R/server.R
In lucidif/HiCeekR: GUI for Hi-C data analysis
options(shiny.maxRequestSize=700*1024^2,stringsAsFactors = FALSE)
#shiny::addResourcePath("www", "./www")
#R.home
#require(R6)
#source ('requirement.R')
#===================================my ws===================================================================
# myDrop<<-TRUE #metti myDrop<-FALSE se stai lavorando con cartelle progetto all'interno del main folder di HiCeekR
# workingPC<<- 'myPC_cln' # 1) 'labPC' 2) 'stebbidone' 3)travelmatto 4)homePC 5)homePC_cln 6)labPC_cln 7)myPC_cln
# source('1_preliminaryStatements.R')
#==============================================================================
#wk<<-getwd()
#======mainStataments==========================================================
server<-shiny::shinyServer(function(input, output, session , rea, wdDir) {
#print (session$ns)
configFilePath<-paste0(getwd(),"/HCR.config")
print(paste0("server wd: ",getwd()))
shinyjs::hide(id = "loading-content", anim = TRUE, animType = "fade")
shinyjs::show("app-content")
print(paste0("server wd2: ",getwd()))
shiny::addResourcePath("hcrimg", system.file("www",package = "HiCeekR"))
print(sessionInfo())
print(system.file("hcrtmpimg","HiCeekR"))
if (file.exists("./SysVal.Robj")==FALSE){
print(paste0("server wd3: ",getwd()))
SysVal<-matrix(nrow=1,ncol=1)
SysVal[1,1]<-TRUE
rownames(SysVal)<-"restart"
save(SysVal,file=paste0(getwd(),"/SysVal.Robj"))
print("sysGenerate")
print(paste0("server wd4: ",getwd()))
}
if (file.exists(paste0(getwd(),"/HCR.config"))==TRUE){
print("preWd")
paste0(getwd(),"/HCR.config")
print(paste0("load config wd:",getwd(),"/HCR.config"))
#configFilePath<-paste0(getwd(),"/HCR.config")
workingDir<-as.character(
paste0(
(read.table(configFilePath))[2,1],
(read.table(configFilePath))[1,1])
)
print(paste0("config: ", configFilePath))
print(paste0("working dir:",workingDir))
print("postWd")
print("workingDir")
####confTable<-matrix(ncol=1,nrow=2)
####confTable[1,1]<-workingDir
#####confTable[2,1]<-projectName
write.table(workingDir,"HCRtmp.config", col.names=FALSE, row.names=FALSE,
quote=FALSE, sep="\t")
}
load("./SysVal.Robj")
rea<-shiny::reactiveValues()
if (dir.exists(paste0(getwd(),"/www"))){
#rea$delend<-FALSE
delend<-reactiveVal(FALSE)
shiny::stopApp()
#file.rename(from=paste0(getwd(),"/www"), to=paste0(getwd(),"/wwwhcr"),recursive=TRUE)
stop(paste0("there is 'www' folder in working directory: ", getwd(),", please try to delete manualy www folder. You can show manual for more details \n"))
#geterrmessage("there are 'www' folder in working directory, please try to delete manualy www folder. You can show manual for more details \n")
} else {
file.copy(from=system.file("www",package = "HiCeekR"),to=getwd(),recursive=TRUE)
#rea$delend<-TRUE
#rea$delend<-TRUE
delend<-reactiveVal(FALSE)
}
# output$multipleSlot<-renderUI({
# #prjLoadName
# print(paste0("wd path:",getwd()))
# shiny::checkboxGroupInput("prjSelector",
# label="",
# choices=list.dirs(path=paste(rea$workingDir)
# ))
# })
#rea$volumes<-c(root = "/")
#rea$volumes<-c(root = getVolumes)
#rea$volumes<-shinyFiles::getVolumes()
rea$volumes<-c(root=getwd()) #shinyFiles::getVolumes()
rea$rStart<-as.logical(SysVal["restart",1])
print (isolate(rea$rStart))
if (isolate(rea$rStart==TRUE)){
SysVal["restart",1]<-"FALSE"
save(SysVal,file="./SysVal.Robj")
session$reload()
}
restart<-FALSE
shiny::onStop(function(){
if (file.exists(paste0(getwd(),"/www/fragments.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/fragments.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/inOutWard.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/inOutWard.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/fragments_trimmed.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/fragments_trimmed.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/inOutWard_trimmed.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/inOutWard_trimmed.jpeg"))
}
# if (delend==TRUE){
# file.remove(paste0(getwd(),"/www"),recursive=TRUE)
# }
unlink(paste0(getwd(),"/www"),recursive=TRUE)
# if (file.exists("./SysVal.Robj")==TRUE){
# load("./SysVal.Robj")
# if (SysVal["restart",1]==FALSE){
# file.remove("./SysVal.Robj")
# print("Sys removed")
# }
# }
})
prjManExport<-shiny::reactiveValues()
shinyFiles::shinyFileChoose(input,
"bamFile",
root=isolate(rea$volumes),
filetypes=c("bam"))
shinyFiles::shinyDirChoose(input,
"wdPath",
root=isolate(rea$volumes)
)
shinyFiles::shinyFileChoose(input,
"configPath",
root=isolate(rea$volumes),
filetypes=c("config")
)
shinyFiles::shinyFileChoose(input,
"refGenome",
root=isolate(rea$volumes),
filetypes=c("fa")
)
shiny::observeEvent(input$restart,{
#rea$runmodState<-"restart"
print("start ok")
})
shiny::observeEvent(input$wdPath,{
output$dataPh <-shiny::renderText({
"data path selected"
})
#output$wdPathText<-shiny::renderText({
output$phLoc<-shiny::renderText({
if (is.atomic(input$wdPath)==FALSE){
# paste0(
# "path selected: ",
# shinyDirPath(unlist(input$wdPath))
# )
shinyDirPath(unlist(input$wdPath))
}
})
})
shiny::observeEvent(input$configPath,{
# output$configTxt<-shiny::renderText({
# if (is.atomic(input$configPath)==FALSE){
#
# "file selected: "
# #shinyFilesPath(unlist(input$configPath))
# }
# })
output$dataPh <-shiny::renderText({
"data path selected"
})
#output$configPathText<-shiny::renderText({
output$phLoc<-shiny::renderText({
if (is.atomic(input$configPath)==FALSE){
# paste0(
# "file selected: ",
# shinyFilesPath(unlist(input$configPath$files))
# #shinyFilesPath(unlist(input$configPath))
# )
shinyFilesPath(unlist(input$configPath$files))
}
})
})
shiny::observeEvent(input$bamFile,{
output$bamPathShow<-shiny::renderText({
if (is.atomic(input$bamFile)==FALSE){
paste0("file selected:", rea$volumes,
shinyFilesPath(unlist(input$bamFile$files)))
}
})
})
shiny::observeEvent(input$refGenome,{
output$textReference<-shiny::renderText({
if (is.atomic(input$refGenome)==FALSE){
paste0("file selected:", rea$volumes,
shinyFilesPath(unlist(input$refGenome$files)))
}
})
})
output$welcomeSlot<-shiny::renderUI({
prjManPanel_welcome()
})
if (file.exists("HCRtmp.config")==TRUE){
#print("temp exist")
#print(getwd())
output$configFileText<-shiny::renderText({""})
#ttCfg<<-read.table('HCRtmp.config')
#rea$workingDir<-as.character((read.table('HCRtmp.config'))[1,1])
# rea$workingDir<-as.character(paste0((read.table('HCRtmp.config'))[2,1],
# (read.table('HCRtmp.config'))[1,1],
# "HiCeekRwd/"))
rea$workingDir<-as.character(paste0(
(read.table('HCRtmp.config'))[1,1],
"HiCeekRwd/"))
#print (paste0("baseDir:", (read.table('HCRtmp.config'))[2,1]))
print (paste0("prjDir:", (read.table('HCRtmp.config'))[1,1]))
print (paste0("wkDir: ", isolate(rea$workingDir)))
#prjName<-as.character((read.table('HCRtmp.config'))[2,1])
file.remove("HCRtmp.config")
# refGenomeDir<-paste0(isolate(rea$workingDir), "RefGenomes/")
# print(paste0("referenceGenomes:", refGenomeDir))
# output$refgenSlot <- renderUI({
# selectFile(
# id="refGenome",
# path = refGenomeDir,
# label= "reference"
# )
# })
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
output$multipleSlot<-renderUI({
#prjLoadName
#print(paste0("wd path:",getwd()))
foLs<-list.dirs(path=paste0(rea$workingDir,"Projects/",input$prjLoadName),
full.names=FALSE,recursive = FALSE)
foLs<-foLs[!foLs %in% "ProjectData" ]
shiny::fluidRow(
shiny::column(6,
shiny::checkboxGroupInput("prjSelector",
label="",
choices=foLs
)
),
shiny::column(6,
shiny::actionButton("newMultiAnalysis",
label = shiny::h5("make new analysis"),
class = "btn-primary",
width = "100%"
)
)
)
})
} else {
rea$config<-"none"
output$configFileText<-shiny::renderText({"no config file found, please make a config file with panel below"})
#print(isolate(rea$config))
}
shiny::observeEvent(input$loadOrNewConf, {
if (input$loadOrNewConf=="new"){
output$configHelper<-shiny::renderText({
paste0("create new config file in: ",getwd())
})
} else {#input$loadOrNewConf=="load"
output$configHelper<-shiny::renderText({
"select existent HCR.config"
})
}
})
shiny::observeEvent(input$showBut,{
output$navSlot<-shiny::renderUI({
mainNav()
})
})
shiny::observeEvent(input$resetBut,{
#output$navSlot<-shiny::renderUI({})
print ("reset")
session$reload()
})
#======prjManager =============================================================
#rea$resetVal<-"noReset"
#rea$volumes <- c("R Installation" = "")
#print(paste0("isolate", isolate(rea$volumes)))
output$prjState<-shiny::renderText({
"Select Project"
})
output$selector<-shiny::renderUI({
prjManPanel_prjSelector()
})
shiny::observeEvent(input$loadNewPrj,{
#pointTest<<-pointin(rea$workingDir,
# "Projects")
if (input$loadNewPrj == "load"){
output$prjName<-shiny::renderUI({
prjManPanel_loadProject(rea$workingDir)
})
} else { #input$loadNewPrj == "new"
output$prjName<-shiny::renderUI({
prjManPanel_newProject()
})
}
})
shiny::observeEvent(input$loadNewAn,{
if(input$loadNewAn == "new"){
output$anNames<-shiny::renderUI({
shiny::textInput("anNewName", label=h5("Analysis"))
})
output$anOptionsSlot2<-shiny::renderUI({
prjManPanel_anlysisInputType()
})
} else {#input$loadNewAn == "load"
output$anNames<-shiny::renderUI({
shiny::selectInput("anLoadNames", label=h5("Analysis"),
choices=c(folderList(rea$prjDir, ecception=TRUE, ecceptionName="ProjectData"))
)
})
output$anExecuteBut<-shiny::renderUI({
shiny::actionButton("anButtonLoad", label="load")
})
output$anOptionsSlot2<-shiny::renderUI({})
output$anOptionsSlot3<-shiny::renderUI({})
}
output$pathViewer<-shiny::renderDataTable({
folderFrame(rea$prjDir)
})
})
#=======prjMan actionButton========================================
shiny::observeEvent(input$makeConfig,{
busyIndServer("makeConfig",{
#workingDir<-as.character((read.table('HCRtmp.config'))[1,1])
#============================================
makeConfig(shinyDirPath(unlist(input$wdPath)))
#============================================
rea$workingDir<-as.character(paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1],
"HiCeekRwd/"))
# dir.create(paste0((read.table('HCR.config'))[2,1],
# (read.table('HCR.config'))[1,1],
# "HiCeekRwd/"),
# showWarnings = TRUE
# )
#dir.create(paste0(rea$working))
makeHCRwd(path=paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1]
))
output$configFileText<-renderText({""})
print (paste0("wkDir: ", rea$workingDir))
#prjName<-as.character((read.table('HCR.config'))[2,1])
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
})
})
shiny::observeEvent(input$loadConfig,{
busyIndServer("loadConfig",{
#file.copy(from=shinyFilesPath(input$configPath),to=paste0(getwd(),"/HCR.config"))
print("config copy")
#print(paste0("from: ",shinyFilesPath(unlist(input$configPath$files))))
# print(paste0("from: ",
# shinyFiles::getVolumes()()["Computer"],
# shinyFiles::getVolumes()()[Sys.info()["user"]],
# shinyFilesPath(unlist(input$configPath$files))))
# flPath<-paste0(shinyFiles::getVolumes()()["Computer"],
# shinyFiles::getVolumes()()[Sys.info()["user"]],
# shinyFilesPath(unlist(input$configPath$files)))
setwd((read.table(shinyFilesPath(unlist(input$configPath$files))))[2,1])
print(paste0("to: ", paste0(getwd(),"/HCR.config")))
file.copy(from=shinyFilesPath(unlist(input$configPath$files)),to=paste0(getwd(),"/HCR.config"))
#unlist(input$configPath$files)
output$configFileText<-shiny::renderText({""})
#rea$workingDir<-as.character(paste0((read.table('HCR.config'))[1,1],"HiCeekRwd/"))
rea$workingDir<-as.character(paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1],
"HiCeekRwd/"))
print(paste0("wkDir: ", rea$workingDir))
#prjName<-as.character((read.table('HCR.config'))[2,1])
prjName<-"NONE" #<- va definito dopo
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
})
})
shiny::observeEvent(input$resetPrj,{
output$prjState<-shiny::renderText({
"Select Project"
})
output$selector<-shiny::renderUI({prjManPanel_prjSelector()})
if (input$loadNewPrj == "load"){
output$prjName<-shiny::renderUI({prjManPanel_loadProject()})
}else{#input$loadNewPrj == "new"
output$prjName<-shiny::renderUI({prjManPanel_newProject()})
}
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
output$anSetted<-shiny::renderUI({})
output$anSettings<-shiny::renderUI({})
session$reload()
})
shiny::observeEvent(input$prjButton,{
refGenomeDir<-paste0(isolate(rea$workingDir), "RefGenomes/")
print(paste0("referenceGenomes:", refGenomeDir))
output$refgenSlot <- shiny::renderUI({
selectFile(
id="refGenome",
path = refGenomeDir,
label= h5("reference")
)
})
busyIndServer("prjButton",{
if (input$loadNewPrj == "new"){
if (input$prjNewName == ""){
stop("please give a name to project")
# if (input$loadNewPrj == "error"){
# stop("please give a name to project")
# }
} else {
makeHCRprj(input$prjNewName, paste0(rea$workingDir,"Projects/"))
prjManExport$prjFolder <- paste0(rea$workingDir,"Projects/",
input$prjNewName, "/"
)
pName<-input$prjNewName
print(prjManExport$prjFolder)
}
} else { #input$loadNewPrj == "load"
prjManExport$prjFolder <- paste0(rea$workingDir,"Projects/",
input$prjLoadName, "/"
)
pName<-input$prjLoadName
print(prjManExport$prjFolder)
}
output$prjState<-shiny::renderText({
"Project Selected"
})
#rea$anFolder<-paste0(rea$workingDir, "Projects/", pName, "/")
rea$prjDir<-paste0(rea$workingDir, "Projects/", pName, "/")
#print(paste0("rea$anFolder=",rea$anFolder))
output$selector<-shiny::renderUI({})
output$prjName<-shiny::renderUI({})
output$anSetted<-shiny::renderUI({prjManPanel_reset(pName)})
#output$pNameSlot<- shiny::renderText({pName})
output$anSettings<-shiny::renderUI({prjManPanel_analysisSettings()})
})
})
shiny::observeEvent(input$newMultiAnalysis,{
print("make multiple analysis")
#paste0(rea$workingDir,"Projects/",input$prjLoadName)
print(input$prjSelector)
for (i in 1:length(input$prjSelector)){
print(paste0(rea$workingDir,"Projects/",
input$prjLoadName,"/",
input$prjSelector[i]))
}
output$navSlot<-shiny::renderUI({
mainNav(inType="Multiple")
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anNewName)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
#input.inputType==
})
shiny::observeEvent(input$newAnalysis,{
#store run time
#runTime1<<-proc.time()
busyIndServer("newAnalysis",{
if (input$loadNewPrj=="new"){
prjName<-input$prjNewName
print(paste0("prjName: ",input$prjNewName))
} else {#input$loadNewPrj=="load"
prjName<-input$prjLoadName
}
rea$anDir <- paste0(rea$prjDir,input$anNewName,"/")
print("rea$anDir....ok")
if (input$inputType == "BAM"){
it<-matrix(ncol=2, nrow=5)
#itTT<<-it
# print(paste0("inputpath: ",
# #parseFilePaths(rea$volumes, input$bamFile)
# shinyFilesPath(input$bamFile)
# ))
#parseFilePaths(roots, input$bamFile)
itNames<-c("InputPath", "Resolution", "Type",
"ProjectName", "AnalysisName","comment")
#print(shinyFilesPath(input$bamFile))
#print(shinyFilesPath(input$refGenome))
#print(shinyFilesPath(input$refGenome, last=TRUE))
#print(unlist(input$bamFile$files))
itValues<-c(shinyFilesPath(paste0(
rea$volumes,
unlist(input$bamFile$files))) ,
input$binSize,
input$inputType, prjName, input$anNewName,
paste0("Reference Genome:", rea$volumes,
shinyFilesPath(unlist(input$refGenome$files), last=TRUE)
)
)
#itValuesTT<<-itValues
it<-data.frame(itNames,itValues)
it<-as.matrix(it)
#itTT<<-it
print ("it.....ok")
if (input$anNewName==""){
stop("no name for new analysis")
} else {
makeHCRan(input$anNewName, prjManExport$prjFolder, infoTable=it)
}
print ("analysis created !!!")
aN<-input$anNewName
output$pNameSlot<- shiny::renderText({aN})
#============================================================================
print("before Param")
print(unlist(input$refGenome$files))
param<-refGenomeEdit(refGenome = paste0(rea$volumes,
shinyFilesPath(unlist(input$refGenome$files)
)
),
enzyme = input$cutSite,
overhang = input$overhang,
name = "refGenFrag",
cutGenomeOutDir = pointin(rea$anDir,
"Pre-Processing",
sys=TRUE)
)
print("param obtained")
reportTable<-bamMatching(
bam.datapath=paste0(rea$volumes,shinyFilesPath(#paste0(getwd(),
unlist(input$bamFile$files)
#)
)),
param=param,
h5PathOut=pointin(rea$anDir,
"Pre-Processing",
sys=TRUE
)
)
#fagli salvare al reportTable
reportTable<-unlist(reportTable)
write.table(reportTable, paste0(pointin(rea$anDir,
"Pre-Processing", sys=TRUE),
"reportTable.tsv"),
sep="\t",
quote=FALSE,
col.names=FALSE
)
print("bamMatching executed")
#print("beforePlot execution")
rFrags<- read.table(paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),
"refGenFrag.cutGenome.tsv"), sep='\t', header=TRUE)
#print("beforePlot execution 1")
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
#print("beforePlot execution 2")
paramFil <- diffHic::pairParam(rFragsGrange)
#print("beforePlot execution 3")
diags <- diffHic::getPairData(paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),
"h5file.h5"),
paramFil)
#print("beforePlot execution 4")
save(diags, file=paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),"diags.Robj"))
#print("beforePlot completed")
#=================================================================
output$navSlot<-shiny::renderUI({
mainNav(inType="BAM")
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anNewName)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
#======================================esporta plot
rea$diags<-diags
rea$llinsert <- log2(rea$diags$insert + 1L)
rea$intra <- !is.na(rea$llinsert)
rea$breaks <- seq(min(rea$llinsert[rea$intra]),
max(rea$llinsert[rea$intra]), length.out=30)
rea$inward <- hist(rea$llinsert[rea$diags$orientation==1L],
plot=FALSE, breaks=rea$breaks)
rea$outward <- hist(rea$llinsert[rea$diags$orientation==2L] ,
plot=FALSE, breaks=rea$breaks)
rea$samestr <- hist(rea$llinsert[rea$diags$orientation==0L | rea$diags$orientation==3L],
plot=FALSE, breaks=rea$breaks)
rea$samestr$counts <- rea$samestr$counts/2
# Setting up the axis limits.
rea$ymax <- max(rea$inward$counts, rea$outward$counts,
rea$samestr$counts)/1e6
rea$xmax <- max(rea$inward$mids, rea$outward$mids,
rea$samestr$mids)
rea$xmin <- min(rea$inward$mids, rea$outward$mids,
rea$samestr$mids)
##=======================================================================
jpeg(file=paste0(pointin(rea$anDir, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
hist(rea$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
dev.off()
jpeg(file=paste0(pointin(rea$anDir, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
plot(0,0,type="n", xlim=c(rea$xmin, rea$xmax), ylim=c(0, rea$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(rea$inward$mids, rea$inward$counts/1e6, col="darkgreen", lwd=2)
#abline(v=log2(rea$min.inward), col="darkgrey")
lines(rea$outward$mids, rea$outward$counts/1e6, col="red", lwd=2)
#abline(v=log2(rea$min.outward), col="darkgrey", lty=2)
lines(rea$samestr$mids, rea$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
dev.off()
#=================================================
} else {
if (input$inputType == "Multiple"){
print("make multiple analysis")
#controls
}
}
})
#run time end
#runTime1<<-proc.time()-runTime1
})
#====================================================Initizialize Module Selection Panels
shiny::observeEvent(input$anButtonLoad,{
rea$anDir <- paste0(rea$prjDir,input$anLoadNames,"/")
#==========================================================================
output$navSlot<-shiny::renderUI({
#mainNav(inType="BAM")
mainNav(inType=input$inputType)
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anLoadNames)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
aN<-input$anNewName
output$pNameSlot<- shiny::renderText({aN})
print(input$anLoadNames)
print("analysis start")
})
shiny::observeEvent(input$returnToSummary,{
shiny::updateTabsetPanel(session, "mainNav", selected="Summary")
#output$moduleScreen<-shiny::renderUI({})
tool_DetectInteraction<-"sum"
moduleUI_DetectInteraction<- "sum_UI"
moduleLoad_DetectInteraction<- "sum_Server"
output$summarySlot <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
})
#======================================================
shiny::observeEvent(input$Filtering_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
print ("Filtering Restart")
rea$modset<-"Filtering"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel()
# shiny::wellPanel("do you want to restart analysis from this point?2",
# shiny::fluidRow(
# shiny::column(3),
# shiny::column(3,
# shiny::actionButton("startModule2", label="Yes2")
# ),
# shiny::column(3,
# shiny::actionButton("returnToSummary2", label="No2s")
# ),
# shiny::column(3)
# )
# )
})
})
#========================================================
# shiny::observeEvent(input$restart,{
# rea$runmodState<-"restart"
# print("start ok")
# })
#===========botton observer
shiny::observeEvent(input$Filtering_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Filtering"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$Filtering_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Binning_reStart ,{
output$moduleScreen<-shiny::renderUI({})
#salva nelle reactiveValues lo stato restart
print ("binning Restart")
rea$modset<-"Binning"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel()
# shiny::wellPanel("do you want to restart analysis from this point?",
# shiny::fluidRow(
# shiny::column(3),
# shiny::column(3,
# shiny::actionButton("startModule", label="Yes")
# ),
# shiny::column(3,
# shiny::actionButton("returnToSummary", label="No")
# ),
# shiny::column(3)
# )
# )
})
})
shiny::observeEvent(input$Binning_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Binning"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$Binning_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$iterative_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Normalization")
})
})
shiny::observeEvent(input$iterative_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$iterative_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$WavSis_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Normalization")
})
})
shiny::observeEvent(input$WavSis_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$WavSis_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$directionalityIndex_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$directionalityIndex_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$directionalityIndex_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$TopDomTADs_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$TopDomTADs_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$HiCsegTADs_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$HiCsegTADs_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$HiCsegTADs_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$TopDomTADs_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$bed2track_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("bed2track")
})
})
shiny::observeEvent(input$bed2track_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$bed2track_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$CompartmentsPCA_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$EpigeneticFeatures_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Heatmaps_start,{
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Networks_start,{
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
#================================================botton observer end
##======WELCOME================================================================
# tool_prjSettings<-'prjSettings'
# moduleUI_prjSettings<-paste0 (tool_prjSettings, '_UI')
# moduleLoad_prjSettings<-paste0 (tool_prjSettings,'_Server')
# output$prjSettingsSlot<-shiny::renderUI ({
# get(moduleUI_prjSettings)(tool_prjSettings,label='prjSettings')
# })
# loadApp_prjSettings<-shiny::callModule(get(moduleLoad_prjSettings),
# tool_prjSettings)
#
##add new module:
##ogni nuovo modulo da aggiungere devi aggiungere un pezzo
##nell'observe della mainNav e una altro pezzo nell'observe dello startModule
##cerca : input$startModule
##e devi mettere gli observe dei bottini start restart e branch
##MODULE STARTPANELS
shiny::observeEvent (input$mainNav,{
if (input$mainNav == 'Summary' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
tool_DetectInteraction<-"sum"
moduleUI_DetectInteraction<- "sum_UI"
moduleLoad_DetectInteraction<- "sum_Server"
output$summarySlot <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
#addResourcePath("images",pointin(rea$anDir, "tmpimg", sys=TRUE))
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'Filtering' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
print("Filtering tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
# if (exists("rea$moduleSet")==TRUE){
# print(paste0("moduleSet:",rea$moduleSet))
# }else{
# print("moduleSet non difined")
# }
#print(paste0("moduleSet:",rea$moduleSet))
#output$moduleScreen<-renderUI({})
#output$filteringSlot<-renderUI({moduleStartPanel("Filtering",
output$selectPn<-shiny::renderUI({moduleStartPanel("Filtering",
rea$anDir,
callModuleDescription(
"Filtering")
)
})
}
if (input$mainNav == 'Binning' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
print("Binning tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
# if (exists("rea$moduleSet")==TRUE){
# print(paste0("moduleSet:",rea$moduleSet))
# }else{
# print("moduleSet non difined")
# }
#print(paste0("moduleSet:",rea$moduleSet))
#output$moduleScreen<-renderUI({})
#output$binningSlot<-renderUI({moduleStartPanel("Binning",
output$selectPn<-renderUI({moduleStartPanel("Binning",
rea$anDir,
callModuleDescription(
"Binning")
)
})
}
if (input$mainNav == 'iterative' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#print("Filtering tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
#output$iterativeSlot<-renderUI({moduleStartPanel("iterative",
output$selectPn<-shiny::renderUI({moduleStartPanel("iterative",
rea$anDir,
callModuleDescription(
"iterative")
)
})
}
if (input$mainNav == 'WavSis' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$WavSisSlot<-renderUI({moduleStartPanel("WavSis",
output$selectPn<-shiny::renderUI({moduleStartPanel("WavSis",
rea$anDir,
callModuleDescription(
"WavSis")
)
})
}
if (input$mainNav == 'TopDomTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("TopDomTADs",
rea$anDir,
callModuleDescription(
"TopDomTADs")
)
})
}
if (input$mainNav == 'HiCsegTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("HiCsegTADs",
rea$anDir,
callModuleDescription(
"HiCsegTADs")
)
})
}
if (input$mainNav == 'directionalityIndex' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("directionalityIndex",
rea$anDir,
callModuleDescription(
"directionalityIndex")
)
})
}
if (input$mainNav == 'bed2track' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("bed2track",
rea$anDir,
callModuleDescription(
"bed2track")
)
})
}
if (input$mainNav == 'CompartmentsPCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaCompSlot<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
output$selectPn<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
rea$anDir,
callModuleDescription(
"CompartmentsPCA")
)
})
}
if (input$mainNav == 'EpigeneticFeatures' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
rea$anDir,
callModuleDescription(
"EpigeneticFeatures")
)
})
}
if (input$mainNav == 'PCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
rea$anDir,
callModuleDescription(
"CompartmentsPCA")
)
})
}
if (input$mainNav== 'Heatmap' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("Heatmaps",
rea$anDir,
callModuleDescription(
"Heatmaps")
)
})
}
if (input$mainNav== 'Networks' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({moduleStartPanel("Networks",
rea$anDir,
callModuleDescription(
"Networks")
)
})
}
})
#==============================================================================
#startModule pressend condition================================================
#
#===========Initizialize Modules===============================================
#==============================================================================
shiny::observeEvent (#input$mainNav,
input$startModule
,
{
#se questo observe Lo metti su startModule e non su mainNav
# shiny::observeEvent(input$startModule,{
#
# })
# if (input$mainNav == 'Summary' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
# tool_DetectInteraction<-"sum"
# moduleUI_DetectInteraction<- "sum_UI"
# moduleLoad_DetectInteraction<- "sum_Server"
#
# output$summarySlot <- shiny::renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
# })
#
# loadApp_DetectInteraction <- shiny::callModule(
# get(moduleLoad_DetectInteraction)
# , tool_DetectInteraction,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
output$selectPn<-renderUI({})
if (rea$runmodState=="branch"){
print("branch pressed")
makeBranch(input$branchName, rea$modset, infoTsv=paste0(rea$anDir, 'info.tsv'))
session$reload()
#rea$anDir <- paste0(rea$prjDir,input$branchName,"/")
#pName<-input$branchName
#output$anSetted<-shiny::renderUI({prjManPanel_reset(pName)})
#output$pNameSlot<- shiny::renderText({input$branchName})
#session$reload()
}else {
if (rea$runmodState=="restart"){
print("restart pressed")
restartFrom(paste0(rea$anDir, 'info.tsv'),rea$modset)
#print("restartFrom executed")
session$reload()
#print("session end")
} else{
#print("render module")
output$moduleScreen<-shiny::renderUI({})
#leggi in reactive se lo stato è branch o reStart
#se branch crea nuovo progetto
#se reStart cancella fino ad un certo punto e riprendi la là
#agiorna lo stato nel reactive come "ready"
withProgress(message="please wait module pre processing", min=0, max=3, {
setProgress(message = 'Calculation in progress', detail = 'This may take a while...')
if (input$mainNav == 'Filtering' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#source ('DiffHiC_DetectInteraction.R')
tool_DetectInteraction<-"Filmod"
moduleUI_DetectInteraction<- "FilmodUI"
moduleLoad_DetectInteraction<- "FilmodServer"
setProgress(value = 1)
#output$filteringSlot <- shiny::renderUI ({
output$selectPn <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
setProgress(value = 2)
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
setProgress(value = 3)
}
})
if (input$mainNav == 'Binning'
& file.exists(paste0(rea$anDir, 'info.tsv')) == TRUE ){
tool_Binning <- 'DiffHiC_BinningV2'
moduleUI_Binning <- paste0 (tool_Binning, '_UI')
moduleLoad_Binning <- paste0 (tool_Binning,'_Server')
# output$binningSlot <-renderUI ({
output$selectPn <-renderUI ({
get(moduleUI_Binning) (tool_Binning,label='helpingUI')
})
loadApp_Binning <-shiny::callModule(get(moduleLoad_Binning), tool_Binning,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'iterative' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_DiffHiC_Norm <- 'diffHic_Normalization'
moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
#output$iterativeSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='iceUI')
})
loadApp_DiffHiC_Norm <- shiny::callModule(get(moduleLoad_DiffHiC_Norm),
tool_DiffHiC_Norm,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'WavSis' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_chromoR <- 'chromoR_Normalization'
moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
#output$WavSisSlot<- shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
})
loadApp_chromoR <-shiny::callModule(get(moduleLoad_chromoR),
tool_chromoR,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'directionalityIndex' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'directionalityIndex_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'TopDomTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'TopDomTADs_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'HiCsegTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'HiCsegTADs_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'CompartmentsPCA' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'pcaComp_postProcessing'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'TopDomTADs' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_tdtadsComp <- 'TopDomTADs_postProcessing'
moduleUI_tdtadsComp<- paste0 (tool_tdtadsComp, '_UI')
moduleLoad_tdtadsComp<- paste0 (tool_tdtadsComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_tdtadsComp) (tool_tdtadsComp,label='TopDomTADs')
})
loadApp_tdtadsComp <- shiny::callModule(get(moduleLoad_tdtadsComp),
tool_tdtadsComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'bed2track' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_tdtadsComp <- 'bed2track_postProcessing'
moduleUI_tdtadsComp<- paste0 (tool_tdtadsComp, '_UI')
moduleLoad_tdtadsComp<- paste0 (tool_tdtadsComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_tdtadsComp) (tool_tdtadsComp,label='bed2track')
})
loadApp_tdtadsComp <- shiny::callModule(get(moduleLoad_tdtadsComp),
tool_tdtadsComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
#EpigeneticFeatures
if (input$mainNav == 'EpigeneticFeatures' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'EpigeneticFeatures'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == '' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'pcaComp_postProcessing'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'PCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#source ('pca_postProcessing.R')
tool_pca <- 'pca_postProcessing'
moduleUI_pca<- paste0 (tool_pca, '_UI')
moduleLoad_pca<- paste0 (tool_pca,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pca) (tool_pca,label='PCA')
})
loadApp_pca <- shiny::callModule(get(moduleLoad_pca), tool_pca,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'Heatmap' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
){
tool_htm <- 'TADsV2_Visualization'
moduleUI_htm<- paste0 (tool_htm, '_UI')
moduleLoad_htm<- paste0 (tool_htm,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_htm) (tool_htm,label='htmUI')
})
loadApp_htm <- shiny::callModule(get(moduleLoad_htm), tool_htm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'Networks' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
){
tool_ntw <- 'networksV2_Visualization' #networksV2_Visualization_UI
moduleUI_ntw<- paste0 (tool_ntw, '_UI')
moduleLoad_ntw<- paste0 (tool_ntw,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_ntw) (tool_ntw,label='ntwUI')
})
loadApp_ntw <- shiny::callModule(get(moduleLoad_ntw), tool_ntw,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
}
}
# #print("render module")
# output$moduleScreen<-shiny::renderUI({})
#
# #leggi in reactive se lo stato è branch o reStart
# #se branch crea nuovo progetto
# #se reStart cancella fino ad un certo punto e riprendi la là
# #agiorna lo stato nel reactive come "ready"
#
# withProgress(message="please wait module pre processing", min=0, max=3, {
# setProgress(message = 'Calculation in progress', detail = 'This may take a while...')
# if (input$mainNav == 'Filtering' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#
# #source ('DiffHiC_DetectInteraction.R')
# tool_DetectInteraction<-"Filmod"
# moduleUI_DetectInteraction<- "FilmodUI"
# moduleLoad_DetectInteraction<- "FilmodServer"
# setProgress(value = 1)
# #output$filteringSlot <- shiny::renderUI ({
# output$selectPn <- shiny::renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
# })
# setProgress(value = 2)
# loadApp_DetectInteraction <- shiny::callModule(
# get(moduleLoad_DetectInteraction)
# , tool_DetectInteraction,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# setProgress(value = 3)
# }
# })
#
# if (input$mainNav == 'Binning'
# & file.exists(paste0(rea$anDir, 'info.tsv')) == TRUE ){
#
# tool_Binning <- 'DiffHiC_BinningV2'
#
# moduleUI_Binning <- paste0 (tool_Binning, '_UI')
# moduleLoad_Binning <- paste0 (tool_Binning,'_Server')
# # output$binningSlot <-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_Binning) (tool_Binning,label='helpingUI')
# })
# loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
#
# }
#
# if (input$mainNav == 'iterative' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_DiffHiC_Norm <- 'diffHic_Normalization'
# moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
# moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
# #output$iterativeSlot<-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='iceUI')
# })
# loadApp_DiffHiC_Norm <- callModule(get(moduleLoad_DiffHiC_Norm),
# tool_DiffHiC_Norm,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
#
# if (input$mainNav == 'WavSis' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_chromoR <- 'chromoR_Normalization'
# moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
# moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
# #output$WavSisSlot<- shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
# })
# loadApp_chromoR <-shiny::callModule(get(moduleLoad_chromoR),
# tool_chromoR,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
#
# if (input$mainNav == 'TADsHMM' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_hmm <- 'HMM_postProcessing'
# moduleUI_hmm<- paste0 (tool_hmm, '_UI')
# moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
# #output$hmmSlot<-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_hmm) (tool_hmm,label='helpingUI')
# })
# loadApp_hmm <- callModule(get(moduleLoad_hmm), tool_hmm,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'CompartmentsPCA' & file.exists(paste0(
# rea$anDir, 'info.tsv'))==TRUE ){
# #source ('pcaComp_postProcessing.R')
# tool_pcaComp <- 'pcaComp_postProcessing'
# moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
# moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
# #output$pcaCompSlot<- shiny::renderUI({
# output$selectPn <-renderUI ({
# get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
# })
# loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
# tool_pcaComp,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir)
# }
#
# if (input$mainNav == 'EpigeneticFeatures' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
# #source ('pca_postProcessing.R')
# tool_pca <- 'pca_postProcessing'
# moduleUI_pca<- paste0 (tool_pca, '_UI')
# moduleLoad_pca<- paste0 (tool_pca,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_pca) (tool_pca,label='epifUI')
# })
# loadApp_pca <- shiny::callModule(get(moduleLoad_pca), tool_pca,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'Heatmap' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
# ){
# tool_htm <- 'TADsV2_Visualization'
# moduleUI_htm<- paste0 (tool_htm, '_UI')
# moduleLoad_htm<- paste0 (tool_htm,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_htm) (tool_htm,label='htmUI')
# })
# loadApp_htm <- shiny::callModule(get(moduleLoad_htm), tool_htm,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'Networks' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
# ){
# tool_ntw <- 'networksV2_Visualization' #networksV2_Visualization_UI
# moduleUI_ntw<- paste0 (tool_ntw, '_UI')
# moduleLoad_ntw<- paste0 (tool_ntw,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-shiny::renderUI ({
# get(moduleUI_ntw) (tool_ntw,label='ntwUI')
# })
# loadApp_ntw <- shiny::callModule(get(moduleLoad_ntw), tool_ntw,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
# if (input$mainNav == 'Analysis' ){
# source ('anSettings.R')
# tool_anSettings <- 'anSettings'
# moduleUI_anSettings<- paste0 (tool_anSettings, '_UI')
# moduleLoad_anSettings<- paste0 (tool_anSettings,'_Server')
# output$anSetPlot<-renderUI ({
# get(moduleUI_anSettings) (tool_anSettings,label='helpingUI')
# })
# loadApp_anSettings <- callModule(get(moduleLoad_anSettings), tool_anSettings,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Pre-Processing' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('DiffHiC_DetectInteraction.R')
# tool_DetectInteraction <- 'DiffHiC_DetectInteraction'
# moduleUI_DetectInteraction<- paste0 (tool_DetectInteraction, '_UI')
# moduleLoad_DetectInteraction<- paste0 (tool_DetectInteraction,'_Server')
# output$preProSlot<-renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='helpingUI')
# })
# loadApp_DetectInteraction <- callModule(get(moduleLoad_DetectInteraction), tool_DetectInteraction,
# stringsAsFactors = FALSE)
#}
#
# if (input$mainNav == 'Binning' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('DiffHiC_BinningV2.R')
# tool_Binning <- 'DiffHiC_BinningV2'
# moduleUI_Binning<- paste0 (tool_Binning, '_UI')
# moduleLoad_Binning<- paste0 (tool_Binning,'_Server')
# output$binningSlot<-renderUI ({
# get(moduleUI_Binning) (tool_Binning,label='helpingUI')
# })
# loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'WavSis' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('chromoR_Normalization.R')
# tool_chromoR <- 'chromoR_Normalization'
# moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
# moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
# output$WavSisSlot<-renderUI ({
# get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
# })
# loadApp_chromoR <- callModule(get(moduleLoad_chromoR), tool_chromoR,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'iterative' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('diffHic_Normalization.R')
# tool_DiffHiC_Norm <- 'diffHic_Normalization'
# moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
# moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
# output$iterativeSlot<-renderUI ({
# get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='helpingUI')
# })
# loadApp_DiffHiC_Norm <<- callModule(get(moduleLoad_DiffHiC_Norm), tool_DiffHiC_Norm,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Epigenetic Features' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('pca_postProcessing.R')
# tool_pca <- 'pca_postProcessing'
# moduleUI_pca<- paste0 (tool_pca, '_UI')
# moduleLoad_pca<- paste0 (tool_pca,'_Server')
# output$pcaSlot<-renderUI ({
# get(moduleUI_pca) (tool_pca,label='helpingUI')
# })
# loadApp_pca <- callModule(get(moduleLoad_pca), tool_pca,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Compartments-PCA' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('pcaComp_postProcessing.R')
# tool_pcaComp <- 'pcaComp_postProcessing'
# moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
# moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
# output$pcaCompSlot<-renderUI ({
# get(moduleUI_pcaComp) (tool_pcaComp,label='helpingUI')
# })
# loadApp_pcaComp <- callModule(get(moduleLoad_pcaComp), tool_pcaComp,
# stringsAsFactors = FALSE)
# }
#
#
# if (input$mainNav == 'TADs-HMM' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('HMM_postProcessing.R')
# tool_hmm <- 'HMM_postProcessing'
# moduleUI_hmm<- paste0 (tool_hmm, '_UI')
# moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
# output$hmmSlot<-renderUI ({
# get(moduleUI_hmm) (tool_hmm,label='helpingUI')
# })
# loadApp_hmm <- callModule(get(moduleLoad_hmm), tool_hmm,
# stringsAsFactors = FALSE)
# }
#
#
# if (input$mainNav == 'Heatmap' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('TADsV2_Visualization.R')
# tool_tads <- 'TADsV2_Visualization'
# moduleUI_tads<- paste0 (tool_tads, '_UI')
# moduleLoad_tads<- paste0 (tool_tads,'_Server')
# output$TADsModule<-renderUI ({
# get(moduleUI_tads) (tool_tads,label='helpingUI')
# })
# loadApp_tads <- callModule(get(moduleLoad_tads), tool_tads,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Networks' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('networksV2_Visualization.R')
# tool_net <- 'networksV2_Visualization'
# moduleUI_net<- paste0 (tool_net, '_UI')
# moduleLoad_net<- paste0 (tool_net,'_Server')
# output$netModule<-renderUI ({
# get(moduleUI_net) (tool_net,label='nets')
# })
# loadApp_net <- callModule(get(moduleLoad_net), tool_net,
# stringsAsFactors = FALSE)
# }
} #fine observe MainNav
)
})
lucidif/HiCeekR documentation built on Jan. 31, 2021, 10:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
options(shiny.maxRequestSize=700*1024^2,stringsAsFactors = FALSE)
#shiny::addResourcePath("www", "./www")
#R.home
#require(R6)
#source ('requirement.R')
#===================================my ws===================================================================
# myDrop<<-TRUE #metti myDrop<-FALSE se stai lavorando con cartelle progetto all'interno del main folder di HiCeekR
# workingPC<<- 'myPC_cln' # 1) 'labPC' 2) 'stebbidone' 3)travelmatto 4)homePC 5)homePC_cln 6)labPC_cln 7)myPC_cln
# source('1_preliminaryStatements.R')
#==============================================================================
#wk<<-getwd()
#======mainStataments==========================================================
server<-shiny::shinyServer(function(input, output, session , rea, wdDir) {
#print (session$ns)
configFilePath<-paste0(getwd(),"/HCR.config")
print(paste0("server wd: ",getwd()))
shinyjs::hide(id = "loading-content", anim = TRUE, animType = "fade")
shinyjs::show("app-content")
print(paste0("server wd2: ",getwd()))
shiny::addResourcePath("hcrimg", system.file("www",package = "HiCeekR"))
print(sessionInfo())
print(system.file("hcrtmpimg","HiCeekR"))
if (file.exists("./SysVal.Robj")==FALSE){
print(paste0("server wd3: ",getwd()))
SysVal<-matrix(nrow=1,ncol=1)
SysVal[1,1]<-TRUE
rownames(SysVal)<-"restart"
save(SysVal,file=paste0(getwd(),"/SysVal.Robj"))
print("sysGenerate")
print(paste0("server wd4: ",getwd()))
}
if (file.exists(paste0(getwd(),"/HCR.config"))==TRUE){
print("preWd")
paste0(getwd(),"/HCR.config")
print(paste0("load config wd:",getwd(),"/HCR.config"))
#configFilePath<-paste0(getwd(),"/HCR.config")
workingDir<-as.character(
paste0(
(read.table(configFilePath))[2,1],
(read.table(configFilePath))[1,1])
)
print(paste0("config: ", configFilePath))
print(paste0("working dir:",workingDir))
print("postWd")
print("workingDir")
####confTable<-matrix(ncol=1,nrow=2)
####confTable[1,1]<-workingDir
#####confTable[2,1]<-projectName
write.table(workingDir,"HCRtmp.config", col.names=FALSE, row.names=FALSE,
quote=FALSE, sep="\t")
}
load("./SysVal.Robj")
rea<-shiny::reactiveValues()
if (dir.exists(paste0(getwd(),"/www"))){
#rea$delend<-FALSE
delend<-reactiveVal(FALSE)
shiny::stopApp()
#file.rename(from=paste0(getwd(),"/www"), to=paste0(getwd(),"/wwwhcr"),recursive=TRUE)
stop(paste0("there is 'www' folder in working directory: ", getwd(),", please try to delete manualy www folder. You can show manual for more details \n"))
#geterrmessage("there are 'www' folder in working directory, please try to delete manualy www folder. You can show manual for more details \n")
} else {
file.copy(from=system.file("www",package = "HiCeekR"),to=getwd(),recursive=TRUE)
#rea$delend<-TRUE
#rea$delend<-TRUE
delend<-reactiveVal(FALSE)
}
# output$multipleSlot<-renderUI({
# #prjLoadName
# print(paste0("wd path:",getwd()))
# shiny::checkboxGroupInput("prjSelector",
# label="",
# choices=list.dirs(path=paste(rea$workingDir)
# ))
# })
#rea$volumes<-c(root = "/")
#rea$volumes<-c(root = getVolumes)
#rea$volumes<-shinyFiles::getVolumes()
rea$volumes<-c(root=getwd()) #shinyFiles::getVolumes()
rea$rStart<-as.logical(SysVal["restart",1])
print (isolate(rea$rStart))
if (isolate(rea$rStart==TRUE)){
SysVal["restart",1]<-"FALSE"
save(SysVal,file="./SysVal.Robj")
session$reload()
}
restart<-FALSE
shiny::onStop(function(){
if (file.exists(paste0(getwd(),"/www/fragments.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/fragments.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/inOutWard.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/inOutWard.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/fragments_trimmed.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/fragments_trimmed.jpeg"))
}
if (file.exists(paste0(getwd(),"/www/inOutWard_trimmed.jpeg"))==TRUE){
file.remove(paste0(getwd(),"/www/inOutWard_trimmed.jpeg"))
}
# if (delend==TRUE){
# file.remove(paste0(getwd(),"/www"),recursive=TRUE)
# }
unlink(paste0(getwd(),"/www"),recursive=TRUE)
# if (file.exists("./SysVal.Robj")==TRUE){
# load("./SysVal.Robj")
# if (SysVal["restart",1]==FALSE){
# file.remove("./SysVal.Robj")
# print("Sys removed")
# }
# }
})
prjManExport<-shiny::reactiveValues()
shinyFiles::shinyFileChoose(input,
"bamFile",
root=isolate(rea$volumes),
filetypes=c("bam"))
shinyFiles::shinyDirChoose(input,
"wdPath",
root=isolate(rea$volumes)
)
shinyFiles::shinyFileChoose(input,
"configPath",
root=isolate(rea$volumes),
filetypes=c("config")
)
shinyFiles::shinyFileChoose(input,
"refGenome",
root=isolate(rea$volumes),
filetypes=c("fa")
)
shiny::observeEvent(input$restart,{
#rea$runmodState<-"restart"
print("start ok")
})
shiny::observeEvent(input$wdPath,{
output$dataPh <-shiny::renderText({
"data path selected"
})
#output$wdPathText<-shiny::renderText({
output$phLoc<-shiny::renderText({
if (is.atomic(input$wdPath)==FALSE){
# paste0(
# "path selected: ",
# shinyDirPath(unlist(input$wdPath))
# )
shinyDirPath(unlist(input$wdPath))
}
})
})
shiny::observeEvent(input$configPath,{
# output$configTxt<-shiny::renderText({
# if (is.atomic(input$configPath)==FALSE){
#
# "file selected: "
# #shinyFilesPath(unlist(input$configPath))
# }
# })
output$dataPh <-shiny::renderText({
"data path selected"
})
#output$configPathText<-shiny::renderText({
output$phLoc<-shiny::renderText({
if (is.atomic(input$configPath)==FALSE){
# paste0(
# "file selected: ",
# shinyFilesPath(unlist(input$configPath$files))
# #shinyFilesPath(unlist(input$configPath))
# )
shinyFilesPath(unlist(input$configPath$files))
}
})
})
shiny::observeEvent(input$bamFile,{
output$bamPathShow<-shiny::renderText({
if (is.atomic(input$bamFile)==FALSE){
paste0("file selected:", rea$volumes,
shinyFilesPath(unlist(input$bamFile$files)))
}
})
})
shiny::observeEvent(input$refGenome,{
output$textReference<-shiny::renderText({
if (is.atomic(input$refGenome)==FALSE){
paste0("file selected:", rea$volumes,
shinyFilesPath(unlist(input$refGenome$files)))
}
})
})
output$welcomeSlot<-shiny::renderUI({
prjManPanel_welcome()
})
if (file.exists("HCRtmp.config")==TRUE){
#print("temp exist")
#print(getwd())
output$configFileText<-shiny::renderText({""})
#ttCfg<<-read.table('HCRtmp.config')
#rea$workingDir<-as.character((read.table('HCRtmp.config'))[1,1])
# rea$workingDir<-as.character(paste0((read.table('HCRtmp.config'))[2,1],
# (read.table('HCRtmp.config'))[1,1],
# "HiCeekRwd/"))
rea$workingDir<-as.character(paste0(
(read.table('HCRtmp.config'))[1,1],
"HiCeekRwd/"))
#print (paste0("baseDir:", (read.table('HCRtmp.config'))[2,1]))
print (paste0("prjDir:", (read.table('HCRtmp.config'))[1,1]))
print (paste0("wkDir: ", isolate(rea$workingDir)))
#prjName<-as.character((read.table('HCRtmp.config'))[2,1])
file.remove("HCRtmp.config")
# refGenomeDir<-paste0(isolate(rea$workingDir), "RefGenomes/")
# print(paste0("referenceGenomes:", refGenomeDir))
# output$refgenSlot <- renderUI({
# selectFile(
# id="refGenome",
# path = refGenomeDir,
# label= "reference"
# )
# })
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
output$multipleSlot<-renderUI({
#prjLoadName
#print(paste0("wd path:",getwd()))
foLs<-list.dirs(path=paste0(rea$workingDir,"Projects/",input$prjLoadName),
full.names=FALSE,recursive = FALSE)
foLs<-foLs[!foLs %in% "ProjectData" ]
shiny::fluidRow(
shiny::column(6,
shiny::checkboxGroupInput("prjSelector",
label="",
choices=foLs
)
),
shiny::column(6,
shiny::actionButton("newMultiAnalysis",
label = shiny::h5("make new analysis"),
class = "btn-primary",
width = "100%"
)
)
)
})
} else {
rea$config<-"none"
output$configFileText<-shiny::renderText({"no config file found, please make a config file with panel below"})
#print(isolate(rea$config))
}
shiny::observeEvent(input$loadOrNewConf, {
if (input$loadOrNewConf=="new"){
output$configHelper<-shiny::renderText({
paste0("create new config file in: ",getwd())
})
} else {#input$loadOrNewConf=="load"
output$configHelper<-shiny::renderText({
"select existent HCR.config"
})
}
})
shiny::observeEvent(input$showBut,{
output$navSlot<-shiny::renderUI({
mainNav()
})
})
shiny::observeEvent(input$resetBut,{
#output$navSlot<-shiny::renderUI({})
print ("reset")
session$reload()
})
#======prjManager =============================================================
#rea$resetVal<-"noReset"
#rea$volumes <- c("R Installation" = "")
#print(paste0("isolate", isolate(rea$volumes)))
output$prjState<-shiny::renderText({
"Select Project"
})
output$selector<-shiny::renderUI({
prjManPanel_prjSelector()
})
shiny::observeEvent(input$loadNewPrj,{
#pointTest<<-pointin(rea$workingDir,
# "Projects")
if (input$loadNewPrj == "load"){
output$prjName<-shiny::renderUI({
prjManPanel_loadProject(rea$workingDir)
})
} else { #input$loadNewPrj == "new"
output$prjName<-shiny::renderUI({
prjManPanel_newProject()
})
}
})
shiny::observeEvent(input$loadNewAn,{
if(input$loadNewAn == "new"){
output$anNames<-shiny::renderUI({
shiny::textInput("anNewName", label=h5("Analysis"))
})
output$anOptionsSlot2<-shiny::renderUI({
prjManPanel_anlysisInputType()
})
} else {#input$loadNewAn == "load"
output$anNames<-shiny::renderUI({
shiny::selectInput("anLoadNames", label=h5("Analysis"),
choices=c(folderList(rea$prjDir, ecception=TRUE, ecceptionName="ProjectData"))
)
})
output$anExecuteBut<-shiny::renderUI({
shiny::actionButton("anButtonLoad", label="load")
})
output$anOptionsSlot2<-shiny::renderUI({})
output$anOptionsSlot3<-shiny::renderUI({})
}
output$pathViewer<-shiny::renderDataTable({
folderFrame(rea$prjDir)
})
})
#=======prjMan actionButton========================================
shiny::observeEvent(input$makeConfig,{
busyIndServer("makeConfig",{
#workingDir<-as.character((read.table('HCRtmp.config'))[1,1])
#============================================
makeConfig(shinyDirPath(unlist(input$wdPath)))
#============================================
rea$workingDir<-as.character(paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1],
"HiCeekRwd/"))
# dir.create(paste0((read.table('HCR.config'))[2,1],
# (read.table('HCR.config'))[1,1],
# "HiCeekRwd/"),
# showWarnings = TRUE
# )
#dir.create(paste0(rea$working))
makeHCRwd(path=paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1]
))
output$configFileText<-renderText({""})
print (paste0("wkDir: ", rea$workingDir))
#prjName<-as.character((read.table('HCR.config'))[2,1])
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
})
})
shiny::observeEvent(input$loadConfig,{
busyIndServer("loadConfig",{
#file.copy(from=shinyFilesPath(input$configPath),to=paste0(getwd(),"/HCR.config"))
print("config copy")
#print(paste0("from: ",shinyFilesPath(unlist(input$configPath$files))))
# print(paste0("from: ",
# shinyFiles::getVolumes()()["Computer"],
# shinyFiles::getVolumes()()[Sys.info()["user"]],
# shinyFilesPath(unlist(input$configPath$files))))
# flPath<-paste0(shinyFiles::getVolumes()()["Computer"],
# shinyFiles::getVolumes()()[Sys.info()["user"]],
# shinyFilesPath(unlist(input$configPath$files)))
setwd((read.table(shinyFilesPath(unlist(input$configPath$files))))[2,1])
print(paste0("to: ", paste0(getwd(),"/HCR.config")))
file.copy(from=shinyFilesPath(unlist(input$configPath$files)),to=paste0(getwd(),"/HCR.config"))
#unlist(input$configPath$files)
output$configFileText<-shiny::renderText({""})
#rea$workingDir<-as.character(paste0((read.table('HCR.config'))[1,1],"HiCeekRwd/"))
rea$workingDir<-as.character(paste0((read.table('HCR.config'))[2,1],
(read.table('HCR.config'))[1,1],
"HiCeekRwd/"))
print(paste0("wkDir: ", rea$workingDir))
#prjName<-as.character((read.table('HCR.config'))[2,1])
prjName<-"NONE" #<- va definito dopo
output$prjManagerSlot<-shiny::renderUI({
prjManagerMainUI()
})
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
})
})
shiny::observeEvent(input$resetPrj,{
output$prjState<-shiny::renderText({
"Select Project"
})
output$selector<-shiny::renderUI({prjManPanel_prjSelector()})
if (input$loadNewPrj == "load"){
output$prjName<-shiny::renderUI({prjManPanel_loadProject()})
}else{#input$loadNewPrj == "new"
output$prjName<-shiny::renderUI({prjManPanel_newProject()})
}
output$pathViewer<-shiny::renderDataTable({
folderFrame(paste0(rea$workingDir, "Projects/"))
})
output$anSetted<-shiny::renderUI({})
output$anSettings<-shiny::renderUI({})
session$reload()
})
shiny::observeEvent(input$prjButton,{
refGenomeDir<-paste0(isolate(rea$workingDir), "RefGenomes/")
print(paste0("referenceGenomes:", refGenomeDir))
output$refgenSlot <- shiny::renderUI({
selectFile(
id="refGenome",
path = refGenomeDir,
label= h5("reference")
)
})
busyIndServer("prjButton",{
if (input$loadNewPrj == "new"){
if (input$prjNewName == ""){
stop("please give a name to project")
# if (input$loadNewPrj == "error"){
# stop("please give a name to project")
# }
} else {
makeHCRprj(input$prjNewName, paste0(rea$workingDir,"Projects/"))
prjManExport$prjFolder <- paste0(rea$workingDir,"Projects/",
input$prjNewName, "/"
)
pName<-input$prjNewName
print(prjManExport$prjFolder)
}
} else { #input$loadNewPrj == "load"
prjManExport$prjFolder <- paste0(rea$workingDir,"Projects/",
input$prjLoadName, "/"
)
pName<-input$prjLoadName
print(prjManExport$prjFolder)
}
output$prjState<-shiny::renderText({
"Project Selected"
})
#rea$anFolder<-paste0(rea$workingDir, "Projects/", pName, "/")
rea$prjDir<-paste0(rea$workingDir, "Projects/", pName, "/")
#print(paste0("rea$anFolder=",rea$anFolder))
output$selector<-shiny::renderUI({})
output$prjName<-shiny::renderUI({})
output$anSetted<-shiny::renderUI({prjManPanel_reset(pName)})
#output$pNameSlot<- shiny::renderText({pName})
output$anSettings<-shiny::renderUI({prjManPanel_analysisSettings()})
})
})
shiny::observeEvent(input$newMultiAnalysis,{
print("make multiple analysis")
#paste0(rea$workingDir,"Projects/",input$prjLoadName)
print(input$prjSelector)
for (i in 1:length(input$prjSelector)){
print(paste0(rea$workingDir,"Projects/",
input$prjLoadName,"/",
input$prjSelector[i]))
}
output$navSlot<-shiny::renderUI({
mainNav(inType="Multiple")
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anNewName)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
#input.inputType==
})
shiny::observeEvent(input$newAnalysis,{
#store run time
#runTime1<<-proc.time()
busyIndServer("newAnalysis",{
if (input$loadNewPrj=="new"){
prjName<-input$prjNewName
print(paste0("prjName: ",input$prjNewName))
} else {#input$loadNewPrj=="load"
prjName<-input$prjLoadName
}
rea$anDir <- paste0(rea$prjDir,input$anNewName,"/")
print("rea$anDir....ok")
if (input$inputType == "BAM"){
it<-matrix(ncol=2, nrow=5)
#itTT<<-it
# print(paste0("inputpath: ",
# #parseFilePaths(rea$volumes, input$bamFile)
# shinyFilesPath(input$bamFile)
# ))
#parseFilePaths(roots, input$bamFile)
itNames<-c("InputPath", "Resolution", "Type",
"ProjectName", "AnalysisName","comment")
#print(shinyFilesPath(input$bamFile))
#print(shinyFilesPath(input$refGenome))
#print(shinyFilesPath(input$refGenome, last=TRUE))
#print(unlist(input$bamFile$files))
itValues<-c(shinyFilesPath(paste0(
rea$volumes,
unlist(input$bamFile$files))) ,
input$binSize,
input$inputType, prjName, input$anNewName,
paste0("Reference Genome:", rea$volumes,
shinyFilesPath(unlist(input$refGenome$files), last=TRUE)
)
)
#itValuesTT<<-itValues
it<-data.frame(itNames,itValues)
it<-as.matrix(it)
#itTT<<-it
print ("it.....ok")
if (input$anNewName==""){
stop("no name for new analysis")
} else {
makeHCRan(input$anNewName, prjManExport$prjFolder, infoTable=it)
}
print ("analysis created !!!")
aN<-input$anNewName
output$pNameSlot<- shiny::renderText({aN})
#============================================================================
print("before Param")
print(unlist(input$refGenome$files))
param<-refGenomeEdit(refGenome = paste0(rea$volumes,
shinyFilesPath(unlist(input$refGenome$files)
)
),
enzyme = input$cutSite,
overhang = input$overhang,
name = "refGenFrag",
cutGenomeOutDir = pointin(rea$anDir,
"Pre-Processing",
sys=TRUE)
)
print("param obtained")
reportTable<-bamMatching(
bam.datapath=paste0(rea$volumes,shinyFilesPath(#paste0(getwd(),
unlist(input$bamFile$files)
#)
)),
param=param,
h5PathOut=pointin(rea$anDir,
"Pre-Processing",
sys=TRUE
)
)
#fagli salvare al reportTable
reportTable<-unlist(reportTable)
write.table(reportTable, paste0(pointin(rea$anDir,
"Pre-Processing", sys=TRUE),
"reportTable.tsv"),
sep="\t",
quote=FALSE,
col.names=FALSE
)
print("bamMatching executed")
#print("beforePlot execution")
rFrags<- read.table(paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),
"refGenFrag.cutGenome.tsv"), sep='\t', header=TRUE)
#print("beforePlot execution 1")
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
#print("beforePlot execution 2")
paramFil <- diffHic::pairParam(rFragsGrange)
#print("beforePlot execution 3")
diags <- diffHic::getPairData(paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),
"h5file.h5"),
paramFil)
#print("beforePlot execution 4")
save(diags, file=paste0(pointin(rea$anDir,"Pre-Processing", sys = TRUE),"diags.Robj"))
#print("beforePlot completed")
#=================================================================
output$navSlot<-shiny::renderUI({
mainNav(inType="BAM")
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anNewName)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
#======================================esporta plot
rea$diags<-diags
rea$llinsert <- log2(rea$diags$insert + 1L)
rea$intra <- !is.na(rea$llinsert)
rea$breaks <- seq(min(rea$llinsert[rea$intra]),
max(rea$llinsert[rea$intra]), length.out=30)
rea$inward <- hist(rea$llinsert[rea$diags$orientation==1L],
plot=FALSE, breaks=rea$breaks)
rea$outward <- hist(rea$llinsert[rea$diags$orientation==2L] ,
plot=FALSE, breaks=rea$breaks)
rea$samestr <- hist(rea$llinsert[rea$diags$orientation==0L | rea$diags$orientation==3L],
plot=FALSE, breaks=rea$breaks)
rea$samestr$counts <- rea$samestr$counts/2
# Setting up the axis limits.
rea$ymax <- max(rea$inward$counts, rea$outward$counts,
rea$samestr$counts)/1e6
rea$xmax <- max(rea$inward$mids, rea$outward$mids,
rea$samestr$mids)
rea$xmin <- min(rea$inward$mids, rea$outward$mids,
rea$samestr$mids)
##=======================================================================
jpeg(file=paste0(pointin(rea$anDir, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
hist(rea$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
dev.off()
jpeg(file=paste0(pointin(rea$anDir, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
plot(0,0,type="n", xlim=c(rea$xmin, rea$xmax), ylim=c(0, rea$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(rea$inward$mids, rea$inward$counts/1e6, col="darkgreen", lwd=2)
#abline(v=log2(rea$min.inward), col="darkgrey")
lines(rea$outward$mids, rea$outward$counts/1e6, col="red", lwd=2)
#abline(v=log2(rea$min.outward), col="darkgrey", lty=2)
lines(rea$samestr$mids, rea$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
dev.off()
#=================================================
} else {
if (input$inputType == "Multiple"){
print("make multiple analysis")
#controls
}
}
})
#run time end
#runTime1<<-proc.time()-runTime1
})
#====================================================Initizialize Module Selection Panels
shiny::observeEvent(input$anButtonLoad,{
rea$anDir <- paste0(rea$prjDir,input$anLoadNames,"/")
#==========================================================================
output$navSlot<-shiny::renderUI({
#mainNav(inType="BAM")
mainNav(inType=input$inputType)
})
output$prjState<-shiny::renderText({
"Analysis Selected"
})
output$prjManagerSlot<-shiny::renderUI({prjManPanel_reset(input$anLoadNames)})
##devi creare uno specifico panel per il reset dall'analisi
#output$prjManagerSlot<-shiny::renderUI({})
output$welcomeSlot<-shiny::renderUI({})
output$pathViewer<-shiny::renderUI({})
output$multipleSlot<-shiny::renderUI({})
aN<-input$anNewName
output$pNameSlot<- shiny::renderText({aN})
print(input$anLoadNames)
print("analysis start")
})
shiny::observeEvent(input$returnToSummary,{
shiny::updateTabsetPanel(session, "mainNav", selected="Summary")
#output$moduleScreen<-shiny::renderUI({})
tool_DetectInteraction<-"sum"
moduleUI_DetectInteraction<- "sum_UI"
moduleLoad_DetectInteraction<- "sum_Server"
output$summarySlot <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
})
#======================================================
shiny::observeEvent(input$Filtering_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
print ("Filtering Restart")
rea$modset<-"Filtering"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel()
# shiny::wellPanel("do you want to restart analysis from this point?2",
# shiny::fluidRow(
# shiny::column(3),
# shiny::column(3,
# shiny::actionButton("startModule2", label="Yes2")
# ),
# shiny::column(3,
# shiny::actionButton("returnToSummary2", label="No2s")
# ),
# shiny::column(3)
# )
# )
})
})
#========================================================
# shiny::observeEvent(input$restart,{
# rea$runmodState<-"restart"
# print("start ok")
# })
#===========botton observer
shiny::observeEvent(input$Filtering_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Filtering"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$Filtering_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Binning_reStart ,{
output$moduleScreen<-shiny::renderUI({})
#salva nelle reactiveValues lo stato restart
print ("binning Restart")
rea$modset<-"Binning"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel()
# shiny::wellPanel("do you want to restart analysis from this point?",
# shiny::fluidRow(
# shiny::column(3),
# shiny::column(3,
# shiny::actionButton("startModule", label="Yes")
# ),
# shiny::column(3,
# shiny::actionButton("returnToSummary", label="No")
# ),
# shiny::column(3)
# )
# )
})
})
shiny::observeEvent(input$Binning_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Binning"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$Binning_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$iterative_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Normalization")
})
})
shiny::observeEvent(input$iterative_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$iterative_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$WavSis_reStart ,{
#salva nelle reactiveValues lo stato restart
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Normalization")
})
})
shiny::observeEvent(input$WavSis_branch,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Normalization"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$WavSis_start,{
#salva nella reactiveValues lo stato branch
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$directionalityIndex_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$directionalityIndex_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$directionalityIndex_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$TopDomTADs_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$TopDomTADs_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$HiCsegTADs_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$HiCsegTADs_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("Downstream")
})
})
shiny::observeEvent(input$HiCsegTADs_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$TopDomTADs_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$bed2track_reStart,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"restart"
output$moduleScreen<-shiny::renderUI({
moduleRestartPanel("bed2track")
})
})
shiny::observeEvent(input$bed2track_branch,{
#output$moduleScreen<-shiny::renderUI({})
rea$modset<-"Downstream"
rea$runmodState<-"branch"
output$moduleScreen<-shiny::renderUI({
moduleBranchPanel()
})
})
shiny::observeEvent(input$bed2track_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$CompartmentsPCA_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$EpigeneticFeatures_start,{
#output$moduleScreen<-shiny::renderUI({})
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Heatmaps_start,{
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
shiny::observeEvent(input$Networks_start,{
rea$runmodState<-"start"
output$moduleScreen<-shiny::renderUI({
moduleStartPanel2()
})
})
#================================================botton observer end
##======WELCOME================================================================
# tool_prjSettings<-'prjSettings'
# moduleUI_prjSettings<-paste0 (tool_prjSettings, '_UI')
# moduleLoad_prjSettings<-paste0 (tool_prjSettings,'_Server')
# output$prjSettingsSlot<-shiny::renderUI ({
# get(moduleUI_prjSettings)(tool_prjSettings,label='prjSettings')
# })
# loadApp_prjSettings<-shiny::callModule(get(moduleLoad_prjSettings),
# tool_prjSettings)
#
##add new module:
##ogni nuovo modulo da aggiungere devi aggiungere un pezzo
##nell'observe della mainNav e una altro pezzo nell'observe dello startModule
##cerca : input$startModule
##e devi mettere gli observe dei bottini start restart e branch
##MODULE STARTPANELS
shiny::observeEvent (input$mainNav,{
if (input$mainNav == 'Summary' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
tool_DetectInteraction<-"sum"
moduleUI_DetectInteraction<- "sum_UI"
moduleLoad_DetectInteraction<- "sum_Server"
output$summarySlot <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
#addResourcePath("images",pointin(rea$anDir, "tmpimg", sys=TRUE))
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'Filtering' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
print("Filtering tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
# if (exists("rea$moduleSet")==TRUE){
# print(paste0("moduleSet:",rea$moduleSet))
# }else{
# print("moduleSet non difined")
# }
#print(paste0("moduleSet:",rea$moduleSet))
#output$moduleScreen<-renderUI({})
#output$filteringSlot<-renderUI({moduleStartPanel("Filtering",
output$selectPn<-shiny::renderUI({moduleStartPanel("Filtering",
rea$anDir,
callModuleDescription(
"Filtering")
)
})
}
if (input$mainNav == 'Binning' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
print("Binning tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
# if (exists("rea$moduleSet")==TRUE){
# print(paste0("moduleSet:",rea$moduleSet))
# }else{
# print("moduleSet non difined")
# }
#print(paste0("moduleSet:",rea$moduleSet))
#output$moduleScreen<-renderUI({})
#output$binningSlot<-renderUI({moduleStartPanel("Binning",
output$selectPn<-renderUI({moduleStartPanel("Binning",
rea$anDir,
callModuleDescription(
"Binning")
)
})
}
if (input$mainNav == 'iterative' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#print("Filtering tab")
output$selectPn<-shiny::renderUI({})
output$moduleScreen<-shiny::renderUI({})
#output$iterativeSlot<-renderUI({moduleStartPanel("iterative",
output$selectPn<-shiny::renderUI({moduleStartPanel("iterative",
rea$anDir,
callModuleDescription(
"iterative")
)
})
}
if (input$mainNav == 'WavSis' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$WavSisSlot<-renderUI({moduleStartPanel("WavSis",
output$selectPn<-shiny::renderUI({moduleStartPanel("WavSis",
rea$anDir,
callModuleDescription(
"WavSis")
)
})
}
if (input$mainNav == 'TopDomTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("TopDomTADs",
rea$anDir,
callModuleDescription(
"TopDomTADs")
)
})
}
if (input$mainNav == 'HiCsegTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("HiCsegTADs",
rea$anDir,
callModuleDescription(
"HiCsegTADs")
)
})
}
if (input$mainNav == 'directionalityIndex' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("directionalityIndex",
rea$anDir,
callModuleDescription(
"directionalityIndex")
)
})
}
if (input$mainNav == 'bed2track' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$hmmSlot<-renderUI({moduleStartPanel("TADsHMM",
output$selectPn<-shiny::renderUI({moduleStartPanel("bed2track",
rea$anDir,
callModuleDescription(
"bed2track")
)
})
}
if (input$mainNav == 'CompartmentsPCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaCompSlot<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
output$selectPn<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
rea$anDir,
callModuleDescription(
"CompartmentsPCA")
)
})
}
if (input$mainNav == 'EpigeneticFeatures' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
rea$anDir,
callModuleDescription(
"EpigeneticFeatures")
)
})
}
if (input$mainNav == 'PCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("CompartmentsPCA",
rea$anDir,
callModuleDescription(
"CompartmentsPCA")
)
})
}
if (input$mainNav== 'Heatmap' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
#output$pcaSlot<-shiny::renderUI({moduleStartPanel("EpigeneticFeatures",
output$selectPn<-shiny::renderUI({moduleStartPanel("Heatmaps",
rea$anDir,
callModuleDescription(
"Heatmaps")
)
})
}
if (input$mainNav== 'Networks' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
output$moduleScreen<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({})
output$selectPn<-shiny::renderUI({moduleStartPanel("Networks",
rea$anDir,
callModuleDescription(
"Networks")
)
})
}
})
#==============================================================================
#startModule pressend condition================================================
#
#===========Initizialize Modules===============================================
#==============================================================================
shiny::observeEvent (#input$mainNav,
input$startModule
,
{
#se questo observe Lo metti su startModule e non su mainNav
# shiny::observeEvent(input$startModule,{
#
# })
# if (input$mainNav == 'Summary' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
# tool_DetectInteraction<-"sum"
# moduleUI_DetectInteraction<- "sum_UI"
# moduleLoad_DetectInteraction<- "sum_Server"
#
# output$summarySlot <- shiny::renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
# })
#
# loadApp_DetectInteraction <- shiny::callModule(
# get(moduleLoad_DetectInteraction)
# , tool_DetectInteraction,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
output$selectPn<-renderUI({})
if (rea$runmodState=="branch"){
print("branch pressed")
makeBranch(input$branchName, rea$modset, infoTsv=paste0(rea$anDir, 'info.tsv'))
session$reload()
#rea$anDir <- paste0(rea$prjDir,input$branchName,"/")
#pName<-input$branchName
#output$anSetted<-shiny::renderUI({prjManPanel_reset(pName)})
#output$pNameSlot<- shiny::renderText({input$branchName})
#session$reload()
}else {
if (rea$runmodState=="restart"){
print("restart pressed")
restartFrom(paste0(rea$anDir, 'info.tsv'),rea$modset)
#print("restartFrom executed")
session$reload()
#print("session end")
} else{
#print("render module")
output$moduleScreen<-shiny::renderUI({})
#leggi in reactive se lo stato è branch o reStart
#se branch crea nuovo progetto
#se reStart cancella fino ad un certo punto e riprendi la là
#agiorna lo stato nel reactive come "ready"
withProgress(message="please wait module pre processing", min=0, max=3, {
setProgress(message = 'Calculation in progress', detail = 'This may take a while...')
if (input$mainNav == 'Filtering' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#source ('DiffHiC_DetectInteraction.R')
tool_DetectInteraction<-"Filmod"
moduleUI_DetectInteraction<- "FilmodUI"
moduleLoad_DetectInteraction<- "FilmodServer"
setProgress(value = 1)
#output$filteringSlot <- shiny::renderUI ({
output$selectPn <- shiny::renderUI ({
get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
})
setProgress(value = 2)
loadApp_DetectInteraction <- shiny::callModule(
get(moduleLoad_DetectInteraction)
, tool_DetectInteraction,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
setProgress(value = 3)
}
})
if (input$mainNav == 'Binning'
& file.exists(paste0(rea$anDir, 'info.tsv')) == TRUE ){
tool_Binning <- 'DiffHiC_BinningV2'
moduleUI_Binning <- paste0 (tool_Binning, '_UI')
moduleLoad_Binning <- paste0 (tool_Binning,'_Server')
# output$binningSlot <-renderUI ({
output$selectPn <-renderUI ({
get(moduleUI_Binning) (tool_Binning,label='helpingUI')
})
loadApp_Binning <-shiny::callModule(get(moduleLoad_Binning), tool_Binning,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'iterative' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_DiffHiC_Norm <- 'diffHic_Normalization'
moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
#output$iterativeSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='iceUI')
})
loadApp_DiffHiC_Norm <- shiny::callModule(get(moduleLoad_DiffHiC_Norm),
tool_DiffHiC_Norm,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'WavSis' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_chromoR <- 'chromoR_Normalization'
moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
#output$WavSisSlot<- shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
})
loadApp_chromoR <-shiny::callModule(get(moduleLoad_chromoR),
tool_chromoR,
stringsAsFactors = FALSE,
wdPath = rea$anDir
)
}
if (input$mainNav == 'directionalityIndex' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'directionalityIndex_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'TopDomTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'TopDomTADs_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'HiCsegTADs' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
tool_hmm <- 'HiCsegTADs_postProcessing'
moduleUI_hmm<- paste0 (tool_hmm, '_UI')
moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#output$hmmSlot<-renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_hmm) (tool_hmm,label='helpingUI')
})
loadApp_hmm <- shiny::callModule(get(moduleLoad_hmm), tool_hmm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'CompartmentsPCA' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'pcaComp_postProcessing'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'TopDomTADs' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_tdtadsComp <- 'TopDomTADs_postProcessing'
moduleUI_tdtadsComp<- paste0 (tool_tdtadsComp, '_UI')
moduleLoad_tdtadsComp<- paste0 (tool_tdtadsComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_tdtadsComp) (tool_tdtadsComp,label='TopDomTADs')
})
loadApp_tdtadsComp <- shiny::callModule(get(moduleLoad_tdtadsComp),
tool_tdtadsComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'bed2track' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_tdtadsComp <- 'bed2track_postProcessing'
moduleUI_tdtadsComp<- paste0 (tool_tdtadsComp, '_UI')
moduleLoad_tdtadsComp<- paste0 (tool_tdtadsComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_tdtadsComp) (tool_tdtadsComp,label='bed2track')
})
loadApp_tdtadsComp <- shiny::callModule(get(moduleLoad_tdtadsComp),
tool_tdtadsComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
#EpigeneticFeatures
if (input$mainNav == 'EpigeneticFeatures' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'EpigeneticFeatures'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == '' & file.exists(paste0(
rea$anDir, 'info.tsv'))==TRUE ){
#source ('pcaComp_postProcessing.R')
tool_pcaComp <- 'pcaComp_postProcessing'
moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#output$pcaCompSlot<- shiny::renderUI({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
})
loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
tool_pcaComp,
stringsAsFactors = FALSE,
wdPath=rea$anDir)
}
if (input$mainNav == 'PCA' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#source ('pca_postProcessing.R')
tool_pca <- 'pca_postProcessing'
moduleUI_pca<- paste0 (tool_pca, '_UI')
moduleLoad_pca<- paste0 (tool_pca,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_pca) (tool_pca,label='PCA')
})
loadApp_pca <- shiny::callModule(get(moduleLoad_pca), tool_pca,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'Heatmap' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
){
tool_htm <- 'TADsV2_Visualization'
moduleUI_htm<- paste0 (tool_htm, '_UI')
moduleLoad_htm<- paste0 (tool_htm,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_htm) (tool_htm,label='htmUI')
})
loadApp_htm <- shiny::callModule(get(moduleLoad_htm), tool_htm,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
if (input$mainNav == 'Networks' &
file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
){
tool_ntw <- 'networksV2_Visualization' #networksV2_Visualization_UI
moduleUI_ntw<- paste0 (tool_ntw, '_UI')
moduleLoad_ntw<- paste0 (tool_ntw,'_Server')
#output$pcaSlot<-shiny::renderUI ({
output$selectPn <-shiny::renderUI ({
get(moduleUI_ntw) (tool_ntw,label='ntwUI')
})
loadApp_ntw <- shiny::callModule(get(moduleLoad_ntw), tool_ntw,
stringsAsFactors = FALSE,
wdPath=rea$anDir
)
}
}
}
# #print("render module")
# output$moduleScreen<-shiny::renderUI({})
#
# #leggi in reactive se lo stato è branch o reStart
# #se branch crea nuovo progetto
# #se reStart cancella fino ad un certo punto e riprendi la là
# #agiorna lo stato nel reactive come "ready"
#
# withProgress(message="please wait module pre processing", min=0, max=3, {
# setProgress(message = 'Calculation in progress', detail = 'This may take a while...')
# if (input$mainNav == 'Filtering' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#
# #source ('DiffHiC_DetectInteraction.R')
# tool_DetectInteraction<-"Filmod"
# moduleUI_DetectInteraction<- "FilmodUI"
# moduleLoad_DetectInteraction<- "FilmodServer"
# setProgress(value = 1)
# #output$filteringSlot <- shiny::renderUI ({
# output$selectPn <- shiny::renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
# })
# setProgress(value = 2)
# loadApp_DetectInteraction <- shiny::callModule(
# get(moduleLoad_DetectInteraction)
# , tool_DetectInteraction,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# setProgress(value = 3)
# }
# })
#
# if (input$mainNav == 'Binning'
# & file.exists(paste0(rea$anDir, 'info.tsv')) == TRUE ){
#
# tool_Binning <- 'DiffHiC_BinningV2'
#
# moduleUI_Binning <- paste0 (tool_Binning, '_UI')
# moduleLoad_Binning <- paste0 (tool_Binning,'_Server')
# # output$binningSlot <-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_Binning) (tool_Binning,label='helpingUI')
# })
# loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
#
# }
#
# if (input$mainNav == 'iterative' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_DiffHiC_Norm <- 'diffHic_Normalization'
# moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
# moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
# #output$iterativeSlot<-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='iceUI')
# })
# loadApp_DiffHiC_Norm <- callModule(get(moduleLoad_DiffHiC_Norm),
# tool_DiffHiC_Norm,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
#
# if (input$mainNav == 'WavSis' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_chromoR <- 'chromoR_Normalization'
# moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
# moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
# #output$WavSisSlot<- shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
# })
# loadApp_chromoR <-shiny::callModule(get(moduleLoad_chromoR),
# tool_chromoR,
# stringsAsFactors = FALSE,
# wdPath = rea$anDir
# )
# }
#
# if (input$mainNav == 'TADsHMM' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
# tool_hmm <- 'HMM_postProcessing'
# moduleUI_hmm<- paste0 (tool_hmm, '_UI')
# moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
# #output$hmmSlot<-renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_hmm) (tool_hmm,label='helpingUI')
# })
# loadApp_hmm <- callModule(get(moduleLoad_hmm), tool_hmm,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'CompartmentsPCA' & file.exists(paste0(
# rea$anDir, 'info.tsv'))==TRUE ){
# #source ('pcaComp_postProcessing.R')
# tool_pcaComp <- 'pcaComp_postProcessing'
# moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
# moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
# #output$pcaCompSlot<- shiny::renderUI({
# output$selectPn <-renderUI ({
# get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
# })
# loadApp_pcaComp <- shiny::callModule(get(moduleLoad_pcaComp),
# tool_pcaComp,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir)
# }
#
# if (input$mainNav == 'EpigeneticFeatures' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
# #source ('pca_postProcessing.R')
# tool_pca <- 'pca_postProcessing'
# moduleUI_pca<- paste0 (tool_pca, '_UI')
# moduleLoad_pca<- paste0 (tool_pca,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_pca) (tool_pca,label='epifUI')
# })
# loadApp_pca <- shiny::callModule(get(moduleLoad_pca), tool_pca,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'Heatmap' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
# ){
# tool_htm <- 'TADsV2_Visualization'
# moduleUI_htm<- paste0 (tool_htm, '_UI')
# moduleLoad_htm<- paste0 (tool_htm,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-renderUI ({
# get(moduleUI_htm) (tool_htm,label='htmUI')
# })
# loadApp_htm <- shiny::callModule(get(moduleLoad_htm), tool_htm,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
#
# if (input$mainNav == 'Networks' &
# file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE
# ){
# tool_ntw <- 'networksV2_Visualization' #networksV2_Visualization_UI
# moduleUI_ntw<- paste0 (tool_ntw, '_UI')
# moduleLoad_ntw<- paste0 (tool_ntw,'_Server')
# #output$pcaSlot<-shiny::renderUI ({
# output$selectPn <-shiny::renderUI ({
# get(moduleUI_ntw) (tool_ntw,label='ntwUI')
# })
# loadApp_ntw <- shiny::callModule(get(moduleLoad_ntw), tool_ntw,
# stringsAsFactors = FALSE,
# wdPath=rea$anDir
# )
# }
# if (input$mainNav == 'Analysis' ){
# source ('anSettings.R')
# tool_anSettings <- 'anSettings'
# moduleUI_anSettings<- paste0 (tool_anSettings, '_UI')
# moduleLoad_anSettings<- paste0 (tool_anSettings,'_Server')
# output$anSetPlot<-renderUI ({
# get(moduleUI_anSettings) (tool_anSettings,label='helpingUI')
# })
# loadApp_anSettings <- callModule(get(moduleLoad_anSettings), tool_anSettings,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Pre-Processing' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('DiffHiC_DetectInteraction.R')
# tool_DetectInteraction <- 'DiffHiC_DetectInteraction'
# moduleUI_DetectInteraction<- paste0 (tool_DetectInteraction, '_UI')
# moduleLoad_DetectInteraction<- paste0 (tool_DetectInteraction,'_Server')
# output$preProSlot<-renderUI ({
# get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='helpingUI')
# })
# loadApp_DetectInteraction <- callModule(get(moduleLoad_DetectInteraction), tool_DetectInteraction,
# stringsAsFactors = FALSE)
#}
#
# if (input$mainNav == 'Binning' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('DiffHiC_BinningV2.R')
# tool_Binning <- 'DiffHiC_BinningV2'
# moduleUI_Binning<- paste0 (tool_Binning, '_UI')
# moduleLoad_Binning<- paste0 (tool_Binning,'_Server')
# output$binningSlot<-renderUI ({
# get(moduleUI_Binning) (tool_Binning,label='helpingUI')
# })
# loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'WavSis' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('chromoR_Normalization.R')
# tool_chromoR <- 'chromoR_Normalization'
# moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
# moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
# output$WavSisSlot<-renderUI ({
# get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
# })
# loadApp_chromoR <- callModule(get(moduleLoad_chromoR), tool_chromoR,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'iterative' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('diffHic_Normalization.R')
# tool_DiffHiC_Norm <- 'diffHic_Normalization'
# moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
# moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
# output$iterativeSlot<-renderUI ({
# get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='helpingUI')
# })
# loadApp_DiffHiC_Norm <<- callModule(get(moduleLoad_DiffHiC_Norm), tool_DiffHiC_Norm,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Epigenetic Features' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('pca_postProcessing.R')
# tool_pca <- 'pca_postProcessing'
# moduleUI_pca<- paste0 (tool_pca, '_UI')
# moduleLoad_pca<- paste0 (tool_pca,'_Server')
# output$pcaSlot<-renderUI ({
# get(moduleUI_pca) (tool_pca,label='helpingUI')
# })
# loadApp_pca <- callModule(get(moduleLoad_pca), tool_pca,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Compartments-PCA' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('pcaComp_postProcessing.R')
# tool_pcaComp <- 'pcaComp_postProcessing'
# moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
# moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
# output$pcaCompSlot<-renderUI ({
# get(moduleUI_pcaComp) (tool_pcaComp,label='helpingUI')
# })
# loadApp_pcaComp <- callModule(get(moduleLoad_pcaComp), tool_pcaComp,
# stringsAsFactors = FALSE)
# }
#
#
# if (input$mainNav == 'TADs-HMM' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('HMM_postProcessing.R')
# tool_hmm <- 'HMM_postProcessing'
# moduleUI_hmm<- paste0 (tool_hmm, '_UI')
# moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
# output$hmmSlot<-renderUI ({
# get(moduleUI_hmm) (tool_hmm,label='helpingUI')
# })
# loadApp_hmm <- callModule(get(moduleLoad_hmm), tool_hmm,
# stringsAsFactors = FALSE)
# }
#
#
# if (input$mainNav == 'Heatmap' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('TADsV2_Visualization.R')
# tool_tads <- 'TADsV2_Visualization'
# moduleUI_tads<- paste0 (tool_tads, '_UI')
# moduleLoad_tads<- paste0 (tool_tads,'_Server')
# output$TADsModule<-renderUI ({
# get(moduleUI_tads) (tool_tads,label='helpingUI')
# })
# loadApp_tads <- callModule(get(moduleLoad_tads), tool_tads,
# stringsAsFactors = FALSE)
# }
#
# if (input$mainNav == 'Networks' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
# source ('networksV2_Visualization.R')
# tool_net <- 'networksV2_Visualization'
# moduleUI_net<- paste0 (tool_net, '_UI')
# moduleLoad_net<- paste0 (tool_net,'_Server')
# output$netModule<-renderUI ({
# get(moduleUI_net) (tool_net,label='nets')
# })
# loadApp_net <- callModule(get(moduleLoad_net), tool_net,
# stringsAsFactors = FALSE)
# }
} #fine observe MainNav
)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.