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server-og.R
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# library(shinyIncubator)
shinyServer(function(input, output) {
sessionID<-paste(gsub(":","_",gsub(" ","_",date())),trunc(10000000*runif(1)),sep="_")
print(sessionID)
# wd<-"/opt/raid10/genomics/Web/GenomicsPortals/ilincs/gimm"
# wwd<-"http://eh3.uc.edu/genomics/GenomicsPortals/ilincs/gimm"
wd<-"/mnt/raid/tmp/gimm"
wwd<-"http://eh3.uc.edu/tmp/gimm"
setwd(wd)
output$fileName<-renderText({
if(is.null(input$inputFile)) return(NULL)
as.character(input$inputFile[1,"datapath"])
})
inputDataTable<-reactive({
if(input$example){
inputData<-read.table(file="/opt/raid10/genomics/mario/r/shiny/DCE_Genes_GSE11121.txt", sep="\t", header=T, quote="", stringsAsFactors=F)
# info(paste("Loaded dataset with ",dim(inputData)[1]," genes and ",dim(inputData)[2]-2," samples",sep=""))
return(inputData)
}
if(is.null(input$inputFile)) return(NULL)
inputData<-read.table(file=as.character(input$inputFile[1,"datapath"]), sep="\t", header=T, stringsAsFactors=F)
return(inputData)
})
observe({
if(!is.null(inputDataTable())){
enable("cluster")
}
})
# observe({
# if(!is.null(inputDataTable())){
# # enable("cluster")
# info(paste("Loaded dataset with ",dim(inputDataTable())[1]," genes and ",dim(inputDataTable())[2]-2," samples",sep=""))
# }
# })
output$toCluster<-renderDataTable(
# {
inputDataTable(),
options = list(pageLength = 5)
# output$clustButton<-renderUI({
# if(is.null(input$inputFile)) return(NULL)
# actionButton("cluster",label="Cluster")
# # p("Current Value")
# # verbatimTextOutput("cluster")
# }
)
observe({
print(input$cluster)
if(is.null(inputDataTable())){
disable("cluster")
# disable("treeview")
# disable("download")
}
})
# observe({
# if(input$treeview) browseURL(paste(wwd,"/",sessionID,".jnlp",sep=""), browser="konqueror")
# })
#
output$clustResults<-renderText({
# finishesClustering<-reactive({
print(1)
print(dim(inputDataTable()))
# if(is.null(input$inputFile)) return(NULL)
if(is.null(inputDataTable())) return(NULL)
print(input$cluster)
if(input$cluster){
library(gimmR)
# progress <- shiny::Progress$new()
# Make sure it closes when we exit this reactive, even if there's an error
# on.exit(progress$close())
# progress$set(message = "Analysis in Progress", detail="Reading Data", value = 0)
# setwd("/opt/raid10/genomics/Web/GenomicsPortals/ilincs/gimm")
print("running gimm")
#print(inputDataTable())
# progress$inc(1/3, detail = "Cluster Analysis")
gimmOut<-runGimmNPosthoc(inputDataTable(),dataFile=sessionID,M=dim(inputDataTable())[2]-2, T=dim(inputDataTable())[1], nIter=50, nreplicates=1, burnIn=20,verbose=F, contextSpecific = "y", nContexts = dim(inputDataTable())[2]-2, contextLengths = rep(1,dim(inputDataTable())[2]-2),estimate_contexts = "y",intFiles=F)
# progress$inc(1/3, detail = "Creating TreeView Files")
source("/opt/raid10/genomics/software/RPrograms/source/createJnlpFile.R")
junk<-createJnlpFileGenomics(ilincs=F,fileName=paste(sessionID,".jnlp",sep=""),location=wd, webLocation=wwd, targetFilesLocation=wd, targetFilesName=paste(sessionID,".cdt",sep=""), targetWebLocation=wwd)
print(junk)
system(paste("zip ",sessionID,".zip ",sessionID,".cdt ",sessionID,".gtr ",sessionID,".atr",sep=""))
# progress$inc(1/3, detail = "Done")
# enable("treeview")
# enable("download")
# paste(names(gimmOut),sep="separator")
"Finished"
}
})
# output$clustResults<-reactive({
# finishesClustering()
# })
# output$clustResults<-
output$treeviewLink <- renderUI({
tags$a(href = paste(wwd,"/",sessionID,".jnlp",sep=""), "View resluts with FTreeView")
})
output$downloadLink <- renderUI({
tags$a(href = paste(wwd,"/",sessionID,".zip",sep=""), "Download clustering results")
})
# observe({
# if(input$download){
# system(paste("zip ",sessionID,".zip ",sessionID,".cdt ",sessionID,".gtr ",sessionID,".atr",sep=""))
# browseURL(paste(wwd,"/",sessionID,".zip",sep=""), browser="konqueror")
# }
# })
#output$toCluster<-renderTable({
# if(is.null(input$inputFile)) return(NULL)
# inputDataTable<-read.table(file=as.character(input$inputFile[1,"datapath"]), sep="\t", header=T, stringsAsFactors=F)
# head(inputDataTable)[,head(colnames(inputDataTable))]
# data.frame(x=1:3,y=1:3)
# })
})