmentAnalysis_rows_selected)>0){
idSel<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,1])
nameSel<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,2])
enrichment<-list("enrichID"=idSel,"enrichName"=nameSel)
enrichIDlength<-length(enrichment$enrichID)
from<-c()
to<-c()
for(i in 1:enrichIDlength){
addGO<-genesInEnrichedCategories(enrichment$enrichID[i], netData$geneID, funcCategories = "GO", species = "Hs")
for(j in 1:ncol(addGO)){
if(addGO[,j]==TRUE){
geneConversion<-substring( colnames(addGO)[j],2)
GOnodeName<-geneConversion
from<-c(from,enrichment$enrichID[i])
to<-c(to,GOnodeName)
}
}
}
if(input$PPI==1){
GOdataframe<-data.frame(from,to,title=NA,weight=NA,X=NA,f.neighborhood=NA,f.fusion=NA,f.cooccurence=NA,f.coexpression=NA,f.experimental=NA,f.database=NA,f.textmining=NA,f.combined_score=NA,a_symbols=NA,b_symbols=NA)
}
else if (input$PPI==2){
GOdataframe<-data.frame(from,to)
}
netconGO<-rbind(netcon,GOdataframe) #add from,to edgelist from existing network to newly added GO pathway
l<-nrow(nodecon)
for(i in 1:enrichIDlength){ ##add GO node attributes
nodecon[l+i,1]<-as.character(enrichment$enrichID[i])
nodecon[l+i,2]<-as.character(enrichment$enrichID[i])
nodecon[l+i,3]<-"#ffff00 "
nodecon[l+i,4]<-2
nodecon[l+i,5]<-"black"
nodecon[l+i,6]<-paste0("<p>",enrichment$enrichName[i],"</p>")
nodecon[l+i,7]<-"square"
nodecon[l+i,8]<-20
}
nodeGO<<-nodecon
edgeGO<<-netconGO
}
else{
#Remove GO nodes when no rows are selected
nodeGO<<-NULL
edgeGO<<-NULL
}
})
##END...ADDING GO PATHWAY TO NETWORK
##DETECT CHANGES IN APP FOR REMOVING GO PATHWAYS##
observeEvent(input$algorithm,{
nodeGO<<-NULL
edgeGO<<-NULL
})
observeEvent(input$PPI,{
nodeGO<<-NULL
edgeGO<<-NULL
})
##END..DETECT CHANGES IN APP FOR REMOVING GO PATHWAYS##
##CHANGE TAB WHEN GO PATHWAYS ADDED/DELETED##
observeEvent(input$goAn,{
updateTabsetPanel(session, "tabs", selected = "cytonet")
})
})
##END SERVER FUNCTION##
#
# library(DT)
# library(shiny)
# library(shinyjs)
# library(DLBCL)
# library(BioNet)
# library(igraph)
# library(CLEAN)
# library(CLEAN.Hs)
# library(networkD3)
# library(SigNetA)
# library(visNetwork)
# library(dmGWAS)
# #library(RCurl)
#
# ##hello world!!!
# data(interactome)
# #statNet <- reactiveValues(df_data = NULL)
# #statNet<-statNet$df_data
# statNet<<-NULL
# visImg<<-NULL
# exFile<<-NULL
# en<<-NULL
# tableEnrichment<<-NULL
# shinyServer(function(input,output,session){
# observe({
# query<-parseQueryString(session$clientData$url_search)
#
# if (!is.null(query[["File"]])) {
# File<<-query[['File']]
# ##print(File)
# #print("woohoo")
# # File<<- read.delim(file=File)
# # File<<- read.csv(file=File,sep="\t")
# # #print(class(File))
# # #print(data[[GeneNames]])
# path<-paste("http://www.ilincs.org/tmp/",query[["File"]],sep="")
# # path<-paste("http://dev.ilincs.org/tmp/",query[["File"]],sep="") #get file from url look it up
# # path<-paste("/Users/Rashid/Desktop/Rashid/Career/PhD/Research/Events/BD2KAllHandsMeeting/signatures/",query[["File"]],sep="")
# File<<-path
# # File<<- read.csv(file=path,sep="\t")
# #File<<-File[complete.cases(File),]
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
# toggle(condition = File , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = File, selector = "#tabs li a[data-value=datTable]")
# toggle(condition = File, selector = "#tabs li a[data-value=irich]")
#
# Sys.sleep(2)
#
# # Hide the loading message when the rest of the server function has executed
# hide(id = "loading-content", anim = TRUE, animType = "fade")
# ##print(path)
# #File<<- read.delim(file=path)
# }
#
# else{
# File<<-""
# }
# })
# observeEvent(input$load_example,{
#
# exFile<<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=datTable]")
# toggle(condition = TRUE , selector = "#tabs li a[data-value=irich]")
#
# })
# #shinyjs::toggle(selector = "span.logo",TRUE,condition="[data-collapsed=true]" )
#
# #shinyjs::onclick("[role=button]",shinyjs::hide(selector = "[role=button]"))
#
#
# observe({
# #shinyjs::onclick(".skin-yellow .main-header .navbar .sidebar-toggle ",shinyjs::hide(".skin-yellow .main-header .logo "))
# if (is.null(input$file1) || input$file1 == "" ) {
#
# if(!(grepl("xls",File))){
#
# shinyjs::disable("downloadNetworkImage")
# shinyjs::hide("saveImage")
# shinyjs::disable("downloadEnrich")
# shinyjs::hide("algorithm")
# shinyjs::hide("layout")
# shinyjs::hide("PPI")
# shinyjs::hide("goAn")
# }
# else{
#
# }
#
# } else {
#
# shinyjs::enable("downloadNetworkImage")
# shinyjs::show("saveImage")
# shinyjs::enable("downloadEnrich")
# shinyjs::show("algorithm")
# shinyjs::show("layout")
# shinyjs::show("PPI")
# shinyjs::show("goAn")
#
#
# Sys.sleep(2)
#
# # Hide the loading message when the rest of the server function has executed
# hide(id = "loading-content", anim = TRUE, animType = "fade")
#
# }
#
# if(is.null(File) || File==""){
# toggle(condition = input$file1 , selector = "#tabs li a[data-value=cytonet]")
# toggle(condition = input$file1, selector = "#tabs li a[data-value=datTable]")
# toggle(condition = input$file1, selector = "#tabs li a[data-value=irich]")
# }
#
#
#
#
# })
# observeEvent(input$saveImage, {
#
# session$sendCustomMessage(type="saveImage", message="NULL")
#
# })
#
# observe({
# if(input$algorithm==3 || input$algorithm==4){
# showModal(modalDialog(
# title = "Important message",
# "Please wait.This algorithm takes time to generate the subnetwork."
# ))
# }
# })
#
# output$clickedNode = renderPrint({
# input$clickedNode
# })
#
# output$connectedNodes = renderPrint({
# input$connectedNodes
# })
#
# ##gdgsgds
# output$enrichmentAnalysis<-DT::renderDataTable({
# if (is.null(input$file1) || input$file1 == "" ) {
# if(!is.null(exFile)){
#
# enrichmentChange()
#
# }
# else if(grepl("xls",File)){
# enrichmentChange()
# }
# else{
# paste("No genes analyzed")
# }
#
#
# } else if(!is.null(input$file) || !is.null(input$PPI)){
#
#
# # if(class(err) == "try-error"){
#
# # output$input_error2=renderText("No significant enrichment analysis data generated.Please upload another signature.")
# # stopifnot(class(err) == "try-error")
# #}
# # else{
# # output$input_error2=renderText("")
#
# enrichmentChange()
#
# #this is where enrichment functionality was
#
#
# }
#
#
# # }
# }
#
#
# )
#
# #enrichmentChange<-reactive({
# enrichmentChange<-function(){
# # if((input$algorithm=="1" && input$layout=="1") || (input$algorithm=="1" && input$layout=="2"))
# if(input$algorithm=="1")
# {
# if(is.null(input$file1)){
# if(!(grepl("xls",File))){
# logic<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
# }
# else{
# logic<-read.csv(file=File,sep='\t')
# colnames(logic)<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
# }
# }
#
# else{
# logic<-read.csv(input$file1$datapath,sep="\t")
# }
#
#
# logic<-sortNetwork(logic)
#
#
# geninfo<-geneInfoFromPortals(geneList=as.character(logic$GeneID),symbol=T,names=F)
# geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
#
# if(input$PPI=="2"){
# subnetGenes<-statNet$id
# }
# else{
# ##IMPORTANT CHANGES TO BE MADE HERE
# #subnetGenes<-statNet$id ; Look into applying this
# subnetGenes<-gsub("[\\(\\)]", "", regmatches( statNet$id, gregexpr("\\(.*?\\)", statNet$id)))
# }
# allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
#
#
#
#
# result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory=10, maxGenesInCategory=1000, inBkg=TRUE, sigFDR = 0.1, verbose=TRUE)
#
#
#
#
# options(scipen = 999)
# ID<-result$categories
# Name<-result$Description
# PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
# FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
# NetworkGenes<-result$nGenesInCategory
# AllGenes<-result$nAllGenesInCategory
# logOR<-round(result$logOR,2)
# tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
# datatable(tableEnrichment, options=list(columnDefs=list(list(targets=4)),pageLength = 7))
#
#
# }
#
# # else if((input$algorithm=="2" && input$layout=="2")||(input$algorithm=="2" && input$layout=="1")){
# else if(input$algorithm=="2" || input$algorithm=="4"){
# if(is.null(input$file1)){
# if(!(grepl("xls",File))){
# logic<-read.csv(file=system.file("extdata", "sig_try3.tsv", package = "SigNetA"),sep='\t')
# }
# else{
# logic<-read.csv(file=File,sep='\t')
# colnames(logic)<-c("signatureID","GeneID","GeneNames","coefficients","Pvals")
# }
# }
# else{
# logic<-read.csv(input$file1$datapath,sep="\t")
# }
#
#
#
#
#
# geninfo<-geneInfoFromPortals(geneList=as.character(logic$GeneID),symbol=T,names=F)
# geneLabels<-apply(geninfo,1,function(x) paste(x[2],"(",as.integer(x[1]),")",sep=""))
#
# subnetGenes<-gsub("[\\(\\)]", "", regmatches( statNet$id, gregexpr("\\(.*?\\)", statNet$id)))
# allGenes<-gsub("[\\(\\)]", "", regmatches(geneLabels, gregexpr("\\(.*?\\)", geneLabels)))
#
# result<-geneListEnrichment(subnetGenes, allGenes, functionalCategories = "GO", species = "Hs", minGenesInCategory=10, maxGenesInCategory=1000, inBkg=TRUE, sigFDR = 0.1, verbose=TRUE)
#
#
#
#
# options(scipen = 999)
# ID<-result$categories
# Name<-result$Description
# PValue<-format(result$FisherPValue,digits=2,scientific = TRUE)
# FDR<-format(result$FisherFDR,digits=2,scientific = TRUE)
# NetworkGenes<-result$nGenesInCategory
# AllGenes<-result$nAllGenesInCategory
# logOR<-round(result$logOR,2)
# tableEnrichment<<-data.frame(ID,Name,PValue,FDR,NetworkGenes,AllGenes,logOR)
#
#
# }
#
# }
# #})
#
# # tableChange<-reactive({
# tableChange<-function(){
#
# # if(input$algorithm=="1" ){
# if(!is.null(statNet)){
#
# statNet<-statNet[-c(1,3,4)]
#
# colnames(statNet)<-c("geneName","NCBI Information","geneID","Diff_Exp")
# statNet<-statNet[c("geneName","geneID","Diff_Exp","NCBI Information")]
#
#
# }
#
# statNet
# # }
# }
# # })
#
# output$contents <-DT::renderDataTable({
#
# if (is.null(input$file1) || input$file1 == "" ) {
# if(!is.null(exFile) || is.null(input$PPI)){
#
# tableChange()
#
# }
# else if(grepl("xls",File)){
#
# tableChange()
# }
#
# else{
# paste("No genes analyzed")
# }
# }
#
# else if(!is.null(input$file) || !is.null(input$PPI)){
#
#
#
# tableChange()
#
# }
#
#
# })
#
#
# observeEvent(input$algorithm,{
#
# tableChange()
# })
#
#
# observeEvent(input$goAn,{
#
#
# idSel<<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,1])
# nameSel<<-as.character(tableEnrichment[input$enrichmentAnalysis_rows_selected,2])
# en<<-data.frame(idSel,nameSel)
#
#
# if(nrow(en)>0){
#
# }
# else{
#
# en<<-NULL
#
# }
#
#
#
# # output$plot<-renderVisNetwork({
# #
# # ret<-topHundredNetwork(input$file1$datapath,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=en,package=FALSE)
# #
# # })
# #
#
#
# })
# output$genenodes <- renderText({
#
# if (is.null(input$file1) || input$file1 == "") {
# paste("No genes analyzed")
# } else {
#
#
# newlist<-c()
#
#
# for (i in 1:length(statNet$id)){
# append(statNet$id,"\n",i)
# newlist[i]<-statNet$id[i]
# }
#
# newlist
#
#
#
#
# }
#
#
#
#
# })
#
#
#
#
#
#
#
#
# output$general_ui <- renderUI({
# if(input$algorithm=="1" && input$layout=="1"){
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
# else if(input$algorithm=="2" && input$layout=="1"){
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
#
#
# #LAYOUT
# else if(input$algorithm=="1" && input$layout=="2"){
# simpleNetworkOutput("simple")
# }
# else if(input$algorithm=="2" && input$layout=="2"){
# simpleNetworkOutput("simple")
# }
#
# else{
# #rcytoscapejsOutput("plot", height="800px",width="900px")
# visNetworkOutput("plot")
# }
#
#
#
#
# })
#
# enrichAdd<-function(){
#
# if(is.null(en)){
# retu<-NULL;
# }
# else{
# retu<-en
# }
# }
#
#
# datasetInput <- reactive({
# if(input$algorithm=="1" && (!grepl("xls",File))){
# #if(!is.null(File))
# #{ print(File)
# # ret<-topHundredNetwork(File,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
# #}
# # else{
#
# # print("algo 1")
# RWR(input$file1$datapath,upload5="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
#
# #}
#
# }
# else if(input$algorithm=="1" && (grepl("xls",File))){
# #print("algo 1 1")
# RWR(File,upload5="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
#
# }
#
#
#
# else if(input$algorithm=="2" && (!grepl("xls",File))){
# # print("algo 2")
# print(File)
# ret<-bioNetwork(input$file1$datapath,upload2="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="2" && (grepl("xls",File))){
# # print("algo 2 2")
# ret<-bioNetwork(File,upload2="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="3" && (!grepl("xls",File))){
# # print("algo 3")
# ret<-dmGWAS(input$file1$datapath,upload3="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="3" && (grepl("xls",File))){
# ret<-dmGWAS(File,upload3="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
#
# else if(input$algorithm=="4" && (!grepl("xls",File))){
# # print("algo4")
# modifiedBioNetwork(input$file1$datapath,upload4="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="4" && (grepl("xls",File))){
# # print("algo4 4")
# modifiedBioNetwork(File,upload4="yes",phy=input$phyactive,layOut=input$layout,package=FALSE)
# }
# else if(input$algorithm=="5" && (!grepl("xls",File))){
# ret<-topHundredNetwork(input$file1$datapath,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
#
# }
# else if(input$algorithm=="5" && (grepl("xls",File))){
#
# ret<-topHundredNetwork(File,upload1="yes",layOut=input$layout,proteinN=input$PPI,phy=input$phyactive,enrich=enrichAdd())
# }
#
#
#
#
#
#
#
# })
#
# layoutInput<-reactive({
#
# #if(input$layout=="2"){
# if(input$algorithm=="1"){
# #source("D3layout.R")
# ret<-D3layout(input$file1$datapath,upload3="yes")
# }
# else if(input$algorithm=="2"){
# #source("D3bioNetwork.R")
# ret<-D3bioNetwork(input$file1$datapath,upload4="yes")
# }
# }
#
#
# # }
#
# )
#
#
#
# output$plot<-renderVisNetwork({
#
# Sys.sleep(2);
#
# datasetInput()
#
#
#
#
#
#
#
#
#
#
#
# })
#
# output$simple<-renderSimpleNetwork({
#
# layoutInput()
#
# })
#
#
#
# observe({
# visNetworkProxy("plot") %>%
#
#
# visOptions(highlightNearest = TRUE,nodesIdSelection=list(enabled=TRUE,values=input$nodeSelect))
#
#
#
#
# })
# observe({
# visNetworkProxy("plot") %>%
#
# visPhysics(enabled=input$phyactive)
#
#
# })
# observe({
# visNetworkProxy("plot") %>%
#
# visNodes(size=input$nodeSize)
#
#
# })
#
#
# observe({
# visNetworkProxy("plot") %>%
#
# visPhysics(solver=input$solve,barnesHut=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav),repulsion=list(centralGravity=input$centralGrav),forceAtlas2Based=list(gravitationalConstant=input$grav,centralGravity=input$centralGrav))
#
#
#
# })
#
#
#
#
# ##VISNETWORK INPUT END##
#
# plotInput <- function(network,nodes,edges){
#
# cyNetwork <- network
#
# rashidcytoscapejs(nodes,edges,showPanzoom=TRUE)
# }
#
#
#
# output$downloadNetworkImage <- downloadHandler(
# filename = "Shinynet.csv",
#
# content = function(file) {
# statNet<-statNet[-c(1,3,4)]
# colnames(statNet)<-c("geneName","NCBI Information","geneID","Diff_Exp","score")
# statNet<-statNet[c("geneName","geneID","Diff_Exp","score","NCBI Information")]
# write.csv(statNet, file)
#
#
# })
# output$downloadEnrich <- downloadHandler(
# filename = "Shinynet.csv",
#
# content = function(file) {
#
# write.csv(tableEnrichment, file)
#
#
# })
#
#
#
# observeEvent(input$compDataSave, {
# filename=paste("files/",input$compData)
# write.csv(statNet,file=paste(filename,".csv",sep=""),row.names=FALSE,sep = "\t")
#
# session$sendCustomMessage(type = 'testmessage',
# message = 'Thank you for clicking')
# })
#
# sig_name<-reactive({
#
# return(listfiles())
# })
# observeEvent(input$choices,{
# sigFileName<-paste("files/",input$choices,sep = "")
# sigFile<<-read.csv(file=sigFileName,sep='\t')
#
#
#
#
# })
# output$Signatures <- renderUI({
# selectInput("choices","Select Signatures",choices = as.vector(sig_name()))
# })
# output$text <- renderPrint({
# paste("you selected",input$choices,sep=" ")
# })
#
#
#
#
#
# }
# )
# ##other functions##
# #list all files
# listfiles <- function(){
#
# files <- Sys.glob("files/*.csv")
#
# l = list()
# for(i in 1:length(files)){
#
# l[[i]]=strsplit(files[i],"/")
#
# }
#
# vect = c()
# for(i in 1:length(files)){
#
# vect[i] = l[[i]][[1]][2]
# }
#
#
# return (vect)
# }
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