R/vMod4_EpigeneticFeatures.R
In lucidif/HiCeekR: GUI for Hi-C data analysis
##pca_postProcessing
#' pca_postProcessing_UI
#'
#' @param id
#' @param label
#'
#' @return
#' @keywords internal
#'
#' @examples
EpigeneticFeatures_UI <- function (id, label='epiFea' ){
pcaNS<- shiny::NS (id)
shiny::fluidPage(
shiny::tabsetPanel ( #pcaNS('tabSetPCA'),
shiny::tabPanel( 'EpigeneticFeatures'
,shiny::wellPanel (
shiny::fluidRow (
shiny::column (12,
shiny::selectInput (pcaNS('dataType'),
label='data type',
choices = c('bint.tsv'
,'epiCounts'
#,'EpiCounts.bed'
)
)
)
),
shiny::fluidRow (
shiny::column (8,
#fileInput (pcaNS('binTable'), label='select binTable file')
#selectFile (pcaNS('binTable'), path=pointin (wdPath, 'Binning') ,label='select binTable file', subset=TRUE, pattern='.bint')
shiny::uiOutput (pcaNS('selFileSlot'))
)
#column (3,
# textInput (pcaNS('name'), label='name')
# )
#,
,
shiny::column (2,
shiny::br(),
shiny::br(),
shiny::actionButton (pcaNS('genPcaMod'),
label='generate')
)
#,
#column(1,br(),
# uiOutput (pcaNS('finish'))
# )
),
shiny::uiOutput (pcaNS('secondRow')),
shiny::uiOutput (pcaNS('thirdRow')),
shiny::fluidRow (
shiny::dataTableOutput(pcaNS('tableScreen'))
#dataTableOutput(pcaNS('tableScreen'))
)
)
)
# ,shiny::tabPanel ('PCA'
#
# ,shiny::wellPanel (
#
# shiny::fluidRow (
#
# shiny::column (10,
#
# #fileInput (pcaNS ('pcaTableLoaded'), 'pca table')
# #selectFile (pcaNS('pcaTableLoaded'), path=pointin(wdPath, 'PCA') ,'pca table', subset=TRUE, pattern='.epiCounts.tsv')
# shiny::uiOutput (pcaNS('pcaTableSlot'))
# ),
#
# shiny::column (2, shiny::br(),
#
# shiny::actionButton (pcaNS('startPca'),
# 'start PCA')
#
# )
#
# ),
#
#
# shiny::fluidRow(
#
# shiny::column (12, plotOutput(pcaNS('pcaPlot')) )
#
# ),
#
# shiny::fluidRow (
#
# shiny::column (12,
# shiny::uiOutput(pcaNS('selectPCui')) )
#
# )
#
# )
#
# )
)
)
}
#' pca_postProcessing_Server
#'
#' @param input
#' @param output
#' @param session
#' @param stringsAsFactors
#' @param wdPath
#'
#' @return
#' @keywords internal
#'
#' @examples
EpigeneticFeatures_Server <- function (input, output, session, stringsAsFactors,
wdPath
){
print ("start PCA module")
#plusval<-0
pcaNServer<- session$ns
#require ('Rsamtools')
##reactiveValue
#tPcaRea<- reactiveValues(tP='none')
Reac<- shiny::reactiveValues(tP='none', S_pcaMod='none', S_exportThis='none') #non c'è bisogno che definisci prima la variabile reactiveValues() e poi definisci dopo
print ("pcaTabSlot render")
output$pcaTableSlot<- shiny::renderUI ({
#selectFile (pcaNServer('pcaTableLoaded'), path=pointin(wdPath, 'PCA') ,'.hkr.pca file', subset=TRUE, pattern='.hkr.pca')
shiny::fileInput(pcaNServer('pcaTableLoaded'), label="pca file")
})
print ("start observer")
shiny::observeEvent(input$bamLoadPath,{
print("bamLoadPath")
print (input$bamLoadPath)
if ( input$bamLoadPath!="please select file"){
print(paste0("EpiPath:",pointin(wdPath,'Epi'),input$bamLoadPath))
#Reac$bedTab<-read.table(paste0(pointin(wdPath,'Epi'),input$bamLoadPath), sep="\t")
#rownames(Reac$bedTab)<-rep(paste0(Reac$bedTab[,1],":",Reac$bedTab[,2],"-",Reac$bedTab[,3]))
#Reac$bedTab<-Reac$bedTab[,-c(1:4)]
# output$colSelectorSlot<-shiny::renderUI({
# shiny::selectInput(pcaNServer('colSelector'),
# label="select column",
# choices=c(1:length(Reac$bedTab[1,]))
# )
# })
#bedTabTT<<-bedTab
}
})
shiny::observeEvent (input$genPcaMod,{
print ('generate start')
#plusval<- plusval+1
#nameD<- paste0('data', plusval)
#print (nameD)
#pcaMod<-Reac$A_pcaMod
if (input$dataType=='bint.tsv'){
bintabPath<- paste0 ( pointin(wdPath,'Binning'), input$binTable)
Reac$pcaMod<-pcaMatrixModel(bintabPath)
Reac$A_pcaMod<-Reac$pcaMod
}
if (input$dataType=='epiCounts'){
print ('in epiCounts')
bintabPath<- paste0 ( pointin(wdPath,'PCA'), input$epicTable)
Reac$pcaMod<-HCRread('',path=bintabPath)
Reac$A_pcaMod<-Reac$pcaMod
regionsN<- rownames (Reac$pcaMod)
regions<- matrix (ncol=1,nrow=length(regionsN))
rownames(regions)<-rownames (Reac$pcaMod)
colnames(regions)<-'regions'
regions[,1]<-regionsN
#View (regions)
rm (regionsN)
#print (regions)
Reac$pcaMod <- cbind (regions,Reac$pcaMod)
#View (pcaMod)
#print (pcaMod)
}
if (input$dataType=='EpiCounts.bed'){
#testTT<<-mergeBed(input$epicBed$datapath)
#testTTnames<<-input$epicBed$name
clnm<-gsub(".bed","",input$epicBed$name)
Reac$pcaMod<-mergeBed(input$epicBed$datapath, customHeader=TRUE,
header=clnm
)
regionsN<- rownames (Reac$pcaMod)
regions<- matrix (ncol=1,nrow=length(regionsN))
rownames(regions)<-rownames (Reac$pcaMod)
colnames(regions)<-'regions'
regions[,1]<-regionsN
#View (regions)
rm (regionsN)
#print (regions)
Reac$pcaMod <- cbind (regions,Reac$pcaMod)
}
#bintabPath<- paste0 ( pointin(wdPath,'Binning'), input$binTable)
#print (c('bintabPath'), bintabPath)
#tagAlignPath<- input$tagAlignFiles$datapath
#bintab<- read.table (bintabPath, sep='\t')
#pcaMod<-pcaMatrixModel(bintabPath)
#colnames(pcaMod)<-'regions'
#pcaModReduct<- pcaMod [1:10,]
print ('pcaMod.....Generated')
#print (c('typeof pcaMod', typeof(pcaMod)))
#View (pcaMod)
output$tableScreen<- shiny::renderDataTable ({
as.data.frame(Reac$pcaMod)
})#, colnames=TRUE)
output$secondRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column (5, shiny::br(), # esce quando selezioni bin table bin table
#textInput(pcaNServer('bamLoadPath'), label='bam file path')
# 3=================================================
selectFile (pcaNServer('bamLoadPath'),
path=pointin (wdPath,'Epi') ,
label='bam file path',
pattern=".bed"
)
),
shiny::column(3,
shiny::uiOutput(pcaNServer("colSelectorSlot"))
),
shiny::column (3, shiny::br(),
textInput (pcaNServer('name'), label='col name')
),
shiny::column (1, shiny::br(), shiny::br(),
shiny::checkboxInput(pcaNServer('addBox'), 'add', value=FALSE)
)
),
shiny::fluidRow(
shiny::column (3,
shiny::actionButton (pcaNServer('addData'),'add data')
)
)
)
})
if (Reac$pcaMod[1,]>=2){
output$thirdRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column(4,
shiny::textInput(pcaNServer('fileName'),'file name') ),
shiny::column(2,shiny::br(),
shiny::actionButton (pcaNServer('export'), 'export table')),
shiny::column(2,shiny::br(),
shiny::checkboxInput(pcaNServer("checkNorm"), label = "Normalization", value = FALSE)),
shiny::column(4,
shiny::uiOutput(pcaNServer('normTypeIn')) )
),
shiny::fluidRow(shiny::column(12,
shiny::uiOutput(pcaNServer('normOpt_slot')) ))
)
})
}
Reac$A_pcaMod<-Reac$pcaMod
})
shiny::observeEvent(input$addData,{ #============addData 2 prima volta
print ("addData 2")
Reac$pcaMod<-Reac$A_pcaMod
print ('add pressed')
output$secondRow<- shiny::renderUI({
shiny::wellPanel (shiny::h5('please wait', width='100%'))
})
print ('please wait')
if (input$dataType=='bint.tsv'){
pcaTable<-bamPca(paste0 ( pointin(wdPath,'Binning'),
input$binTable),
paste0 ( pointin(wdPath,'Epi'),
input$bamLoadPath)
, Reac$pcaMod, columnName=input$name, add=input$addBox )
print (paste0(pointin(wdPath,'Epi'),input$bamLoadPath))
# bedLoad<-read.table(paste0 ( pointin(wdPath,'Epi'),
# input$bamLoadPath),
# sep="\t"
# )
#bedLoadTT<<-bedLoad
#tabTT<<-merge(Reac$pcaMod, paste0 ( pointin(wdPath,'Epi'), input$bamLoadPath))
# )
if (input$addBox==TRUE){
} else {#input$addBox==FALSE
}
}
if (input$dataType=='epiCounts'){
pcaTable<-bamPca (paste0 ( pointin(wdPath,'Binning'),
input$binTableM),
paste0 ( pointin(wdPath,'Epi'),
input$bamLoadPath)
, pcaMod, columnName=input$name,
add=input$addBox )
}
# pcaTable<-bamPca (paste0 ( pointin(wdPath,'Binning'), input$binTable), paste0 ( pointin(wdPath,'Epi'), input$bamLoadPath)
# , pcaMod, columnName=input$name, add=input$addBox )
print ('bamPca.....OK')
Reac$pcaMod<-pcaTable
output$tableScreen<- renderDataTable ({
as.data.frame(Reac$pcaMod)
})
output$thirdRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column(4,
shiny::textInput(pcaNServer('fileName'),'file name') ),
shiny::column(2,shiny::br(),
shiny::actionButton (pcaNServer('export'),
'export table')),
shiny::column(2,shiny::br(),
shiny::checkboxInput(pcaNServer("checkNorm"),
label = "Normalization",
value = FALSE)),
shiny::column(4, shiny::uiOutput(pcaNServer('normTypeIn')) )
),
shiny::fluidRow(
shiny::column(12,
shiny::uiOutput(pcaNServer('normOpt_slot')) ))
)
})
output$secondRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column (5,
#textInput(pcaNServer('bamLoadPath'), label='bam file path')
# 4 =======================================
selectFile (pcaNServer('bamLoadPath'),
path=pointin (wdPath,'Epi') ,
label='bad file path',
pattern=".bed"
)
),
shiny::column(3,
shiny::uiOutput(pcaNServer("colSelectorSlot"))
),
shiny::column (3, shiny::br(),
shiny::textInput (pcaNServer('name'), label='col name')
),
shiny::column (1, shiny::br(), shiny::br(),
shiny::checkboxInput(pcaNServer('addBox'),
'add',
value=FALSE)
)
),
shiny::fluidRow(
shiny::column (3,
shiny::actionButton (pcaNServer('addData'),'add data')
)
)
)
})
Reac$A_pcaMod<-Reac$pcaMod
})
shiny::observeEvent (input$export,{
print ('export table start')
nameToAssign<-paste0(input$fileName,'.epiCounts')
#write.table ( pcaMod , nameF, sep='\t', quote=FALSE )
pcaMod<-Reac$A_pcaMod
#normalization
if (input$checkNorm==TRUE){
if (input$normType=='RPM'){
# epiNorm<-pcaMod
for (i in 2:length (Reac$pcaMod[1,])) {
somma<-sum (as.numeric(Reac$pcaMod[,i]))
ratio<-somma/1000000
Reac$pcaMod[,i] <- rep (as.numeric(Reac$pcaMod[,i])/ratio)
}
} else {
if (input$normType=='byInput'){
print ('byInput norm start')
#pcaModTT2<<-pcaMod
pcaMod2<-Reac$pcaMod[,-which(colnames(pcaMod) %in% input$choiceInput)] #così puoi rimuovere la colonna specifica
#pcaMod2<-pcaMod[,-which(colnames(TTpcaMod) %in% 'H4K20me1')] #così puoi rimuovere la colonna specifica
pcaMod3= as.matrix(Reac$pcaMod[,input$choiceInput]) #generi matrice dei soli input
m<-sum(as.numeric(pcaMod3))
for (i in 2:length(pcaMod2[1,])){
n<-sum(as.numeric(pcaMod2[,i]))
pcaMod2[,i]<- rep ( ((as.numeric(pcaMod2[,i]))*(as.numeric(m))) / ( (as.numeric(pcaMod3[,1])) * (as.numeric(n)) ) )
}
Reac$pcaMod<-pcaMod2
}
}
}
Reac$A_pcaMod<-Reac$pcaMod
HCRwrite (Reac$pcaMod, nameToAssign , path=pointin(wdPath, 'PCA') , quote=FALSE )
output$pcaTableSlot<- shiny::renderUI ({
# selectFile (pcaNServer('pcaTableLoaded'),
# path=pointin(wdPath, 'PCA') ,
# 'pca table',
# subset=TRUE,
# pattern='.epiCounts.tsv')
shiny::fileInput(pcaNServer('pcaTableLoaded'),
lebel="pca table"
)
})
print ('table export SUCCESS')
})
shiny::observeEvent(input$startPca,{
print ('.....start pca.....')
# pcaTable3<- read.table (paste0 (pointin(wdPath,'PCA'),
# #input$pcaTableLoaded
# input$pcaTableLoaded$datapa
# ),
# sep='\t',
# header=TRUE)
pcaTable3<- read.table (input$pcaTableLoaded$datapath, sep='\t', header=TRUE)
columnsNames<- pcaTable3[,1]
pcaTable3<- pcaTable3[,-1]
#View (pcaTable3)
#print ('readTable.....OK')
zScoreTable<- zScore (pcaTable3)
#print ('zscore.....OK')
#zScoreTable[is.na(zScoreTable)] <- 0
tTable3<- t(zScoreTable)
colnames (tTable3)<-columnsNames
#View (tTable3)
print ('traspose.....OK')
tPca<- prcomp (tTable3)
Reac$tP<-tPca$rotation
#print (tPca)
#View (tPca)
#regions <-c('regions',colnames(tTable3))
regions <-colnames(tTable3)
exportThis<- cbind (regions,tPca$rotation)
Reac$S_exportThis<-exportThis
#View (exportThis)
print ('pca.....OK')
pcNum<- length (tPca$rotation[1,])
print (c('pcNum.....OK', pcNum))
output$pcaPlot <- shiny::renderPlot ({
barplot(tPca$rotation[1:100,1])
})
print ('plot.....OK')
output$selectPCui<- shiny::renderUI ({
shiny::wellPanel (
shiny::fluidRow (
shiny::column (4,
shiny::selectInput(pcaNServer("select"),
label = h5("PC to show"),
choices = 1:pcNum,
selected = 1)
),
shiny::column (4,
shiny::textInput (pcaNServer("exportEvName"),
label=h5('File Name'),
value =('evToPlot'))
),
shiny::column (4, shiny::br(), shiny::br(),
shiny::actionButton (pcaNServer("exportEvButton"),
label='Save')
)
)
)
# selectInput(pcaNServer("select"), label = h5("PC to show"),
# choices = 1:pcNum,
# selected = 1)
})
# observeEvent (input$exportEvButton, {
# print ('PCA esport start')
# tabName<-paste0 (input$exportEvName)
# #write.table (tPca$rotation, tabName, sep= "\t", quote=FALSE )
# # View (tPca$rotation)
# # print (paste0 (wdPath, 'Post-Processing'))
# HCRwrite (exportThis, tabName, path=pointin (wdPath,'PCA') , quote=FALSE)
#
# })
})
shiny::observeEvent (input$exportEvButton, {
print ('PCA export start')
tabName<-paste0 (input$exportEvName)
#write.table (tPca$rotation, tabName, sep= "\t", quote=FALSE )
# View (tPca$rotation)
# print (paste0 (wdPath, 'Post-Processing'))
HCRwrite (Reac$S_exportThis, tabName,
path=pointin (wdPath,'PCA') ,
quote=FALSE)
})
shiny::observeEvent (input$select, {
pc<- as.numeric(input$select)
print (Reac$tP[1:100,pc])
output$pcaPlot <- shiny::renderPlot ({
barplot(Reac$tP[1:100,pc])
})
})
shiny::observeEvent (input$checkNorm,{
if (input$checkNorm==TRUE) {
output$normTypeIn<- shiny::renderUI ({
shiny::wellPanel (
shiny::selectInput (pcaNServer ('normType'),
label='type',
choices=c('RPM','byInput'),
selected='RPM'))
})
# if (input$normType=='RPM'){
# # output$normOpt_slot<- renderUI ({
# #
# # wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
# #
# # })
# } else {
#
# if (input$normType=='byInput'){
# pcaMod<-Reac$A_pcaMod
# output$normOpt_slot<- renderUI ({
#
# #wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
# fluidRow (column(12,
#
# selectInput(pcaNServer('choiceInput'), label='Input Column', choices=colnames(pcaMod))
#
# ))
#
# })
# }
#
# }
} else
output$normTypeIn<- shiny::renderUI ({
shiny::wellPanel ()
})
{
}
})
shiny::observeEvent (input$dataType,{
if (input$dataType=='bint.tsv'){
output$selFileSlot <- shiny::renderUI ({
selectFile (pcaNServer('binTable'),
path=pointin (wdPath, 'Binning') ,
label='select binTable file',
subset=TRUE,
pattern='.bint')
})
}
if (input$dataType=='epiCounts'){
output$selFileSlot <- shiny::renderUI ({
shiny::wellPanel (
# shiny::fluidRow(
# selectFile (pcaNServer('binTableM'),
# path=pointin (wdPath, 'Binning') ,
# label='select binTable file',
# subset=TRUE,
# pattern='.bint')
# ),
shiny::fluidRow(
selectFile (pcaNServer('epicTable'),
path=pointin (wdPath, 'PCA') ,
label='select epiCounts file',
subset=TRUE,
pattern='.epiCounts.tsv')
)
)
})
}
if (input$dataType=="EpiCounts.bed"){
output$selFileSlot <- shiny::renderUI ({
shiny::wellPanel (
# shiny::fluidRow(
# selectFile (pcaNServer('binTableM'),
# path=pointin (wdPath, 'Binning') ,
# label='select binTable file',
# subset=TRUE,
# pattern='.bint')
# ),
shiny::fluidRow(
shiny::fileInput(
pcaNServer('epicBed'),
label='select EpiCounts.bed',
multiple=TRUE
)
# selectFile (pcaNServer('epicTable'),
# path=pointin (wdPath, 'PCA') ,
# label='select epiCounts file',
# subset=TRUE,
# pattern='.epiCounts.tsv')
)
)
})
}
})
shiny::observeEvent (input$normType,{
if (input$normType=='RPM'){
# output$normOpt_slot<- renderUI ({
#
# wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
#
# })
} else {
if (input$normType=='byInput'){
Reac$pcaMod<-Reac$A_pcaMod
output$normOpt_slot<- shiny::renderUI ({
#wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
shiny::fluidRow (
shiny::column(12,
shiny::selectInput(pcaNServer('choiceInput'),
label='Input Column',
choices=colnames(Reac$pcaMod)[2:length(colnames(Reac$pcaMod))])
))
})
}
}
})
}
lucidif/HiCeekR documentation built on Jan. 31, 2021, 10:30 p.m.
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##pca_postProcessing
#' pca_postProcessing_UI
#'
#' @param id
#' @param label
#'
#' @return
#' @keywords internal
#'
#' @examples
EpigeneticFeatures_UI <- function (id, label='epiFea' ){
pcaNS<- shiny::NS (id)
shiny::fluidPage(
shiny::tabsetPanel ( #pcaNS('tabSetPCA'),
shiny::tabPanel( 'EpigeneticFeatures'
,shiny::wellPanel (
shiny::fluidRow (
shiny::column (12,
shiny::selectInput (pcaNS('dataType'),
label='data type',
choices = c('bint.tsv'
,'epiCounts'
#,'EpiCounts.bed'
)
)
)
),
shiny::fluidRow (
shiny::column (8,
#fileInput (pcaNS('binTable'), label='select binTable file')
#selectFile (pcaNS('binTable'), path=pointin (wdPath, 'Binning') ,label='select binTable file', subset=TRUE, pattern='.bint')
shiny::uiOutput (pcaNS('selFileSlot'))
)
#column (3,
# textInput (pcaNS('name'), label='name')
# )
#,
,
shiny::column (2,
shiny::br(),
shiny::br(),
shiny::actionButton (pcaNS('genPcaMod'),
label='generate')
)
#,
#column(1,br(),
# uiOutput (pcaNS('finish'))
# )
),
shiny::uiOutput (pcaNS('secondRow')),
shiny::uiOutput (pcaNS('thirdRow')),
shiny::fluidRow (
shiny::dataTableOutput(pcaNS('tableScreen'))
#dataTableOutput(pcaNS('tableScreen'))
)
)
)
# ,shiny::tabPanel ('PCA'
#
# ,shiny::wellPanel (
#
# shiny::fluidRow (
#
# shiny::column (10,
#
# #fileInput (pcaNS ('pcaTableLoaded'), 'pca table')
# #selectFile (pcaNS('pcaTableLoaded'), path=pointin(wdPath, 'PCA') ,'pca table', subset=TRUE, pattern='.epiCounts.tsv')
# shiny::uiOutput (pcaNS('pcaTableSlot'))
# ),
#
# shiny::column (2, shiny::br(),
#
# shiny::actionButton (pcaNS('startPca'),
# 'start PCA')
#
# )
#
# ),
#
#
# shiny::fluidRow(
#
# shiny::column (12, plotOutput(pcaNS('pcaPlot')) )
#
# ),
#
# shiny::fluidRow (
#
# shiny::column (12,
# shiny::uiOutput(pcaNS('selectPCui')) )
#
# )
#
# )
#
# )
)
)
}
#' pca_postProcessing_Server
#'
#' @param input
#' @param output
#' @param session
#' @param stringsAsFactors
#' @param wdPath
#'
#' @return
#' @keywords internal
#'
#' @examples
EpigeneticFeatures_Server <- function (input, output, session, stringsAsFactors,
wdPath
){
print ("start PCA module")
#plusval<-0
pcaNServer<- session$ns
#require ('Rsamtools')
##reactiveValue
#tPcaRea<- reactiveValues(tP='none')
Reac<- shiny::reactiveValues(tP='none', S_pcaMod='none', S_exportThis='none') #non c'è bisogno che definisci prima la variabile reactiveValues() e poi definisci dopo
print ("pcaTabSlot render")
output$pcaTableSlot<- shiny::renderUI ({
#selectFile (pcaNServer('pcaTableLoaded'), path=pointin(wdPath, 'PCA') ,'.hkr.pca file', subset=TRUE, pattern='.hkr.pca')
shiny::fileInput(pcaNServer('pcaTableLoaded'), label="pca file")
})
print ("start observer")
shiny::observeEvent(input$bamLoadPath,{
print("bamLoadPath")
print (input$bamLoadPath)
if ( input$bamLoadPath!="please select file"){
print(paste0("EpiPath:",pointin(wdPath,'Epi'),input$bamLoadPath))
#Reac$bedTab<-read.table(paste0(pointin(wdPath,'Epi'),input$bamLoadPath), sep="\t")
#rownames(Reac$bedTab)<-rep(paste0(Reac$bedTab[,1],":",Reac$bedTab[,2],"-",Reac$bedTab[,3]))
#Reac$bedTab<-Reac$bedTab[,-c(1:4)]
# output$colSelectorSlot<-shiny::renderUI({
# shiny::selectInput(pcaNServer('colSelector'),
# label="select column",
# choices=c(1:length(Reac$bedTab[1,]))
# )
# })
#bedTabTT<<-bedTab
}
})
shiny::observeEvent (input$genPcaMod,{
print ('generate start')
#plusval<- plusval+1
#nameD<- paste0('data', plusval)
#print (nameD)
#pcaMod<-Reac$A_pcaMod
if (input$dataType=='bint.tsv'){
bintabPath<- paste0 ( pointin(wdPath,'Binning'), input$binTable)
Reac$pcaMod<-pcaMatrixModel(bintabPath)
Reac$A_pcaMod<-Reac$pcaMod
}
if (input$dataType=='epiCounts'){
print ('in epiCounts')
bintabPath<- paste0 ( pointin(wdPath,'PCA'), input$epicTable)
Reac$pcaMod<-HCRread('',path=bintabPath)
Reac$A_pcaMod<-Reac$pcaMod
regionsN<- rownames (Reac$pcaMod)
regions<- matrix (ncol=1,nrow=length(regionsN))
rownames(regions)<-rownames (Reac$pcaMod)
colnames(regions)<-'regions'
regions[,1]<-regionsN
#View (regions)
rm (regionsN)
#print (regions)
Reac$pcaMod <- cbind (regions,Reac$pcaMod)
#View (pcaMod)
#print (pcaMod)
}
if (input$dataType=='EpiCounts.bed'){
#testTT<<-mergeBed(input$epicBed$datapath)
#testTTnames<<-input$epicBed$name
clnm<-gsub(".bed","",input$epicBed$name)
Reac$pcaMod<-mergeBed(input$epicBed$datapath, customHeader=TRUE,
header=clnm
)
regionsN<- rownames (Reac$pcaMod)
regions<- matrix (ncol=1,nrow=length(regionsN))
rownames(regions)<-rownames (Reac$pcaMod)
colnames(regions)<-'regions'
regions[,1]<-regionsN
#View (regions)
rm (regionsN)
#print (regions)
Reac$pcaMod <- cbind (regions,Reac$pcaMod)
}
#bintabPath<- paste0 ( pointin(wdPath,'Binning'), input$binTable)
#print (c('bintabPath'), bintabPath)
#tagAlignPath<- input$tagAlignFiles$datapath
#bintab<- read.table (bintabPath, sep='\t')
#pcaMod<-pcaMatrixModel(bintabPath)
#colnames(pcaMod)<-'regions'
#pcaModReduct<- pcaMod [1:10,]
print ('pcaMod.....Generated')
#print (c('typeof pcaMod', typeof(pcaMod)))
#View (pcaMod)
output$tableScreen<- shiny::renderDataTable ({
as.data.frame(Reac$pcaMod)
})#, colnames=TRUE)
output$secondRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column (5, shiny::br(), # esce quando selezioni bin table bin table
#textInput(pcaNServer('bamLoadPath'), label='bam file path')
# 3=================================================
selectFile (pcaNServer('bamLoadPath'),
path=pointin (wdPath,'Epi') ,
label='bam file path',
pattern=".bed"
)
),
shiny::column(3,
shiny::uiOutput(pcaNServer("colSelectorSlot"))
),
shiny::column (3, shiny::br(),
textInput (pcaNServer('name'), label='col name')
),
shiny::column (1, shiny::br(), shiny::br(),
shiny::checkboxInput(pcaNServer('addBox'), 'add', value=FALSE)
)
),
shiny::fluidRow(
shiny::column (3,
shiny::actionButton (pcaNServer('addData'),'add data')
)
)
)
})
if (Reac$pcaMod[1,]>=2){
output$thirdRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column(4,
shiny::textInput(pcaNServer('fileName'),'file name') ),
shiny::column(2,shiny::br(),
shiny::actionButton (pcaNServer('export'), 'export table')),
shiny::column(2,shiny::br(),
shiny::checkboxInput(pcaNServer("checkNorm"), label = "Normalization", value = FALSE)),
shiny::column(4,
shiny::uiOutput(pcaNServer('normTypeIn')) )
),
shiny::fluidRow(shiny::column(12,
shiny::uiOutput(pcaNServer('normOpt_slot')) ))
)
})
}
Reac$A_pcaMod<-Reac$pcaMod
})
shiny::observeEvent(input$addData,{ #============addData 2 prima volta
print ("addData 2")
Reac$pcaMod<-Reac$A_pcaMod
print ('add pressed')
output$secondRow<- shiny::renderUI({
shiny::wellPanel (shiny::h5('please wait', width='100%'))
})
print ('please wait')
if (input$dataType=='bint.tsv'){
pcaTable<-bamPca(paste0 ( pointin(wdPath,'Binning'),
input$binTable),
paste0 ( pointin(wdPath,'Epi'),
input$bamLoadPath)
, Reac$pcaMod, columnName=input$name, add=input$addBox )
print (paste0(pointin(wdPath,'Epi'),input$bamLoadPath))
# bedLoad<-read.table(paste0 ( pointin(wdPath,'Epi'),
# input$bamLoadPath),
# sep="\t"
# )
#bedLoadTT<<-bedLoad
#tabTT<<-merge(Reac$pcaMod, paste0 ( pointin(wdPath,'Epi'), input$bamLoadPath))
# )
if (input$addBox==TRUE){
} else {#input$addBox==FALSE
}
}
if (input$dataType=='epiCounts'){
pcaTable<-bamPca (paste0 ( pointin(wdPath,'Binning'),
input$binTableM),
paste0 ( pointin(wdPath,'Epi'),
input$bamLoadPath)
, pcaMod, columnName=input$name,
add=input$addBox )
}
# pcaTable<-bamPca (paste0 ( pointin(wdPath,'Binning'), input$binTable), paste0 ( pointin(wdPath,'Epi'), input$bamLoadPath)
# , pcaMod, columnName=input$name, add=input$addBox )
print ('bamPca.....OK')
Reac$pcaMod<-pcaTable
output$tableScreen<- renderDataTable ({
as.data.frame(Reac$pcaMod)
})
output$thirdRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column(4,
shiny::textInput(pcaNServer('fileName'),'file name') ),
shiny::column(2,shiny::br(),
shiny::actionButton (pcaNServer('export'),
'export table')),
shiny::column(2,shiny::br(),
shiny::checkboxInput(pcaNServer("checkNorm"),
label = "Normalization",
value = FALSE)),
shiny::column(4, shiny::uiOutput(pcaNServer('normTypeIn')) )
),
shiny::fluidRow(
shiny::column(12,
shiny::uiOutput(pcaNServer('normOpt_slot')) ))
)
})
output$secondRow<- shiny::renderUI ({
shiny::wellPanel(
shiny::fluidRow(
shiny::column (5,
#textInput(pcaNServer('bamLoadPath'), label='bam file path')
# 4 =======================================
selectFile (pcaNServer('bamLoadPath'),
path=pointin (wdPath,'Epi') ,
label='bad file path',
pattern=".bed"
)
),
shiny::column(3,
shiny::uiOutput(pcaNServer("colSelectorSlot"))
),
shiny::column (3, shiny::br(),
shiny::textInput (pcaNServer('name'), label='col name')
),
shiny::column (1, shiny::br(), shiny::br(),
shiny::checkboxInput(pcaNServer('addBox'),
'add',
value=FALSE)
)
),
shiny::fluidRow(
shiny::column (3,
shiny::actionButton (pcaNServer('addData'),'add data')
)
)
)
})
Reac$A_pcaMod<-Reac$pcaMod
})
shiny::observeEvent (input$export,{
print ('export table start')
nameToAssign<-paste0(input$fileName,'.epiCounts')
#write.table ( pcaMod , nameF, sep='\t', quote=FALSE )
pcaMod<-Reac$A_pcaMod
#normalization
if (input$checkNorm==TRUE){
if (input$normType=='RPM'){
# epiNorm<-pcaMod
for (i in 2:length (Reac$pcaMod[1,])) {
somma<-sum (as.numeric(Reac$pcaMod[,i]))
ratio<-somma/1000000
Reac$pcaMod[,i] <- rep (as.numeric(Reac$pcaMod[,i])/ratio)
}
} else {
if (input$normType=='byInput'){
print ('byInput norm start')
#pcaModTT2<<-pcaMod
pcaMod2<-Reac$pcaMod[,-which(colnames(pcaMod) %in% input$choiceInput)] #così puoi rimuovere la colonna specifica
#pcaMod2<-pcaMod[,-which(colnames(TTpcaMod) %in% 'H4K20me1')] #così puoi rimuovere la colonna specifica
pcaMod3= as.matrix(Reac$pcaMod[,input$choiceInput]) #generi matrice dei soli input
m<-sum(as.numeric(pcaMod3))
for (i in 2:length(pcaMod2[1,])){
n<-sum(as.numeric(pcaMod2[,i]))
pcaMod2[,i]<- rep ( ((as.numeric(pcaMod2[,i]))*(as.numeric(m))) / ( (as.numeric(pcaMod3[,1])) * (as.numeric(n)) ) )
}
Reac$pcaMod<-pcaMod2
}
}
}
Reac$A_pcaMod<-Reac$pcaMod
HCRwrite (Reac$pcaMod, nameToAssign , path=pointin(wdPath, 'PCA') , quote=FALSE )
output$pcaTableSlot<- shiny::renderUI ({
# selectFile (pcaNServer('pcaTableLoaded'),
# path=pointin(wdPath, 'PCA') ,
# 'pca table',
# subset=TRUE,
# pattern='.epiCounts.tsv')
shiny::fileInput(pcaNServer('pcaTableLoaded'),
lebel="pca table"
)
})
print ('table export SUCCESS')
})
shiny::observeEvent(input$startPca,{
print ('.....start pca.....')
# pcaTable3<- read.table (paste0 (pointin(wdPath,'PCA'),
# #input$pcaTableLoaded
# input$pcaTableLoaded$datapa
# ),
# sep='\t',
# header=TRUE)
pcaTable3<- read.table (input$pcaTableLoaded$datapath, sep='\t', header=TRUE)
columnsNames<- pcaTable3[,1]
pcaTable3<- pcaTable3[,-1]
#View (pcaTable3)
#print ('readTable.....OK')
zScoreTable<- zScore (pcaTable3)
#print ('zscore.....OK')
#zScoreTable[is.na(zScoreTable)] <- 0
tTable3<- t(zScoreTable)
colnames (tTable3)<-columnsNames
#View (tTable3)
print ('traspose.....OK')
tPca<- prcomp (tTable3)
Reac$tP<-tPca$rotation
#print (tPca)
#View (tPca)
#regions <-c('regions',colnames(tTable3))
regions <-colnames(tTable3)
exportThis<- cbind (regions,tPca$rotation)
Reac$S_exportThis<-exportThis
#View (exportThis)
print ('pca.....OK')
pcNum<- length (tPca$rotation[1,])
print (c('pcNum.....OK', pcNum))
output$pcaPlot <- shiny::renderPlot ({
barplot(tPca$rotation[1:100,1])
})
print ('plot.....OK')
output$selectPCui<- shiny::renderUI ({
shiny::wellPanel (
shiny::fluidRow (
shiny::column (4,
shiny::selectInput(pcaNServer("select"),
label = h5("PC to show"),
choices = 1:pcNum,
selected = 1)
),
shiny::column (4,
shiny::textInput (pcaNServer("exportEvName"),
label=h5('File Name'),
value =('evToPlot'))
),
shiny::column (4, shiny::br(), shiny::br(),
shiny::actionButton (pcaNServer("exportEvButton"),
label='Save')
)
)
)
# selectInput(pcaNServer("select"), label = h5("PC to show"),
# choices = 1:pcNum,
# selected = 1)
})
# observeEvent (input$exportEvButton, {
# print ('PCA esport start')
# tabName<-paste0 (input$exportEvName)
# #write.table (tPca$rotation, tabName, sep= "\t", quote=FALSE )
# # View (tPca$rotation)
# # print (paste0 (wdPath, 'Post-Processing'))
# HCRwrite (exportThis, tabName, path=pointin (wdPath,'PCA') , quote=FALSE)
#
# })
})
shiny::observeEvent (input$exportEvButton, {
print ('PCA export start')
tabName<-paste0 (input$exportEvName)
#write.table (tPca$rotation, tabName, sep= "\t", quote=FALSE )
# View (tPca$rotation)
# print (paste0 (wdPath, 'Post-Processing'))
HCRwrite (Reac$S_exportThis, tabName,
path=pointin (wdPath,'PCA') ,
quote=FALSE)
})
shiny::observeEvent (input$select, {
pc<- as.numeric(input$select)
print (Reac$tP[1:100,pc])
output$pcaPlot <- shiny::renderPlot ({
barplot(Reac$tP[1:100,pc])
})
})
shiny::observeEvent (input$checkNorm,{
if (input$checkNorm==TRUE) {
output$normTypeIn<- shiny::renderUI ({
shiny::wellPanel (
shiny::selectInput (pcaNServer ('normType'),
label='type',
choices=c('RPM','byInput'),
selected='RPM'))
})
# if (input$normType=='RPM'){
# # output$normOpt_slot<- renderUI ({
# #
# # wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
# #
# # })
# } else {
#
# if (input$normType=='byInput'){
# pcaMod<-Reac$A_pcaMod
# output$normOpt_slot<- renderUI ({
#
# #wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
# fluidRow (column(12,
#
# selectInput(pcaNServer('choiceInput'), label='Input Column', choices=colnames(pcaMod))
#
# ))
#
# })
# }
#
# }
} else
output$normTypeIn<- shiny::renderUI ({
shiny::wellPanel ()
})
{
}
})
shiny::observeEvent (input$dataType,{
if (input$dataType=='bint.tsv'){
output$selFileSlot <- shiny::renderUI ({
selectFile (pcaNServer('binTable'),
path=pointin (wdPath, 'Binning') ,
label='select binTable file',
subset=TRUE,
pattern='.bint')
})
}
if (input$dataType=='epiCounts'){
output$selFileSlot <- shiny::renderUI ({
shiny::wellPanel (
# shiny::fluidRow(
# selectFile (pcaNServer('binTableM'),
# path=pointin (wdPath, 'Binning') ,
# label='select binTable file',
# subset=TRUE,
# pattern='.bint')
# ),
shiny::fluidRow(
selectFile (pcaNServer('epicTable'),
path=pointin (wdPath, 'PCA') ,
label='select epiCounts file',
subset=TRUE,
pattern='.epiCounts.tsv')
)
)
})
}
if (input$dataType=="EpiCounts.bed"){
output$selFileSlot <- shiny::renderUI ({
shiny::wellPanel (
# shiny::fluidRow(
# selectFile (pcaNServer('binTableM'),
# path=pointin (wdPath, 'Binning') ,
# label='select binTable file',
# subset=TRUE,
# pattern='.bint')
# ),
shiny::fluidRow(
shiny::fileInput(
pcaNServer('epicBed'),
label='select EpiCounts.bed',
multiple=TRUE
)
# selectFile (pcaNServer('epicTable'),
# path=pointin (wdPath, 'PCA') ,
# label='select epiCounts file',
# subset=TRUE,
# pattern='.epiCounts.tsv')
)
)
})
}
})
shiny::observeEvent (input$normType,{
if (input$normType=='RPM'){
# output$normOpt_slot<- renderUI ({
#
# wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
#
# })
} else {
if (input$normType=='byInput'){
Reac$pcaMod<-Reac$A_pcaMod
output$normOpt_slot<- shiny::renderUI ({
#wellPanel (selectInput (pcaNServer ('normType'), label='type', choices=c('RPM','byInput')))
shiny::fluidRow (
shiny::column(12,
shiny::selectInput(pcaNServer('choiceInput'),
label='Input Column',
choices=colnames(Reac$pcaMod)[2:length(colnames(Reac$pcaMod))])
))
})
}
}
})
}
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