R/vMod1_filtering.R
In lucidif/HiCeekR: GUI for Hi-C data analysis
Defines functions
FilmodServer
FilmodUI
Documented in
FilmodServer
FilmodUI
##filModule
# Module UI function
#' FilmodUI
#'
#' @param id
#' @param label
#'
#' @return
#' @keywords internal
#'
#' @examples
FilmodUI <- function(id, label = "filtering") {
filns <- shiny::NS(id)
#print (filns)
shiny::fluidPage(
# shiny::fluidRow(
# shiny::column(12,
# shiny::uiOutput(
# filns("startSlot")
# )
# )
# ),
# shiny::conditionalPanel(condition = javaNs(filns,
# name = "reStart",
# type = "input",
# condition = ">0"
# ),
shiny::fluidRow(
shiny::column(12,
shiny::fluidRow (
shiny::column (3,
shiny::wellPanel (
shiny::fluidRow(
shiny::column(12,
shiny::numericInput(filns("maxFrag"),
label="max frag length",
value=600
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::checkboxInput(filns("fixValue"),
label="fix values",
value= FALSE
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::conditionalPanel(
condition=javaNs(filns,
name="fixValue",
type="input",
"==true"),
shiny::fluidRow(
shiny::column(6,
shiny::numericInput(
filns("minInward"),
label="min inward",
value=1500
)
),
shiny::column(6,
shiny::numericInput(
filns("minOutward"),
label="min outward",
value=25000
)
)
)
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::conditionalPanel(
condition =
javaNs(filns,
name="fixValue",
type="input",
"==false"
),
shiny::fluidRow(
shiny::column(12,
shiny::fluidRow(
shiny::column(12,
shiny::sliderInput(
filns("minInwardSlider"),
label="min inward",
min=0,
max=25000,
step=100,
value=1000
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::sliderInput(
filns("minOutwardSlider"),
label= "min outward",
min=0,
max=25000,
step=100,
value=25000
)
)
)
)
)
)
)
),
shiny::fluidRow(
# shiny::column(5,
# selectFile (filns("refgenFrag"), path=pointin(wdPath,'Pre-Processing') , label=".cutGenome.tsv file", subset=TRUE, pattern='.cutGenome')
# ),
#
# shiny::column(5,
# selectFile(filns("h5"),path=pointin(anFolder$hisave,'Pre-Processing'), label = "h5 file", subset=TRUE, pattern='.h5')
# ),
shiny::column(12, br(),
shiny::actionButton(filns('filBut'),
'start Filtering',
class="btn-primary"
)
)
)
)
),
shiny::column(8,
shiny::fluidRow(
shiny::column(12,
plotOutput(filns("beforePlot"))
)
),
shiny::fluidRow(
shiny::column(12,
plotOutput(filns("beforePlot2"))
)
)
)
),
shiny::fluidRow(
shiny::column (10,
shiny::fluidRow(
shiny::uiOutput(filns('mainscreen')))
),
shiny::column (2,
shiny::uiOutput (filns('mainPanel'))
)
# column (8,
# fluidRow (uiOutput(filns('mainscreen')))
# )
)
)
)
# ) #conditional end Bracket
)#fluidPage end
}
#==================================================================================
# Module server function
#' FilmodServer
#'
#' @param input
#' @param output
#' @param session
#' @param stringsAsFactors
#' @param wdPath
#'
#' @return
#' @keywords internal
#'
#' @examples
FilmodServer <- function(input, output, session,
stringsAsFactors, wdPath) {
#print (input$bamSel)
rhdf5::h5closeAll()
filns<-session$ns
#prova<-QCmodServer(filns('hsparam'))
#print('param FilmodServer')
#print(prova)
#======================================================================
# > filteringTable<-matrix(ncol=2, nrow=3)
# > filteringTable<-matrix(ncol=1, nrow=3)
# > rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
# > filteringTable[,1]<-c("600", "1500", "25000")
# > write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
#
#======================================================================
values <- shiny::reactiveValues()
values$h5_pa<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
"h5file.h5")
print(paste0("h5_pa: ",values$h5_pa))
values$refgenFrag<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
"refGenFrag.cutGenome.tsv")
print(paste0("refgenFrag: ", values$refgenFrag))
# ##beforePlot operation====================================================
# #questa va eseguita nella sezione di prima e diags nei sysout
# print("beforePlot execution")
# values$rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
# print("beforePlot execution 1")
# values$rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(values$rFrags)
# print("beforePlot execution 2")
# values$paramFil <- diffHic::pairParam(values$rFragsGrange)
# print("beforePlot execution 3")
# values$diags <- diffHic::getPairData(values$h5_pa, values$paramFil)
load(paste0(pointin(wdPath, "Pre-Processing", sys=TRUE ), "diags.Robj"))
values$diags<-diags
# print("beforePlot completed")
#
#
# # Constructing the histograms for each orientation.
#
#questi vanno trasfromrati in widgets
# output$startSlot<-shiny::renderUI({
# controlFile<-paste0(pointin(wdPath,"Filtering", sys=TRUE), "trimmed.h5")
# output$stateText<-shiny::renderText({
# "filtering already executed"
# })
# if (file.exists(controlFile)==TRUE){
# shiny::wellPanel(
# shiny::fluidRow(
# shiny::column(12,
# shiny::helpText("filtering already executed")
# )
# ),
# shiny::fluidRow(
# shiny::column(6,
# shiny::actionButton(filns("reStart"),
# label="Re-Start")
# ),
# shiny::column(6,
# shiny::actionButton(filns("branch"),
# label="branch"
# )
# )
# )
# )
# } else {
# shiny::wellPanel( "Filtering:" ,
# shiny::fluidRow(
# shiny::column(12,
# shiny::helpText("the mapped reads should be
# filtered to ensure that only
# informative and reliable
# read pairs pro- ceedto further
# analysis.")
# )
# ),
# shiny::fluidRow(
# shiny::column(6,
# shiny::actionButton(filns("start"),
# label="Start")
# )
# # ,shiny::column(6,
# # shiny::actionButton(filns("branch"),
# # label="branch"
# # )
# # )
# )
# )
# }
# })
observeEvent(input$minOutward,{
values$min.outward <- input$minOutward
})
observeEvent(input$minInward,{
values$min.inward <- input$minInward
})
observeEvent(input$minInwardSlider,{
values$min.inward <- input$minInwardSlider
})
observeEvent(input$minOutwardSlider,{
values$min.outward <- input$minOutwardSlider
})
#
# #=======================================================================
values$llinsert <- log2(values$diags$insert + 1L)
values$intra <- !is.na(values$llinsert)
values$breaks <- seq(min(values$llinsert[values$intra]),
max(values$llinsert[values$intra]), length.out=30)
values$inward <- hist(values$llinsert[values$diags$orientation==1L],
plot=FALSE, breaks=values$breaks)
values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
plot=FALSE, breaks=values$breaks)
values$samestr <- hist(values$llinsert[values$diags$orientation==0L | values$diags$orientation==3L],
plot=FALSE, breaks=values$breaks)
values$samestr$counts <- values$samestr$counts/2
# Setting up the axis limits.
values$ymax <- max(values$inward$counts, values$outward$counts,
values$samestr$counts)/1e6
values$xmax <- max(values$inward$mids, values$outward$mids,
values$samestr$mids)
values$xmin <- min(values$inward$mids, values$outward$mids,
values$samestr$mids)
##=======================================================================
# jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
# hist(values$diags$length[diags$length < 1000], ylab="Frequency",
# xlab="Spacing (bp)", main="", col="grey80")
# dev.off()
#
# jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
# plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
# xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
# #abline(v=log2(values$min.inward), col="darkgrey")
# lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
# #abline(v=log2(values$min.outward), col="darkgrey", lty=2)
# lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
# legend("topright", c("inward", "outward", "same"),
# col=c("darkgreen", "red", "blue"), lwd=2)
# dev.off()
##1) show previous results results
output$beforePlot<-shiny::renderPlot({
shiny::withProgress(message="Making Plot", min=0, max=1, {
# #=================================================================
# values$llinsert <- log2(values$diags$insert + 1L)
# shiny::setProgress(1)
#
# values$intra <- !is.na(values$llinsert)
# shiny::setProgress(2)
#
# values$breaks <- seq(min(values$llinsert[values$intra]),
# max(values$llinsert[values$intra]), length.out=30)
# shiny::setProgress(3)
#
# values$inward <- hist(values$llinsert[values$diags$orientation==1L],
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(4)
#
# values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(5)
#
# values$samestr <- hist(values$llinsert[values$diags$orientation==0L
# | values$diags$orientation==3L],
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(6)
#
# values$samestr$counts <- values$samestr$counts/2
# shiny::setProgress(7)
#
# # Setting up the axis limits.
# values$ymax <- max(values$inward$counts, values$outward$counts,
# values$samestr$counts)/1e6
# shiny::setProgress(8)
#
# values$xmax <- max(values$inward$mids, values$outward$mids,
# values$samestr$mids)
# shiny::setProgress(9)
#
# values$xmin <- min(values$inward$mids, values$outward$mids,
# values$samestr$mids)
# shiny::setProgress(10)
#
#
#=================================================================
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
})
#dev.off()
})
output$beforePlot2<-shiny::renderPlot({
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
#dev.off()
})
observeEvent(input$filBut,{
busyIndServer("filBut",{
#store run time
runTime2<<-proc.time()
#print(runTime2)
shiny::withProgress("filtering start", min=0, max=13 , {
shiny::setProgress(message = 'Filtering in progress',
detail = 'This may take a while...')
rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
setProgress(value = 1)
# #print (rFrags)
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
setProgress(value = 2)
paramFil <- diffHic::pairParam(rFragsGrange)
setProgress(value = 3)
print(paste0("min.inward=",values$min.inward))
print(paste0("min.outward=",values$min.outward))
counted <- diffHic::prunePairs(paste0(pointin(wdPath, "Pre-Processing", sys=TRUE)
,"h5file.h5"),
paramFil,
file.out= paste0(pointin(wdPath,
"Filtering",
sys=TRUE),
"trimmed.h5"
),
max.frag=input$maxFrag,
min.inward=values$min.inward,
min.outward=values$min.outward)
setProgress(value = 4)
rFrags<- read.table(paste0(pointin(wdPath,"Pre-Processing", sys = TRUE),
"refGenFrag.cutGenome.tsv"), sep='\t', header=TRUE)
#print("beforePlot execution 1")
setProgress(value = 5)
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
#print("beforePlot execution 2")
setProgress(value = 6)
paramFil <- diffHic::pairParam(rFragsGrange)
setProgress(value = 7)
#print("beforePlot execution 3")
diags <- diffHic::getPairData(paste0(pointin(wdPath,"Filtering", sys = TRUE),
"trimmed.h5"),
paramFil)
setProgress(value = 8)
#print("beforePlot execution 4")
save(diags, file=paste0(pointin(wdPath,"Filtering", sys = TRUE),"diags.Robj"))
setProgress(value = 9)
load(paste0(pointin(wdPath, "Filtering", sys=TRUE ), "diags.Robj"))
values$diags<-diags
setProgress(value = 10)
values$llinsert <- log2(values$diags$insert + 1L)
values$intra <- !is.na(values$llinsert)
values$breaks <- seq(min(values$llinsert[values$intra]),
max(values$llinsert[values$intra]), length.out=30)
values$inward <- hist(values$llinsert[values$diags$orientation==1L],
plot=FALSE, breaks=values$breaks)
values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
plot=FALSE, breaks=values$breaks)
values$samestr <- hist(values$llinsert[values$diags$orientation==0L | values$diags$orientation==3L],
plot=FALSE, breaks=values$breaks)
values$samestr$counts <- values$samestr$counts/2
# Setting up the axis limits.
values$ymax <- max(values$inward$counts, values$outward$counts,
values$samestr$counts)/1e6
values$xmax <- max(values$inward$mids, values$outward$mids,
values$samestr$mids)
values$xmin <- min(values$inward$mids, values$outward$mids,
values$samestr$mids)
setProgress(value = 11)
##=======================================================================
jpeg(file=paste0(pointin(wdPath, "Filtering", sys=TRUE),"fragments_trimmed.jpeg"))
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
dev.off()
jpeg(file=paste0(pointin(wdPath, "Filtering", sys=TRUE),"inOutWard_trimmed.jpeg"))
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
dev.off()
##1) show previous results results
output$beforePlot<-shiny::renderPlot({
shiny::withProgress(message="Making Plot", min=0, max=1, {
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
})
})
setProgress(value = 12)
output$beforePlot2<-shiny::renderPlot({
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
})
#saveParameters
filteringTable<-matrix(ncol=2, nrow=3)
filteringTable<-matrix(ncol=1, nrow=3)
rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
if (input$fixValue==FALSE){
mini=input$minInwardSlider
mino=input$minOutwardSlider
} else {
mini=input$minInward
mino=input$minOutward
}
filteringTable[,1]<-c(input$maxFrag, mini, mino)
print(paste("writing filtering parameters",pointin(wdPath, "Filtering", sys=TRUE)))
write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
print("filtering parameters writted")
setProgress(value = 13)
#run time end
runTime2<<-proc.time()-runTime2
})
})
})
# shiny::observeEvent (input$fileVSprevious,{
#
# output$h5<- shiny::renderUI ({
# shiny::fileInput(filns("h5"), label = h6("h5 file"))
# })
#
# if (input$fileVSprevious==1){
#
# output$refgenFrag <- shiny::renderUI ({
# selectFile (filns("refgenFrag"),path=paste0(anFolder$hisave,'Pre-Processing/'))
# #fileInput(filns("refgenFrag"), label = h6("reference genome frags"))
# })
#
# } else {
# output$refgenFrag <- shiny::renderUI ({
# #fileInput(filns("refgenFrag"), label = h6("prova"))
# })
#
# }
#
# })
# shiny::observeEvent (input$startbut,{
#
# fileVSprevious<-1
# print ('startBut.....pressed ')
# #if (input$checkbox==TRUE){
# #
# #} else {
# # refFrags<<-input$refgenFrag$datapath
# # h5file<<-input$h5$datapath
# #}
#
# #values$h5_pa<-input$h5
# # values$h5_pa<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
# # "h5file.h5")
# # print("h5_pa: ",values$h5_pa)
#
# #h5file<<- paste0 ( anFolder$hisave, 'Pre-Processing/' ,input$h5)
# infoImport<- HCRread(file='info.tsv', path=wdPath, header=FALSE)
# print ('info.....imported')
# #bin.size<<-as.numeric(infoImport[2,1])
# #bin.size<<-input$text
#
# #values$refgenFrag_pa<- input$refgenFrag
# # values$refgenFrag<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
# # "refGenFrag.cutGenome.tsv")
# # print(paste0("refgenFrag: ", values$refgenFrag))
# #refFrags<<- paste0 (anFolder$hisave, 'Pre-Processing/' ,input$refgenFrag)
#
# rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
# #print (rFrags)
# rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
# paramFil <- diffHic::pairParam(rFragsGrange)
#
#
# # output$NBbut <-renderUI ({
# # actionButton (filns('NButton'), label = 'get Pair Data')
# # })
#
# #In this model, the overall NB mean across all libraries is (probably) an independent
# #filter statistic. The log-mean-per-million is known as the average abundance and
# #can be computed with the aveLogCPM function in edgeR
# print ('get Pair Data.....START')
#
# #diags<<- getPairData (h5file, paramFil)
#
# diags<- diffHic::getPairData (values$h5_pa, paramFil)
#
# output$LEhist <- shiny::renderPlot({
# hist(diags$length[diags$length < 1000], ylab='frequency', xlab='Spacing (bp)' )
# })
#
# output$minInwardSlot<- shiny::renderUI ({
# numericInput (filns('minInward'), label=h5('min.inward'), value = 1000 )
# })
#
# output$minOutwardSlot<- shiny::renderUI ({
# numericInput (filns('minOutward'), label=h5('min.Outward'), value = 25000 )
# })
#
# output$lengthSlot<- shiny::renderUI ({
# numericInput (filns('fragLength'), label=h5('fragment length'), value = 600 )
# })
#
# output$filteringButSlot<- shiny::renderUI ({
# actionButton (filns('filteringButton'), label=h5('filtering'))
# })
#
# # output$viewButSlot<- renderUI ({
# # actionButton (filns('viewButton'), label=h5('View'))
# # })
#
# intra <- !is.na(diags$insert)
# #min.inward <<- 1000 #as.numeric(input$minInward)
# #min.outward <<- 25000 #as.numeric(input$minOutward)
#
#
#
# #print (c('minInward', 'minOutward', min.inward, min.outward))
#
# llinsert <- log2(diags$insert + 1L)
# values$llinsert2<-llinsert
#
# intra <- !is.na(llinsert)
# values$intra2 <- intra
#
# breaks <- seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
# values$breaks2 <- breaks
#
# inward <- hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
# values$inward2<- inward
#
# outward <- hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
# values$outward2<- outward
#
# #samestr <- hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
# #values$samestr2<-samestr
#
# #samestr$counts <- samestr$counts/2
#
#
# # ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# # xmax <- max(inward$mids, outward$mids, samestr$mids)
# # xmin <- min(inward$mids, outward$mids, samestr$mids)
# ymax <- max(inward$counts, outward$counts)/1e6
# xmax <- max(inward$mids, outward$mids)
# xmin <- min(inward$mids, outward$mids)
#
# output$degSelfGraph <- shiny::renderPlot ({
#
# plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
# abline(v=log2(min.inward), col="darkgrey")
# lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
# abline(v=log2(min.outward), col="darkgrey", lty=2)
# # lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
# # legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
#
# legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
#
#
# })
#
# output$mainPanel<- shiny::renderUI({
# shiny::wellPanel(
#
# ## selectInput(filns("fileVSprevious"), label = h5("Select box"),
# ## choices = list("load from files" = 1, "load previous" = 2),
# ## selected = 1),
# #fileInput(filns("refgenFrag"), label = h6("reference genome frags")),
# #fileInput(filns("h5"), label = h6("h5 file")),
# ###uiOutput(filns('refgenFrag')),
# #selectFile (filns("refgenFrag"),path=wsFolder$hisave),
#
# uiOutput(filns('h5')),
# #textInput(filns('text'),label=h6('bin size'), value="1e5"),
# #checkboxInput("checkbox", label = "no data load", value = TRUE),
# #actionButton(filns('startbut'), 'import')
# shiny::br(),
# shiny::fluidRow (
# shiny::column (1, shiny::uiOutput(filns('NBbut')))
#
# ),
#
# shiny::br(),
#
# shiny::fluidRow(
#
# shiny::column (12, shiny::uiOutput(filns('lengthSlot')))
#
# ),
#
# shiny::fluidRow (
# shiny::column (12, shiny::uiOutput (filns('minInwardSlot')))
# ),
#
# shiny::fluidRow (
#
# shiny::column (12, shiny::uiOutput(filns('minOutwardSlot')))
#
# ),
#
#
# shiny::fluidRow (
#
# shiny::column (12, shiny::uiOutput(filns('viewButSlot')))
#
# ),
#
# shiny::fluidRow (
# shiny::column (12, shiny::uiOutput(filns('filteringButSlot')))
# )
#
#
# )
# })
#
#
# output$mainscreen<- shiny::renderUI ({
# shiny::tabsetPanel (
# shiny::tabPanel('reads length',
# shiny::plotOutput(filns('LEhist')),
# plotOutput(filns ('degSelfGraph'))
# )
# # ,tabPanel('direct filtering', textOutput(filns('difiVal')),
# # fluidRow(column(6,uiOutput(filns('MFCval'))),column(6,br(),br(),uiOutput(filns('MFCBut'))))
# # ,tableOutput (filns('sum2'))
# # )
# )
# })
#
#
#
#
# }
#
# )
#
#
# shiny::observeEvent(input$NBfilButton,{
# count.keep <- ave.ab >= aveLogCPM(5, lib.size=mean(data$totals))
# summary<-capture.output(as.data.frame(show (summary(count.keep))))
# summama<- matrix (nrow=2, ncol=4)
# summaryA<- strsplit (summary[1], split=' ')
# summaryA<- as.vector (summaryA[[1]])
# summaryA<- summaryA[summaryA != ""]
# summaryB<- strsplit (summary[2],split=' ')
# summaryB<- as.vector (summaryB[[1]])
# summaryB<- summaryB[summaryB != ""]
# print(summaryA)
# print(summaryB)
# summama[1,]<-summaryA
# summama[2,]<-summaryB
# print (summama)
# output$sum<- renderTable ({
# summama
# })
#
#
#
# })
#
# shiny::observeEvent (input$minFoldButton,{
# direct.keep <- direct$abundances > log2(5) + direct$threshold
# summary<-capture.output(as.data.frame(show (summary(direct.keep))))
# print (length(summary))
# # summaryC<- strsplit (summary[1], split=' ')
# # summaryC<- as.vector (summaryC[[1]])
# # summaryC<- summaryC[summaryC != ""]
# # lensumC<- length (summaryC)
# # summaryD<- strsplit (summary[2],split=' ')
# # summaryD<- as.vector (summaryD[[1]])
# # summaryD<- summaryD[summaryD != ""]
# # lensumD<- length (summaryD)
# # if (lensumC>=lensumD){
# # summama2<- matrix (nrow=2, ncol=lensumC)
# # } else {summama2<- matrix (nrow=2, ncol=lensumD)}
#
# # summama2[1,]<-summaryC
# # summama2[2,]<-summaryD
# output$sum2<- renderTable ({
# summama2<- tableFromConsole (summary(direct.keep), 1)
# })
# })
#
# shiny::observeEvent (input$viewButton, {
#
# ##diags<- getPairData (h5file, paramFil)
# print ('viewbutton is pressed')
# intra <- !is.na(diags$insert)
# min.inward <<- as.numeric(input$minInward)
# min.outward <<- as.numeric(input$minOutward)
#
# print (c('minInward', 'minOutward', min.inward, min.outward))
# #print (input$minOutwardSlot)
# #print (min.inward)
# #print (min.outward)
# llinsert <- values$llinsert #log2(diags$insert + 1L)
# intra <- !is.na(llinsert)
#
# breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
#
# values$inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
# values$outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
# #samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
# #samestr$counts <- samestr$counts/2
#
# # ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# # xmax <- max(inward$mids, outward$mids, samestr$mids)
# # xmin <- min(inward$mids, outward$mids, samestr$mids)
#
# ymax <- max(inward$counts, outward$counts)/1e6
# xmax <- max(inward$mids, outward$mids)
# xmin <- min(inward$mids, outward$mids)
#
#
# output$degSelfGraph <- shiny::renderPlot ({
#
# plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
# abline(v=log2(min.inward), col="darkgrey")
# lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
# abline(v=log2(min.outward), col="darkgrey", lty=2)
# #lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
# #legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
# legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
#
# })
#
#
# })
shiny::observeEvent(input$filteringButton,{ #deprecated button see filBut
print ('filtering.....START')
##ATTENZIONE: FILTRA SOLO A 600 DI max.frag
fileName<-paste0(anFolder$hisave,'Pre-Processing/',sub('.h5', '' ,values$h5_pa, fixed=TRUE),'_trimmed.h5')
if (min.inward==0){min.inward=NA}
if (min.outward==0){min.outward=NA}
filtered<- prunePairs (h5file, paramFil, file.out='trimmed.h5', max.frag=input$fragLength, min.inward, min.outward)
file.copy("./trimmed.h5", fileName, overwrite = TRUE)
file.remove("trimmed.h5")
#filtered<- prunePairs (h5file, paramFil, file.out=fileName, max.frag=input$fragLength, min.inward, min.outward)
#print(paste0(anFolder$hisave,'Pre-Processing/',sub('.h5', '' ,input$h5, fixed=TRUE),'_trimmed.h5','......CREATED'))
print(paste0(fileName,'......CREATED'))
print ('filtering.....END')
#saveParameters
filteringTable<-matrix(ncol=2, nrow=3)
filteringTable<-matrix(ncol=1, nrow=3)
rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
if (input$fixValue==FALSE){
mini=input$minInwardSlider
mino=input$minOutwardSlider
} else {
mini=input$minInward
mino=input$minOutward
}
filteringTable[,1]<-c(input$maxFrag, mini, mino)
print(paste("writing filtering parameters",pointin(wdPath, "Filtering", sys=TRUE)))
write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
print("filtering parameters writted")
output$mainscreen<- renderUI ({
wellPanel (helpText('filtering Done, please if you want see results load trimmed h5 file'))
})
})
shiny::observeEvent(input$minInward,{
##diags<- getPairData (h5file, paramFil)
#print ('viewbutton is pressed')
intra <- !is.na(diags$insert)
min.inward <- as.numeric(input$minInward)
min.outward <- as.numeric(input$minOutward)
print (c('minInward', 'minOutward', min.inward, min.outward))
#print (input$minOutwardSlot)
#print (min.inward)
#print (min.outward)
llinsert <- values$llinsert #log2(diags$insert + 1L)
intra <- !is.na(llinsert)
breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
samestr$counts <- samestr$counts/2
# ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# xmax <- max(inward$mids, outward$mids, samestr$mids)
# xmin <- min(inward$mids, outward$mids, samestr$mids)
ymax <- max(inward$counts, outward$counts)/1e6
xmax <- max(inward$mids, outward$mids)
xmin <- min(inward$mids, outward$mids)
output$degSelfGraph <- shiny::renderPlot ({
plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(min.inward), col="darkgrey")
lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
abline(v=log2(min.outward), col="darkgrey", lty=2)
#lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
#legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
})
})
shiny::observeEvent(input$minOutward, {
##diags<- getPairData (h5file, paramFil)
#print ('viewbutton is pressed')
intra <- !is.na(diags$insert)
#min.inward <<- as.numeric(input$minInward)
#min.outward <<- as.numeric(input$minOutward)
#print (c('minInward', 'minOutward', min.inward, min.outward))
#print (input$minOutwardSlot)
#print (min.inward)
#print (min.outward)
llinsert <- values$llinsert #log2(diags$insert + 1L)
intra <- !is.na(llinsert)
breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
samestr$counts <- samestr$counts/2
# ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# xmax <- max(inward$mids, outward$mids, samestr$mids)
# xmin <- min(inward$mids, outward$mids, samestr$mids)
ymax <- max(inward$counts, outward$counts)/1e6
xmax <- max(inward$mids, outward$mids)
xmin <- min(inward$mids, outward$mids)
filPlot <- shiny::renderPlot({
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"filplot.jpeg"))
plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(min.inward), col="darkgrey")
lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
abline(v=log2(min.outward), col="darkgrey", lty=2)
#lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
#legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
legend("topright", c("inward", "outward"), col=c("darkgreen", "red", "blue"), lwd=2)
#dev.off()
})
#save (filPlot, file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"filplot.Robj"))
output$degSelfGraph<- filPlot
})
}
lucidif/HiCeekR documentation built on Jan. 31, 2021, 10:30 p.m.
R Package Documentation
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Defines functions FilmodServer FilmodUI
Documented in FilmodServer FilmodUI
##filModule
# Module UI function
#' FilmodUI
#'
#' @param id
#' @param label
#'
#' @return
#' @keywords internal
#'
#' @examples
FilmodUI <- function(id, label = "filtering") {
filns <- shiny::NS(id)
#print (filns)
shiny::fluidPage(
# shiny::fluidRow(
# shiny::column(12,
# shiny::uiOutput(
# filns("startSlot")
# )
# )
# ),
# shiny::conditionalPanel(condition = javaNs(filns,
# name = "reStart",
# type = "input",
# condition = ">0"
# ),
shiny::fluidRow(
shiny::column(12,
shiny::fluidRow (
shiny::column (3,
shiny::wellPanel (
shiny::fluidRow(
shiny::column(12,
shiny::numericInput(filns("maxFrag"),
label="max frag length",
value=600
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::checkboxInput(filns("fixValue"),
label="fix values",
value= FALSE
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::conditionalPanel(
condition=javaNs(filns,
name="fixValue",
type="input",
"==true"),
shiny::fluidRow(
shiny::column(6,
shiny::numericInput(
filns("minInward"),
label="min inward",
value=1500
)
),
shiny::column(6,
shiny::numericInput(
filns("minOutward"),
label="min outward",
value=25000
)
)
)
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::conditionalPanel(
condition =
javaNs(filns,
name="fixValue",
type="input",
"==false"
),
shiny::fluidRow(
shiny::column(12,
shiny::fluidRow(
shiny::column(12,
shiny::sliderInput(
filns("minInwardSlider"),
label="min inward",
min=0,
max=25000,
step=100,
value=1000
)
)
),
shiny::fluidRow(
shiny::column(12,
shiny::sliderInput(
filns("minOutwardSlider"),
label= "min outward",
min=0,
max=25000,
step=100,
value=25000
)
)
)
)
)
)
)
),
shiny::fluidRow(
# shiny::column(5,
# selectFile (filns("refgenFrag"), path=pointin(wdPath,'Pre-Processing') , label=".cutGenome.tsv file", subset=TRUE, pattern='.cutGenome')
# ),
#
# shiny::column(5,
# selectFile(filns("h5"),path=pointin(anFolder$hisave,'Pre-Processing'), label = "h5 file", subset=TRUE, pattern='.h5')
# ),
shiny::column(12, br(),
shiny::actionButton(filns('filBut'),
'start Filtering',
class="btn-primary"
)
)
)
)
),
shiny::column(8,
shiny::fluidRow(
shiny::column(12,
plotOutput(filns("beforePlot"))
)
),
shiny::fluidRow(
shiny::column(12,
plotOutput(filns("beforePlot2"))
)
)
)
),
shiny::fluidRow(
shiny::column (10,
shiny::fluidRow(
shiny::uiOutput(filns('mainscreen')))
),
shiny::column (2,
shiny::uiOutput (filns('mainPanel'))
)
# column (8,
# fluidRow (uiOutput(filns('mainscreen')))
# )
)
)
)
# ) #conditional end Bracket
)#fluidPage end
}
#==================================================================================
# Module server function
#' FilmodServer
#'
#' @param input
#' @param output
#' @param session
#' @param stringsAsFactors
#' @param wdPath
#'
#' @return
#' @keywords internal
#'
#' @examples
FilmodServer <- function(input, output, session,
stringsAsFactors, wdPath) {
#print (input$bamSel)
rhdf5::h5closeAll()
filns<-session$ns
#prova<-QCmodServer(filns('hsparam'))
#print('param FilmodServer')
#print(prova)
#======================================================================
# > filteringTable<-matrix(ncol=2, nrow=3)
# > filteringTable<-matrix(ncol=1, nrow=3)
# > rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
# > filteringTable[,1]<-c("600", "1500", "25000")
# > write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
#
#======================================================================
values <- shiny::reactiveValues()
values$h5_pa<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
"h5file.h5")
print(paste0("h5_pa: ",values$h5_pa))
values$refgenFrag<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
"refGenFrag.cutGenome.tsv")
print(paste0("refgenFrag: ", values$refgenFrag))
# ##beforePlot operation====================================================
# #questa va eseguita nella sezione di prima e diags nei sysout
# print("beforePlot execution")
# values$rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
# print("beforePlot execution 1")
# values$rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(values$rFrags)
# print("beforePlot execution 2")
# values$paramFil <- diffHic::pairParam(values$rFragsGrange)
# print("beforePlot execution 3")
# values$diags <- diffHic::getPairData(values$h5_pa, values$paramFil)
load(paste0(pointin(wdPath, "Pre-Processing", sys=TRUE ), "diags.Robj"))
values$diags<-diags
# print("beforePlot completed")
#
#
# # Constructing the histograms for each orientation.
#
#questi vanno trasfromrati in widgets
# output$startSlot<-shiny::renderUI({
# controlFile<-paste0(pointin(wdPath,"Filtering", sys=TRUE), "trimmed.h5")
# output$stateText<-shiny::renderText({
# "filtering already executed"
# })
# if (file.exists(controlFile)==TRUE){
# shiny::wellPanel(
# shiny::fluidRow(
# shiny::column(12,
# shiny::helpText("filtering already executed")
# )
# ),
# shiny::fluidRow(
# shiny::column(6,
# shiny::actionButton(filns("reStart"),
# label="Re-Start")
# ),
# shiny::column(6,
# shiny::actionButton(filns("branch"),
# label="branch"
# )
# )
# )
# )
# } else {
# shiny::wellPanel( "Filtering:" ,
# shiny::fluidRow(
# shiny::column(12,
# shiny::helpText("the mapped reads should be
# filtered to ensure that only
# informative and reliable
# read pairs pro- ceedto further
# analysis.")
# )
# ),
# shiny::fluidRow(
# shiny::column(6,
# shiny::actionButton(filns("start"),
# label="Start")
# )
# # ,shiny::column(6,
# # shiny::actionButton(filns("branch"),
# # label="branch"
# # )
# # )
# )
# )
# }
# })
observeEvent(input$minOutward,{
values$min.outward <- input$minOutward
})
observeEvent(input$minInward,{
values$min.inward <- input$minInward
})
observeEvent(input$minInwardSlider,{
values$min.inward <- input$minInwardSlider
})
observeEvent(input$minOutwardSlider,{
values$min.outward <- input$minOutwardSlider
})
#
# #=======================================================================
values$llinsert <- log2(values$diags$insert + 1L)
values$intra <- !is.na(values$llinsert)
values$breaks <- seq(min(values$llinsert[values$intra]),
max(values$llinsert[values$intra]), length.out=30)
values$inward <- hist(values$llinsert[values$diags$orientation==1L],
plot=FALSE, breaks=values$breaks)
values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
plot=FALSE, breaks=values$breaks)
values$samestr <- hist(values$llinsert[values$diags$orientation==0L | values$diags$orientation==3L],
plot=FALSE, breaks=values$breaks)
values$samestr$counts <- values$samestr$counts/2
# Setting up the axis limits.
values$ymax <- max(values$inward$counts, values$outward$counts,
values$samestr$counts)/1e6
values$xmax <- max(values$inward$mids, values$outward$mids,
values$samestr$mids)
values$xmin <- min(values$inward$mids, values$outward$mids,
values$samestr$mids)
##=======================================================================
# jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
# hist(values$diags$length[diags$length < 1000], ylab="Frequency",
# xlab="Spacing (bp)", main="", col="grey80")
# dev.off()
#
# jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
# plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
# xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
# #abline(v=log2(values$min.inward), col="darkgrey")
# lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
# #abline(v=log2(values$min.outward), col="darkgrey", lty=2)
# lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
# legend("topright", c("inward", "outward", "same"),
# col=c("darkgreen", "red", "blue"), lwd=2)
# dev.off()
##1) show previous results results
output$beforePlot<-shiny::renderPlot({
shiny::withProgress(message="Making Plot", min=0, max=1, {
# #=================================================================
# values$llinsert <- log2(values$diags$insert + 1L)
# shiny::setProgress(1)
#
# values$intra <- !is.na(values$llinsert)
# shiny::setProgress(2)
#
# values$breaks <- seq(min(values$llinsert[values$intra]),
# max(values$llinsert[values$intra]), length.out=30)
# shiny::setProgress(3)
#
# values$inward <- hist(values$llinsert[values$diags$orientation==1L],
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(4)
#
# values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(5)
#
# values$samestr <- hist(values$llinsert[values$diags$orientation==0L
# | values$diags$orientation==3L],
# plot=FALSE, breaks=values$breaks)
# shiny::setProgress(6)
#
# values$samestr$counts <- values$samestr$counts/2
# shiny::setProgress(7)
#
# # Setting up the axis limits.
# values$ymax <- max(values$inward$counts, values$outward$counts,
# values$samestr$counts)/1e6
# shiny::setProgress(8)
#
# values$xmax <- max(values$inward$mids, values$outward$mids,
# values$samestr$mids)
# shiny::setProgress(9)
#
# values$xmin <- min(values$inward$mids, values$outward$mids,
# values$samestr$mids)
# shiny::setProgress(10)
#
#
#=================================================================
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"fragments.jpeg"))
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
})
#dev.off()
})
output$beforePlot2<-shiny::renderPlot({
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"inOutWard.jpeg"))
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
#dev.off()
})
observeEvent(input$filBut,{
busyIndServer("filBut",{
#store run time
runTime2<<-proc.time()
#print(runTime2)
shiny::withProgress("filtering start", min=0, max=13 , {
shiny::setProgress(message = 'Filtering in progress',
detail = 'This may take a while...')
rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
setProgress(value = 1)
# #print (rFrags)
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
setProgress(value = 2)
paramFil <- diffHic::pairParam(rFragsGrange)
setProgress(value = 3)
print(paste0("min.inward=",values$min.inward))
print(paste0("min.outward=",values$min.outward))
counted <- diffHic::prunePairs(paste0(pointin(wdPath, "Pre-Processing", sys=TRUE)
,"h5file.h5"),
paramFil,
file.out= paste0(pointin(wdPath,
"Filtering",
sys=TRUE),
"trimmed.h5"
),
max.frag=input$maxFrag,
min.inward=values$min.inward,
min.outward=values$min.outward)
setProgress(value = 4)
rFrags<- read.table(paste0(pointin(wdPath,"Pre-Processing", sys = TRUE),
"refGenFrag.cutGenome.tsv"), sep='\t', header=TRUE)
#print("beforePlot execution 1")
setProgress(value = 5)
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
#print("beforePlot execution 2")
setProgress(value = 6)
paramFil <- diffHic::pairParam(rFragsGrange)
setProgress(value = 7)
#print("beforePlot execution 3")
diags <- diffHic::getPairData(paste0(pointin(wdPath,"Filtering", sys = TRUE),
"trimmed.h5"),
paramFil)
setProgress(value = 8)
#print("beforePlot execution 4")
save(diags, file=paste0(pointin(wdPath,"Filtering", sys = TRUE),"diags.Robj"))
setProgress(value = 9)
load(paste0(pointin(wdPath, "Filtering", sys=TRUE ), "diags.Robj"))
values$diags<-diags
setProgress(value = 10)
values$llinsert <- log2(values$diags$insert + 1L)
values$intra <- !is.na(values$llinsert)
values$breaks <- seq(min(values$llinsert[values$intra]),
max(values$llinsert[values$intra]), length.out=30)
values$inward <- hist(values$llinsert[values$diags$orientation==1L],
plot=FALSE, breaks=values$breaks)
values$outward <- hist(values$llinsert[values$diags$orientation==2L] ,
plot=FALSE, breaks=values$breaks)
values$samestr <- hist(values$llinsert[values$diags$orientation==0L | values$diags$orientation==3L],
plot=FALSE, breaks=values$breaks)
values$samestr$counts <- values$samestr$counts/2
# Setting up the axis limits.
values$ymax <- max(values$inward$counts, values$outward$counts,
values$samestr$counts)/1e6
values$xmax <- max(values$inward$mids, values$outward$mids,
values$samestr$mids)
values$xmin <- min(values$inward$mids, values$outward$mids,
values$samestr$mids)
setProgress(value = 11)
##=======================================================================
jpeg(file=paste0(pointin(wdPath, "Filtering", sys=TRUE),"fragments_trimmed.jpeg"))
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
dev.off()
jpeg(file=paste0(pointin(wdPath, "Filtering", sys=TRUE),"inOutWard_trimmed.jpeg"))
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
dev.off()
##1) show previous results results
output$beforePlot<-shiny::renderPlot({
shiny::withProgress(message="Making Plot", min=0, max=1, {
hist(values$diags$length[diags$length < 1000], ylab="Frequency",
xlab="Spacing (bp)", main="", col="grey80")
})
})
setProgress(value = 12)
output$beforePlot2<-shiny::renderPlot({
plot(0,0,type="n", xlim=c(values$xmin, values$xmax), ylim=c(0, values$ymax),
xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(values$inward$mids, values$inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(values$min.inward), col="darkgrey")
lines(values$outward$mids, values$outward$counts/1e6, col="red", lwd=2)
abline(v=log2(values$min.outward), col="darkgrey", lty=2)
lines(values$samestr$mids, values$samestr$counts/1e6, col="blue", lwd=2)
legend("topright", c("inward", "outward", "same"),
col=c("darkgreen", "red", "blue"), lwd=2)
})
#saveParameters
filteringTable<-matrix(ncol=2, nrow=3)
filteringTable<-matrix(ncol=1, nrow=3)
rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
if (input$fixValue==FALSE){
mini=input$minInwardSlider
mino=input$minOutwardSlider
} else {
mini=input$minInward
mino=input$minOutward
}
filteringTable[,1]<-c(input$maxFrag, mini, mino)
print(paste("writing filtering parameters",pointin(wdPath, "Filtering", sys=TRUE)))
write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
print("filtering parameters writted")
setProgress(value = 13)
#run time end
runTime2<<-proc.time()-runTime2
})
})
})
# shiny::observeEvent (input$fileVSprevious,{
#
# output$h5<- shiny::renderUI ({
# shiny::fileInput(filns("h5"), label = h6("h5 file"))
# })
#
# if (input$fileVSprevious==1){
#
# output$refgenFrag <- shiny::renderUI ({
# selectFile (filns("refgenFrag"),path=paste0(anFolder$hisave,'Pre-Processing/'))
# #fileInput(filns("refgenFrag"), label = h6("reference genome frags"))
# })
#
# } else {
# output$refgenFrag <- shiny::renderUI ({
# #fileInput(filns("refgenFrag"), label = h6("prova"))
# })
#
# }
#
# })
# shiny::observeEvent (input$startbut,{
#
# fileVSprevious<-1
# print ('startBut.....pressed ')
# #if (input$checkbox==TRUE){
# #
# #} else {
# # refFrags<<-input$refgenFrag$datapath
# # h5file<<-input$h5$datapath
# #}
#
# #values$h5_pa<-input$h5
# # values$h5_pa<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
# # "h5file.h5")
# # print("h5_pa: ",values$h5_pa)
#
# #h5file<<- paste0 ( anFolder$hisave, 'Pre-Processing/' ,input$h5)
# infoImport<- HCRread(file='info.tsv', path=wdPath, header=FALSE)
# print ('info.....imported')
# #bin.size<<-as.numeric(infoImport[2,1])
# #bin.size<<-input$text
#
# #values$refgenFrag_pa<- input$refgenFrag
# # values$refgenFrag<-paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),
# # "refGenFrag.cutGenome.tsv")
# # print(paste0("refgenFrag: ", values$refgenFrag))
# #refFrags<<- paste0 (anFolder$hisave, 'Pre-Processing/' ,input$refgenFrag)
#
# rFrags<- read.table(values$refgenFrag, sep='\t', header=TRUE)
# #print (rFrags)
# rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
# paramFil <- diffHic::pairParam(rFragsGrange)
#
#
# # output$NBbut <-renderUI ({
# # actionButton (filns('NButton'), label = 'get Pair Data')
# # })
#
# #In this model, the overall NB mean across all libraries is (probably) an independent
# #filter statistic. The log-mean-per-million is known as the average abundance and
# #can be computed with the aveLogCPM function in edgeR
# print ('get Pair Data.....START')
#
# #diags<<- getPairData (h5file, paramFil)
#
# diags<- diffHic::getPairData (values$h5_pa, paramFil)
#
# output$LEhist <- shiny::renderPlot({
# hist(diags$length[diags$length < 1000], ylab='frequency', xlab='Spacing (bp)' )
# })
#
# output$minInwardSlot<- shiny::renderUI ({
# numericInput (filns('minInward'), label=h5('min.inward'), value = 1000 )
# })
#
# output$minOutwardSlot<- shiny::renderUI ({
# numericInput (filns('minOutward'), label=h5('min.Outward'), value = 25000 )
# })
#
# output$lengthSlot<- shiny::renderUI ({
# numericInput (filns('fragLength'), label=h5('fragment length'), value = 600 )
# })
#
# output$filteringButSlot<- shiny::renderUI ({
# actionButton (filns('filteringButton'), label=h5('filtering'))
# })
#
# # output$viewButSlot<- renderUI ({
# # actionButton (filns('viewButton'), label=h5('View'))
# # })
#
# intra <- !is.na(diags$insert)
# #min.inward <<- 1000 #as.numeric(input$minInward)
# #min.outward <<- 25000 #as.numeric(input$minOutward)
#
#
#
# #print (c('minInward', 'minOutward', min.inward, min.outward))
#
# llinsert <- log2(diags$insert + 1L)
# values$llinsert2<-llinsert
#
# intra <- !is.na(llinsert)
# values$intra2 <- intra
#
# breaks <- seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
# values$breaks2 <- breaks
#
# inward <- hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
# values$inward2<- inward
#
# outward <- hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
# values$outward2<- outward
#
# #samestr <- hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
# #values$samestr2<-samestr
#
# #samestr$counts <- samestr$counts/2
#
#
# # ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# # xmax <- max(inward$mids, outward$mids, samestr$mids)
# # xmin <- min(inward$mids, outward$mids, samestr$mids)
# ymax <- max(inward$counts, outward$counts)/1e6
# xmax <- max(inward$mids, outward$mids)
# xmin <- min(inward$mids, outward$mids)
#
# output$degSelfGraph <- shiny::renderPlot ({
#
# plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
# abline(v=log2(min.inward), col="darkgrey")
# lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
# abline(v=log2(min.outward), col="darkgrey", lty=2)
# # lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
# # legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
#
# legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
#
#
# })
#
# output$mainPanel<- shiny::renderUI({
# shiny::wellPanel(
#
# ## selectInput(filns("fileVSprevious"), label = h5("Select box"),
# ## choices = list("load from files" = 1, "load previous" = 2),
# ## selected = 1),
# #fileInput(filns("refgenFrag"), label = h6("reference genome frags")),
# #fileInput(filns("h5"), label = h6("h5 file")),
# ###uiOutput(filns('refgenFrag')),
# #selectFile (filns("refgenFrag"),path=wsFolder$hisave),
#
# uiOutput(filns('h5')),
# #textInput(filns('text'),label=h6('bin size'), value="1e5"),
# #checkboxInput("checkbox", label = "no data load", value = TRUE),
# #actionButton(filns('startbut'), 'import')
# shiny::br(),
# shiny::fluidRow (
# shiny::column (1, shiny::uiOutput(filns('NBbut')))
#
# ),
#
# shiny::br(),
#
# shiny::fluidRow(
#
# shiny::column (12, shiny::uiOutput(filns('lengthSlot')))
#
# ),
#
# shiny::fluidRow (
# shiny::column (12, shiny::uiOutput (filns('minInwardSlot')))
# ),
#
# shiny::fluidRow (
#
# shiny::column (12, shiny::uiOutput(filns('minOutwardSlot')))
#
# ),
#
#
# shiny::fluidRow (
#
# shiny::column (12, shiny::uiOutput(filns('viewButSlot')))
#
# ),
#
# shiny::fluidRow (
# shiny::column (12, shiny::uiOutput(filns('filteringButSlot')))
# )
#
#
# )
# })
#
#
# output$mainscreen<- shiny::renderUI ({
# shiny::tabsetPanel (
# shiny::tabPanel('reads length',
# shiny::plotOutput(filns('LEhist')),
# plotOutput(filns ('degSelfGraph'))
# )
# # ,tabPanel('direct filtering', textOutput(filns('difiVal')),
# # fluidRow(column(6,uiOutput(filns('MFCval'))),column(6,br(),br(),uiOutput(filns('MFCBut'))))
# # ,tableOutput (filns('sum2'))
# # )
# )
# })
#
#
#
#
# }
#
# )
#
#
# shiny::observeEvent(input$NBfilButton,{
# count.keep <- ave.ab >= aveLogCPM(5, lib.size=mean(data$totals))
# summary<-capture.output(as.data.frame(show (summary(count.keep))))
# summama<- matrix (nrow=2, ncol=4)
# summaryA<- strsplit (summary[1], split=' ')
# summaryA<- as.vector (summaryA[[1]])
# summaryA<- summaryA[summaryA != ""]
# summaryB<- strsplit (summary[2],split=' ')
# summaryB<- as.vector (summaryB[[1]])
# summaryB<- summaryB[summaryB != ""]
# print(summaryA)
# print(summaryB)
# summama[1,]<-summaryA
# summama[2,]<-summaryB
# print (summama)
# output$sum<- renderTable ({
# summama
# })
#
#
#
# })
#
# shiny::observeEvent (input$minFoldButton,{
# direct.keep <- direct$abundances > log2(5) + direct$threshold
# summary<-capture.output(as.data.frame(show (summary(direct.keep))))
# print (length(summary))
# # summaryC<- strsplit (summary[1], split=' ')
# # summaryC<- as.vector (summaryC[[1]])
# # summaryC<- summaryC[summaryC != ""]
# # lensumC<- length (summaryC)
# # summaryD<- strsplit (summary[2],split=' ')
# # summaryD<- as.vector (summaryD[[1]])
# # summaryD<- summaryD[summaryD != ""]
# # lensumD<- length (summaryD)
# # if (lensumC>=lensumD){
# # summama2<- matrix (nrow=2, ncol=lensumC)
# # } else {summama2<- matrix (nrow=2, ncol=lensumD)}
#
# # summama2[1,]<-summaryC
# # summama2[2,]<-summaryD
# output$sum2<- renderTable ({
# summama2<- tableFromConsole (summary(direct.keep), 1)
# })
# })
#
# shiny::observeEvent (input$viewButton, {
#
# ##diags<- getPairData (h5file, paramFil)
# print ('viewbutton is pressed')
# intra <- !is.na(diags$insert)
# min.inward <<- as.numeric(input$minInward)
# min.outward <<- as.numeric(input$minOutward)
#
# print (c('minInward', 'minOutward', min.inward, min.outward))
# #print (input$minOutwardSlot)
# #print (min.inward)
# #print (min.outward)
# llinsert <- values$llinsert #log2(diags$insert + 1L)
# intra <- !is.na(llinsert)
#
# breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
#
# values$inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
# values$outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
# #samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
# #samestr$counts <- samestr$counts/2
#
# # ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# # xmax <- max(inward$mids, outward$mids, samestr$mids)
# # xmin <- min(inward$mids, outward$mids, samestr$mids)
#
# ymax <- max(inward$counts, outward$counts)/1e6
# xmax <- max(inward$mids, outward$mids)
# xmin <- min(inward$mids, outward$mids)
#
#
# output$degSelfGraph <- shiny::renderPlot ({
#
# plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
# lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
# abline(v=log2(min.inward), col="darkgrey")
# lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
# abline(v=log2(min.outward), col="darkgrey", lty=2)
# #lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
# #legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
# legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
#
# })
#
#
# })
shiny::observeEvent(input$filteringButton,{ #deprecated button see filBut
print ('filtering.....START')
##ATTENZIONE: FILTRA SOLO A 600 DI max.frag
fileName<-paste0(anFolder$hisave,'Pre-Processing/',sub('.h5', '' ,values$h5_pa, fixed=TRUE),'_trimmed.h5')
if (min.inward==0){min.inward=NA}
if (min.outward==0){min.outward=NA}
filtered<- prunePairs (h5file, paramFil, file.out='trimmed.h5', max.frag=input$fragLength, min.inward, min.outward)
file.copy("./trimmed.h5", fileName, overwrite = TRUE)
file.remove("trimmed.h5")
#filtered<- prunePairs (h5file, paramFil, file.out=fileName, max.frag=input$fragLength, min.inward, min.outward)
#print(paste0(anFolder$hisave,'Pre-Processing/',sub('.h5', '' ,input$h5, fixed=TRUE),'_trimmed.h5','......CREATED'))
print(paste0(fileName,'......CREATED'))
print ('filtering.....END')
#saveParameters
filteringTable<-matrix(ncol=2, nrow=3)
filteringTable<-matrix(ncol=1, nrow=3)
rownames(filteringTable)<-c("maxFragLength", "minInward", "minOutward")
if (input$fixValue==FALSE){
mini=input$minInwardSlider
mino=input$minOutwardSlider
} else {
mini=input$minInward
mino=input$minOutward
}
filteringTable[,1]<-c(input$maxFrag, mini, mino)
print(paste("writing filtering parameters",pointin(wdPath, "Filtering", sys=TRUE)))
write.table(filteringTable, paste0(pointin(wdPath, "Filtering", sys=TRUE),"parameter.tsv"), sep="\t", quote=FALSE, col.names=FALSE)
print("filtering parameters writted")
output$mainscreen<- renderUI ({
wellPanel (helpText('filtering Done, please if you want see results load trimmed h5 file'))
})
})
shiny::observeEvent(input$minInward,{
##diags<- getPairData (h5file, paramFil)
#print ('viewbutton is pressed')
intra <- !is.na(diags$insert)
min.inward <- as.numeric(input$minInward)
min.outward <- as.numeric(input$minOutward)
print (c('minInward', 'minOutward', min.inward, min.outward))
#print (input$minOutwardSlot)
#print (min.inward)
#print (min.outward)
llinsert <- values$llinsert #log2(diags$insert + 1L)
intra <- !is.na(llinsert)
breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
samestr$counts <- samestr$counts/2
# ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# xmax <- max(inward$mids, outward$mids, samestr$mids)
# xmin <- min(inward$mids, outward$mids, samestr$mids)
ymax <- max(inward$counts, outward$counts)/1e6
xmax <- max(inward$mids, outward$mids)
xmin <- min(inward$mids, outward$mids)
output$degSelfGraph <- shiny::renderPlot ({
plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(min.inward), col="darkgrey")
lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
abline(v=log2(min.outward), col="darkgrey", lty=2)
#lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
#legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
legend("topright", c("inward", "outward"), col=c("darkgreen", "red"), lwd=2)
})
})
shiny::observeEvent(input$minOutward, {
##diags<- getPairData (h5file, paramFil)
#print ('viewbutton is pressed')
intra <- !is.na(diags$insert)
#min.inward <<- as.numeric(input$minInward)
#min.outward <<- as.numeric(input$minOutward)
#print (c('minInward', 'minOutward', min.inward, min.outward))
#print (input$minOutwardSlot)
#print (min.inward)
#print (min.outward)
llinsert <- values$llinsert #log2(diags$insert + 1L)
intra <- !is.na(llinsert)
breaks <- values$breaks2 #seq(min(llinsert[intra]), max(llinsert[intra]), length.out=30)
inward <- values$inward2 #hist(llinsert[diags$orientation==1L], plot=FALSE, breaks=breaks)
outward <- values$outward2 #hist(llinsert[diags$orientation==2L] ,plot=FALSE, breaks=breaks)
samestr <- values$samestr2 #hist(llinsert[diags$orientation==0L | diags$orientation==3L], plot=FALSE, breaks=breaks)
samestr$counts <- samestr$counts/2
# ymax <- max(inward$counts, outward$counts, samestr$counts)/1e6
# xmax <- max(inward$mids, outward$mids, samestr$mids)
# xmin <- min(inward$mids, outward$mids, samestr$mids)
ymax <- max(inward$counts, outward$counts)/1e6
xmax <- max(inward$mids, outward$mids)
xmin <- min(inward$mids, outward$mids)
filPlot <- shiny::renderPlot({
#jpeg(file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"filplot.jpeg"))
plot(0,0,type="n", xlim=c(xmin, xmax), ylim=c(0, ymax), xlab=expression(log[2]~"[insert size (bp)]"), ylab="Frequency (millions)")
lines(inward$mids, inward$counts/1e6, col="darkgreen", lwd=2)
abline(v=log2(min.inward), col="darkgrey")
lines(outward$mids, outward$counts/1e6, col="red", lwd=2)
abline(v=log2(min.outward), col="darkgrey", lty=2)
#lines(samestr$mids, samestr$counts/1e6, col="blue", lwd=2)
#legend("topright", c("inward", "outward", "same"), col=c("darkgreen", "red", "blue"), lwd=2)
legend("topright", c("inward", "outward"), col=c("darkgreen", "red", "blue"), lwd=2)
#dev.off()
})
#save (filPlot, file=paste0(pointin(wdPath, "Pre-Processing", sys=TRUE),"filplot.Robj"))
output$degSelfGraph<- filPlot
})
}
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