www/comet/server.R
In TiphaineCMartin/coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
#Load library
library("shiny")
library("grid")
library("grDevices")
library("rtracklayer")
library("biomaRt")
library("Gviz")
library("ggbio")
library("colortools")
library("hash")
library("psych")
library("coMET")
# By default, the file size limit is 5MB. It can be changed by
# setting this option. Here we'll raise limit to 9MB.
options(shiny.maxRequestSize = 9*1024^2)
shinyServer(function(input, output,session) {
filenameImage <- NULL
#### CREATE LIST OF ELEMENTS
output$listCpG <- renderUI ({
cat(file=stderr(), "Create the lsit of CpG sites \n")
inFile1 <- input$datafile
listCpG <- c("")
if (is.null(inFile1)) {
listCpG <- c("")
sizeListCpG <- length(listCpG) - 1
# print(sizeListCpG,digit= 10)
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
listDI<-dataInput[,1]
listCpG <- sapply(listDI,as.character)
sizeListCpG <- length(listCpG)
#print(sizeListCpG,digit=10);
}
cat(file=stderr(), "Number of CpG sites", sizeListCpG, "CpG sites\n")
selectInput("reflistCpG", paste ("among",sizeListCpG) ,
choices = listCpG,selected = NULL,
multiple = FALSE)
})
## Start position
output$startCpG <- renderUI ({
cat(file=stderr(), "Define start position \n")
inFile1 <- input$datafile
startCpG <- 1
if (is.null(inFile1)) {
p('Start position to visualise (nt):')
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
if (input$dataformat == 'region' | input$dataformat == 'region_asso') {
startCpG <- min(dataInput[,3])
} else {
startCpG <- min(dataInput[,3])
}
numericInput("start", "Start position to visualise (nt):", startCpG)
}
})
## Stop position
output$stopCpG <- renderUI ({
cat(file=stderr(), "Define stop position \n")
inFile1 <- input$datafile
stopCpG <- 1
if (is.null(inFile1)) {
p('Stop position to visualise (nt):')
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
if (input$dataformat == 'region' | input$dataformat == 'region_asso') {
stopCpG <- max(dataInput[,4])
} else {
stopCpG <- max(dataInput[,3])
}
numericInput("stop", "Stop position to visualise (nt):", stopCpG)
}
})
#### READ DIFFERENT FILES
## DATASET
output$table <- renderTable({
cat(file=stderr(), "Visualise info data \n")
# input$file1 will be NULL initially. After the user selects
# and uploads a file, it will be a data frame with 'name',
# 'size', 'type', and 'datapath' columns. The 'datapath'
# column will contain the local filenames where the data can
# be found.
inFile <- input$datafile
if (is.null(inFile))
return(NULL)
read.csv(inFile$datapath, header = TRUE,
sep = "\t",quote="")
})
## INFO DATA for help
output$infoHelp <- renderTable({
cat(file=stderr(), "Visualise info data in the help tab \n")
infohelp <- "/var/shiny-server/www/cyp1b1_infofile_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp[1:6,]
})
## INFO DATA for help,region format
output$inforegionHelp <- renderTable({
cat(file=stderr(), "Visualise region example file in the help tab\n")
infohelp <- "/var/shiny-server/www/cyp1b1_infofile_exprGene_region_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp
})
## CONFING FILE for help,region format
output$configFileHelp <- renderTable({
cat(file=stderr(), "Visualise the configuration file in the help tab \n")
infohelp <- "/var/shiny-server/www/config_cyp1b1_zoom_4webserver_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp
})
## INFO DATA to download
# output$downloadINFO <- downloadHandler(
# filename = "cyp1b1_infofile.txt",
# content = function(file){
# dataINFO = "/var/shiny-server/www/cyp1b1_infofile.txt",
# write.csv(dataINFO, file)
# }
# )
## CORRELATION MATRIX
output$cortable <- renderTable({
cat(file=stderr(), "Visualise the correlation file downloaded \n")
corinFile <- input$corfile
if (is.null(corinFile))
return(NULL)
read.csv(corinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## CORRELATION MATRIX for help
output$corHelp <- renderTable({
cat(file=stderr(), "Visualiase the correlation file in the help tab \n")
corhelp <- "/var/shiny-server/www/cyp1b1_res37_rawMatrix.txt"
if (is.null(corhelp))
return(NULL)
data_corhelp <-read.csv(corhelp, header = TRUE,
sep = "\t", quote = "")
data_corhelp[1:6,1:6]
})
## EXTRA DATASET
output$odatatable <- renderTable({
cat(file=stderr(), "Visualisation extra data\n")
oinFile <- input$datalargefile
if (is.null(oinFile))
return(NULL)
read.csv(oinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## ANNOTATION DATA
output$annottable <- renderTable({
cat(file=stderr(), "Visualisation annotation data\n")
annotinFile <- input$annotfile
if (is.null(annotinFile))
return(NULL)
read.csv(annotinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## CONFIGURATION DATA
output$configtable <- renderTable({
cat(file=stderr(), "Visualise the configuration file downloaded \n")
configdatainFile <- input$configfile
if (is.null(configdatainFile))
return(NULL)
configdata<-read.csv(configdatainFile$datapath, header = FALSE,
sep = "=", quote = "")
colnames(configdata)<- c("Parameter","Value")
configdata
})
##### DRAW THE PLOT
#Define the name of file
filenameplot <- function() {
cat(file=stderr(), "Define the name of file \n")
filename = paste(input$plotfilename, "png", sep='.')
filenameImagetmp <- tempfile(fileext=filename)
filenameImagetmp
}
#Create the png
output$cometplotImage <- renderImage({
isize <- as.numeric(input$imagesize) * 100
filenameImage <- filenameplot()
png(file = filenameImage,
width=isize,
height=isize,
fonts=c("sans"))
plotPrintInput()
dev.off()
# Return a list containing the filename
listFile <- list(src = filenameImage,
contentType = 'image/png',
width = isize,
height = isize,
alt = "This is alternate text")
listFile
}, deleteFile = FALSE)
cometplotPrint <- renderPrint({ plotPrintInput() })
#cometplotPrint <- renderPrint({
# cat(file=stderr(), "Start to read the value\n")
# plot(1,2) })
plotPrintInput <- function() {
cat(file=stderr(), "Start to read the value\n")
datainFile <- input$datafile
if (is.null(datainFile))
return(NULL)
cordatainFile <- input$corfile
if (is.null(cordatainFile))
return(NULL)
largedatainFile <- input$datalargefile
largedatainFilepath <- NULL
if (!is.null(largedatainFile))
largedatainFilepath <- largedatainFile$datapath
annotdatainFile <- input$annotfile
annotdatainFilepath <- NULL
if (!is.null(annotdatainFile))
annotdatainFilepath <- annotdatainFile$datapath
configdatainFile <- input$configfile
listTrack <- "geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP"
if (is.null(input$trackAnnot)){
listTrack <-"geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP"
} else if(!is.null(input$trackAnnot) & input$defineTrack){
listTrack<-paste(input$trackAnnot,collapse=',')
}
dataformat <- NULL
if(!is.null(input$dataformat) & (input$defineParm))
dataformat <-input$dataformat
dispAsso <- "FALSE"
if(!is.null(input$dispAsso) & (input$defineParm) & input$dispAsso)
dispAsso <- "TRUE"
dispbetaAsso <- "FALSE"
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
dispbetaAsso <- "TRUE"
dispReg <- "FALSE"
if( !is.null(input$dispReg) & (input$defineParm) & input$dispReg)
dispReg <- "TRUE"
datalab <- NULL
if(!is.null(input$datalabel) & (input$defineParm))
datalab <- input$datalabel
datasymb <- NULL
if(!is.null(input$datasymb) & (input$defineParm))
datasymb <- input$datasymb
datacolor <- "red"
if(!is.null(input$datacolor) & (input$defineParm))
datacolor <- input$datacolor
datalargeformat <- NULL
if(!is.null(input$datalargeformat) & (input$defineextraParm))
datalargeformat <-input$datalargeformat
displargeAsso <- "FALSE"
if(!is.null(input$dispAssolarge) & (input$defineextraParm) & input$dispAssolarge)
displargeAsso <- "TRUE"
dispbetaAssolarge <- "FALSE"
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & input$dispbetaAssolarge)
dispbetaAssolarge <- "TRUE"
dispReglarge <- "FALSE"
if( !is.null(input$dispReglarge) & (input$defineextraParm) & input$dispReglarge)
dispReglarge <- "TRUE"
disReglarge <- as.character(dispReglarge)
datalablarge <- NULL
if(!is.null(input$datalargelabel) & (input$defineextraParm))
datalablarge <- input$datalargelabel
datalargesymb <- NULL
if(!is.null(input$datalargesymb) & (input$defineextraParm))
datalargesymb <- input$datalargesymb
datalargecolor <- "green"
if(!is.null(input$datalargecolor) & (input$defineextraParm))
datalargecolor <- input$datalargecolor
cormethod <- "spearman"
if(!is.null(input$cormethod) & (input$definecorParm))
cormethod <- input$cormethod
corformat <- "raw"
if(!is.null(input$corformat) & (input$definecorParm))
corformat <- input$corformat
coralphaCI <- 0.05
if(!is.null(input$coralphaCI) & (input$definecorParm))
coralphaCI <- input$coralphaCI
copvalThres <- 0.05
if(!is.null(input$corpvalThres) & (input$definecorParm))
corpvalThres <- input$corpvalThres
coradjmethod <- "none"
if(!is.null(input$coradjmethod) & (input$definecorParm))
coradjmethod <- input$coradjmethod
corcolor <- "bluewhitered"
if(!is.null(input$corcolor) & (input$definecorParm))
corcolor <- input$corcolor
genomeCpG <- "hg19"
if(!is.null(input$genome) & (input$defineplotParm))
genomeCpG <- input$genome
startCpG <- NULL
if(!is.null(input$startCpG) & (input$defineplotParm))
startCpG <- input$startCpG
stopCpG <- NULL
if(!is.null(input$stopCpG) & (input$defineplotParm))
stopCpG <- input$stopCpG
myrefCpG <- NULL
if(!is.null(input$reflistCpG) & (!(input$reflistCpG == "" )) & (input$defineplotParm) & input$refCpG)
myrefCpG <- as.character(input$reflistCpG)
dispCpG <- "FALSE"
if(!is.null(input$refCpGcolor) & (input$defineplotParm) & input$refCpGcolor)
dispCpG <- "TRUE"
if(!is.null(input$refCpGcolor) & (!input$defineplotParm))
dispCpG <- "TRUE"
pvalThres <- 0.0000001
if(!is.null(input$pvalThres) & (input$defineParm))
pvalThres <- input$pvalThres
pvalThres2 <- 0.00001
if(!is.null(input$pvalThres2) & (input$defineParm))
pvalThres2 <- input$pvalThres2
fontfactorGviz <- 5
if(!is.null(input$fontfactorGviz) & (input$defineParm))
fontfactorGviz <- input$fontfactorGviz
annotformat <- NULL
if(!is.null(input$annotformat) & input$annotformat != "NULL"
&(input$defineTrack))
annotformat <- as.character(input$annotformat)
annotplot <- NULL
if(!is.null(input$annotplot) & input$annotplot != "NULL"
& (input$defineTrack))
annotplot <- as.character(input$annotplot)
imagetitle <- "coMET plot"
if(!is.null(input$imagetitle))
imagetitle <- as.character(input$imagetitle)
if (is.null(configdatainFile)) {
cat(file=stderr(), "Run coMET.web from values added by hand \n")
cat(file=stderr(), " config ",configdatainFile$datapath,"\n")
cat(file=stderr(), " data ",datainFile$datapath,"\n")
cat(file=stderr(), " cormatrix ",cordatainFile$datapath,"\n")
#plot(1,2)
#comet.web(mydata.file=datainFile$datapath,mydata.format=as.character(input$dataformat))
if(is.null(annotdatainFilepath)){
if(is.null(largedatainFilepath)){
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}
}else{
cat(file=stderr(), " Annotation data ",annotdatainFilepath,"\n")
if(is.null(largedatainFilepath)){
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz, list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,
list.tracks=listTrack, biofeat.user.file=annotdatainFilepath,
biofeat.user.type=annotformat, biofeat.user.type.plot=annotplot, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}
}
} else {
cat(file=stderr(), "Run plotprintInput with configuration files\n")
cat(file=stderr(), " config ",configdatainFile$datapath,"\n")
cat(file=stderr(), " data ",datainFile$datapath,"\n")
cat(file=stderr(), " cormatrix ",cordatainFile$datapath,"\n")
#plot(1,2)
#mydata.large.file=largedatainFilepath,
#configFile="/home/tmartin/git_iop/comet/Rpackage/comet/data/smoking/config_cyp1b1_zoom_local.txt"
#comet.web(config.file=configFile,mydata.file=datainFile$datapath,cormatrix.file=cordatainFile$datapath, print.image=FALSE)
if(is.null(annotdatainFilepath)){
if(is.null(largedatainFilepath)){
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, mydata.large.file=largedatainFilepath,
print.image=FALSE, verbose=TRUE)
}
}else{
cat(file=stderr(), " Annotation data ",annotdatainFilepath,"\n")
if(is.null(largedatainFilepath)){
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, biofeat.user.file=annotdatainFilepath,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, mydata.large.file=largedatainFilepath,
biofeat.user.file=annotdatainFilepath,print.image=FALSE, verbose=TRUE)
}
}
}
# cat(file=stderr(), "comet.web has finished !\n")
}
output$downloadPlot <- downloadHandler(
filename = function() { paste(input$plotfilename, input$imageformat, sep='.') },
content = function(file) {
if(input$imageformat == "pdf"){
cat(file=stderr(), "in pdf \n")
pdf(encoding = "ISOLatin1.enc",
file = file,
onefile=FALSE,
width=as.numeric(input$imagesize),
height=as.numeric(input$imagesize),
paper="special")
}
if(input$imageformat == "eps"){
cat(file=stderr(), "in eps \n")
postscript(encoding = "ISOLatin1.enc",
file = file,
horizontal=FALSE,
onefile=FALSE,
width=as.numeric(input$imagesize),
height=as.numeric(input$imagesize),
paper="special",
pagecentre=TRUE,
fonts=c("sans"))
}
if(input$imageformat == "png"){
cat(file=stderr(), "png \n")
pngsize <- as.numeric(input$imagesize) * 1000
png(file = file,
width=pngsize,
height=pngsize,
fonts=c("sans"))
par(mar=c(1,1,1,1))
}
#lena = readImage(filenameImage)
#display(lena)
cometplotPrint()
# cat(file=stderr(), "finished to do the plot\n")
dev.off()
cat(file=stderr(), "finished to create files \n")
}
)
observe({
if(input$goPlot) {
# cat(file=stderr(), "Ask to run plot in the page \n")
if(is.null(input$datafile)){
output$cometplotUI <- renderUI({
h5("Need to upload data file",style = "color:red")
})
} else if (is.null(input$corfile)) {
output$cometplotUI <- renderUI({
h5("Need to upload correlation file",style = "color:red")
})
} else if (is.null(input$configfile) && ((input$defineParm == FALSE) || (input$definecorParm == FALSE) || (input$defineplotParm == FALSE))) {
output$cometplotUI <- renderUI({
h5("Need to upload configuration file to define parameters of data file, of correlation file and of plot or define from the website",style = "color:red")
})
} else {
cat(file=stderr(), "Run the creation plot \n")
output$cometplotUI <- renderUI({
tagList(
p('your plot is running, please wait....'),
p('Connexion to UCSC and Ensembl'),
hr(),
imageOutput("cometplotImage"),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
h5("Download your image",style = "color:red"),
p('Click on the image and save the image in png or redo in pdf or eps'),
p('It is going to take time because it need to rerun coMET and need to connect to UCSC and ENSEMBL'),
downloadButton('downloadPlot', 'Download')
)
})
}
}else { output$cometplotUI <- renderUI({
h5("Need to upload different files, parameters, and to click on button that launch the plot",style = "color:red")
})
}
})
#### PARAMETERS of coMET PLOT
output$configtableUI <- renderUI({
tagList(
h1('Parameters used in coMET plot'),
h3('Parameters from web interface :'),
#### List of parameters
h4('Info file :'),
p("Info File :",input$datafile),
if(!is.null(input$dataformat) & (input$defineParm))
p('Format of info file:',input$dataformat),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
p('Show association of info file:',input$dispbetaAsso),
if(!is.null(input$dispAsso) & (input$defineParm) & input$dispAsso)
p('Show association of info file:',input$dispAsso),
if(!is.null(input$dispAsso) & (input$defineParm) & !input$dispAsso)
p('Show association of info file: FALSE'),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
p('Show association of info file:',input$dispbetaAsso),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & !input$dispbetaAsso)
p('Show beta of association of info file: FALSE'),
if( !is.null(input$dispReg) & (input$defineParm) & input$dispReg)
p('Show region of info file:',TRUE),
if( !is.null(input$dispReg) & (input$defineParm) & !input$dispReg)
p('Show region of info file:',FALSE),
if(!is.null(input$datalabel) & (input$defineParm))
p('Label of info file:',input$datalabel),
if(!is.null(input$datasymb) & (input$defineParm))
p('Symbol of info file:', input$datasymb),
if(!is.null(input$datacolor) & (input$defineParm))
p('Color of info file:', input$datacolor),
##Correlation
h4('Info file :'),
p('Correlation File :', input$corfile),
if(!is.null(input$cormethod) & (input$definecorParm))
p('Method of Correlation File:',input$cormethod),
if(!is.null(input$corformat) & (input$definecorParm))
p('Format of Correlation File:',input$corformat),
if(!is.null(input$corcolor) & (input$definecorParm))
p('Color Correlation File:',input$corcolor),
#Supplementary file
h4('Supplementary file :'),
if (!is.null(input$datalargefile))
p('Supplementary File :',input$datalargefile),
if(!is.null(input$datalargeformat) & (input$defineextraParm))
p('Format of supplementary file:',input$datalargeformat),
if(!is.null(input$dispAssolarge) & (input$defineextraParm) & input$dispAssolarge)
p('Show association of supplementary file:',input$dispAssolarge),
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & input$dispbetaAssolarge)
p('Show association of supplementary file:',input$dispbetaAssolarge),
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & !input$dispbetaAssolarge)
p('Show beta of association of supplementary file: FALSE'),
if( !is.null(input$dispReglarge) & (input$defineextraParm) & input$dispReglarge)
p('Show region of supplementary file:',input$dispReglarge),
if(!is.null(input$datalargelabel) & (input$defineextraParm))
p('Label of supplementary file:',input$datalargelabel),
if(!is.null(input$datalargesymb) & (input$defineextraParm))
p('Symbole of supplementary file:',input$datalargesymb),
if(!is.null(input$datalargecolor) & (input$defineextraParm))
p('Color of supplementary file:',input$datalargecolor),
#Configuration
h4('Configuration file :'),
p('Configuration File :',input$configfile),
if (is.null(input$trackAnnot))
p('list of tracks:geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP'),
if(!is.null(input$trackAnnot) & input$defineTrack)
p('list of tracks:',paste(input$trackAnnot,collapse=',')),
if(!is.null(input$startCpG) & (input$defineplotParm))
p('Start of genomic region :',input$startCpG),
if(!is.null(input$stopCpG) & (input$defineplotParm))
p('Stop of genomic region :',input$stopCpG),
if(!is.null(input$reflistCpG) & (!(input$reflistCpG == "" )) & (input$defineplotParm) & input$refCpG)
p('Name of reference element:',as.character(input$reflistCpG)),
if(!is.null(input$refCpGcolor) & (input$defineplotParm) & input$refCpGcolor)
p('Show reference element:',input$refCpGcolor),
if(!is.null(input$refCpGcolor) & (!input$defineplotParm))
p('Show reference element:',input$refCpGcolor),
#Annotation
h4('user file for annotation :'),
if (!is.null(input$annotfile))
p('Annotation File :',input$annotfile),
if(!is.null(input$annotformat) & (input$defineTrack))
p('Format of annotation file :',as.character(input$annotformat)),
if(!is.null(input$annotplot) & (input$defineTrack))
p('Type of plot :',as.character(input$annotplot)),
if(!is.null(input$imagetitle))
p('Title of plot :',as.character(input$imagetitle)),
####
h3('Parametres from configuration file'),
tableOutput("configtable")
)
})
##### EXPLANATIONS ABOUT COMET
output$home <- renderUI({
tagList(
h1('Welcome to coMET'),
h3('Overview'),
p('The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest.',
'coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation).',
'The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on such as the ',
a(href = 'http://genome.ucsc.edu/ENCODE/', 'Encode'),' and annotation tracks from', a(href = 'https://genome.ucsc.edu/', 'UCSC Genome Browser website'),
'project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data, e.g. gene expression array data.'
),
h3('coMET webservice'),
p('The webservice is the pre-formated web service of coMET with a reduction of parameters availlable.'),
p('Only 100 omic features can be visualised in the correlation matrix.'),
p('If the region is large or ENSEMBL and UCSC is busy, the creation of plot can take time.'),
h3('Developpers'),
p('coMET is developed by Tiphaine C. Martin in collaboration with Tom Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T.Bell, Department of Twin Research, Kings College London.'),
h3('Cite'),
p('Martin, T.C., Yet, I., Tsai, P-C., Bell and J.T. (2015).',
a(href='http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0568-2','“coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.”'),
' BMC Bioinformatics.'),
p('Martin, T.C, Erte, I, Tsai, P-C, Bell, J.T.,coMET: an R plotting package to visualize regional plots of epigenome-wide association scan results,',
a(href='http://quantgen.soc.srcf.net/qg14/', 'QG14'),
', 2014.'),
h3('Example of coMET plot'),
img(src='http://comet.epigen.kcl.ac.uk:3838/minimal-cometwebPlot.jpeg'),
h3('Contacts'),
p('For any question, you can send an email to',
a(href='mailto:tiphaine.martin@kcl.ac.uk;jordana.bell@kcl.ac.uk?Subject=CoMET', 'Tiphaine Martin and Jordana Bell')),
h3('More information'),
p('Go to the website',
a(href='http://epigen.kcl.ac.uk/comet', ' Department of Twin Research')),
h3('Download'),
p('Want to download the R package :',
a(href='https://github.com/TiphaineCMartin/coMET', ' Department of Twin Research'))
)
})
output$help <- renderUI({
tagList(
h1('Welcome to coMET help'),
h3('Format of info file (mandatory)'),
p('It is mandatory and has to be a file in tabular format with an header.'),
p('The info file can be a list of CpG sites with/without Beta (or direction sign). If it is a CpG-site file then it is mandatory to have 4 columns as shown below with headers in the same order. The beta or direction can be included in the 5th column (optional).'),
tableOutput("infoHelp"),
p('Alternatively, the info file can be region-based and if so, the region-based info file must have the 5 columns (see below) with headers in this order. The beta or direction can be included in the 6th column (optional).'),
tableOutput("inforegionHelp"),
p('There are 4 different options for mydata.format: site (4 columns), region (5 columns), site_asso (5 columns), region_asso (6 columns).'),
h3('Format of correlation matrix (mandatory)'),
p('It is mandatory and has to be a file in tabular format with an header.'),
p('The correlation matrix dataset can either be a pre-calculated correlation matrix or the raw data. There are two format for raw data. The format called RAW is put if the CpG sites/regions are by column and the samples are by row whereas the format called raw_rev is put if the CpG sites/regions are by row and the samples are by column. If it is a raw data then you can select the type of correlation method (spearman, kendall or pearson).'),
p('Example of data at RAW format:'),
tableOutput("corHelp"),
h3('Format of extra info file'),
p('It is optional file or list of files separatated by comma. Files should be in tabular format with an header'),
p('This can be another type of info file (e.g Expression data or replication data) and it follows the same rules than the info file.'),
h3('Format of annotation file'),
p('format accepted by GViz such as BED, GTF, and GFF3 format. It is optional file.'),
h3('Option of config.file'),
p('If you would like to make your own changes to the plot you can download the configuration file from this site. After you make the relative changes you can upload it to the server again and plot.'),
p('It is a file where each line is one option. The name of option is in capital and is separated to its value by "=". If there are multiple values such as for the option list.tracks or the options for exta data.'),
tableOutput("configFileHelp"),
hr(),
h3('Option of comet.web'),
p('Info: ', ?comet.web)
)
})
})
TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#Load library
library("shiny")
library("grid")
library("grDevices")
library("rtracklayer")
library("biomaRt")
library("Gviz")
library("ggbio")
library("colortools")
library("hash")
library("psych")
library("coMET")
# By default, the file size limit is 5MB. It can be changed by
# setting this option. Here we'll raise limit to 9MB.
options(shiny.maxRequestSize = 9*1024^2)
shinyServer(function(input, output,session) {
filenameImage <- NULL
#### CREATE LIST OF ELEMENTS
output$listCpG <- renderUI ({
cat(file=stderr(), "Create the lsit of CpG sites \n")
inFile1 <- input$datafile
listCpG <- c("")
if (is.null(inFile1)) {
listCpG <- c("")
sizeListCpG <- length(listCpG) - 1
# print(sizeListCpG,digit= 10)
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
listDI<-dataInput[,1]
listCpG <- sapply(listDI,as.character)
sizeListCpG <- length(listCpG)
#print(sizeListCpG,digit=10);
}
cat(file=stderr(), "Number of CpG sites", sizeListCpG, "CpG sites\n")
selectInput("reflistCpG", paste ("among",sizeListCpG) ,
choices = listCpG,selected = NULL,
multiple = FALSE)
})
## Start position
output$startCpG <- renderUI ({
cat(file=stderr(), "Define start position \n")
inFile1 <- input$datafile
startCpG <- 1
if (is.null(inFile1)) {
p('Start position to visualise (nt):')
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
if (input$dataformat == 'region' | input$dataformat == 'region_asso') {
startCpG <- min(dataInput[,3])
} else {
startCpG <- min(dataInput[,3])
}
numericInput("start", "Start position to visualise (nt):", startCpG)
}
})
## Stop position
output$stopCpG <- renderUI ({
cat(file=stderr(), "Define stop position \n")
inFile1 <- input$datafile
stopCpG <- 1
if (is.null(inFile1)) {
p('Stop position to visualise (nt):')
} else {
dataInput <- read.csv(inFile1$datapath, header = TRUE,
sep = "\t",quote="")
if (input$dataformat == 'region' | input$dataformat == 'region_asso') {
stopCpG <- max(dataInput[,4])
} else {
stopCpG <- max(dataInput[,3])
}
numericInput("stop", "Stop position to visualise (nt):", stopCpG)
}
})
#### READ DIFFERENT FILES
## DATASET
output$table <- renderTable({
cat(file=stderr(), "Visualise info data \n")
# input$file1 will be NULL initially. After the user selects
# and uploads a file, it will be a data frame with 'name',
# 'size', 'type', and 'datapath' columns. The 'datapath'
# column will contain the local filenames where the data can
# be found.
inFile <- input$datafile
if (is.null(inFile))
return(NULL)
read.csv(inFile$datapath, header = TRUE,
sep = "\t",quote="")
})
## INFO DATA for help
output$infoHelp <- renderTable({
cat(file=stderr(), "Visualise info data in the help tab \n")
infohelp <- "/var/shiny-server/www/cyp1b1_infofile_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp[1:6,]
})
## INFO DATA for help,region format
output$inforegionHelp <- renderTable({
cat(file=stderr(), "Visualise region example file in the help tab\n")
infohelp <- "/var/shiny-server/www/cyp1b1_infofile_exprGene_region_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp
})
## CONFING FILE for help,region format
output$configFileHelp <- renderTable({
cat(file=stderr(), "Visualise the configuration file in the help tab \n")
infohelp <- "/var/shiny-server/www/config_cyp1b1_zoom_4webserver_Grch38.txt"
if (is.null(infohelp))
return(NULL)
data_infohelp <-read.csv(infohelp, header = TRUE,
sep = "\t", quote = "")
data_infohelp
})
## INFO DATA to download
# output$downloadINFO <- downloadHandler(
# filename = "cyp1b1_infofile.txt",
# content = function(file){
# dataINFO = "/var/shiny-server/www/cyp1b1_infofile.txt",
# write.csv(dataINFO, file)
# }
# )
## CORRELATION MATRIX
output$cortable <- renderTable({
cat(file=stderr(), "Visualise the correlation file downloaded \n")
corinFile <- input$corfile
if (is.null(corinFile))
return(NULL)
read.csv(corinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## CORRELATION MATRIX for help
output$corHelp <- renderTable({
cat(file=stderr(), "Visualiase the correlation file in the help tab \n")
corhelp <- "/var/shiny-server/www/cyp1b1_res37_rawMatrix.txt"
if (is.null(corhelp))
return(NULL)
data_corhelp <-read.csv(corhelp, header = TRUE,
sep = "\t", quote = "")
data_corhelp[1:6,1:6]
})
## EXTRA DATASET
output$odatatable <- renderTable({
cat(file=stderr(), "Visualisation extra data\n")
oinFile <- input$datalargefile
if (is.null(oinFile))
return(NULL)
read.csv(oinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## ANNOTATION DATA
output$annottable <- renderTable({
cat(file=stderr(), "Visualisation annotation data\n")
annotinFile <- input$annotfile
if (is.null(annotinFile))
return(NULL)
read.csv(annotinFile$datapath, header = TRUE,
sep = "\t", quote = "")
})
## CONFIGURATION DATA
output$configtable <- renderTable({
cat(file=stderr(), "Visualise the configuration file downloaded \n")
configdatainFile <- input$configfile
if (is.null(configdatainFile))
return(NULL)
configdata<-read.csv(configdatainFile$datapath, header = FALSE,
sep = "=", quote = "")
colnames(configdata)<- c("Parameter","Value")
configdata
})
##### DRAW THE PLOT
#Define the name of file
filenameplot <- function() {
cat(file=stderr(), "Define the name of file \n")
filename = paste(input$plotfilename, "png", sep='.')
filenameImagetmp <- tempfile(fileext=filename)
filenameImagetmp
}
#Create the png
output$cometplotImage <- renderImage({
isize <- as.numeric(input$imagesize) * 100
filenameImage <- filenameplot()
png(file = filenameImage,
width=isize,
height=isize,
fonts=c("sans"))
plotPrintInput()
dev.off()
# Return a list containing the filename
listFile <- list(src = filenameImage,
contentType = 'image/png',
width = isize,
height = isize,
alt = "This is alternate text")
listFile
}, deleteFile = FALSE)
cometplotPrint <- renderPrint({ plotPrintInput() })
#cometplotPrint <- renderPrint({
# cat(file=stderr(), "Start to read the value\n")
# plot(1,2) })
plotPrintInput <- function() {
cat(file=stderr(), "Start to read the value\n")
datainFile <- input$datafile
if (is.null(datainFile))
return(NULL)
cordatainFile <- input$corfile
if (is.null(cordatainFile))
return(NULL)
largedatainFile <- input$datalargefile
largedatainFilepath <- NULL
if (!is.null(largedatainFile))
largedatainFilepath <- largedatainFile$datapath
annotdatainFile <- input$annotfile
annotdatainFilepath <- NULL
if (!is.null(annotdatainFile))
annotdatainFilepath <- annotdatainFile$datapath
configdatainFile <- input$configfile
listTrack <- "geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP"
if (is.null(input$trackAnnot)){
listTrack <-"geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP"
} else if(!is.null(input$trackAnnot) & input$defineTrack){
listTrack<-paste(input$trackAnnot,collapse=',')
}
dataformat <- NULL
if(!is.null(input$dataformat) & (input$defineParm))
dataformat <-input$dataformat
dispAsso <- "FALSE"
if(!is.null(input$dispAsso) & (input$defineParm) & input$dispAsso)
dispAsso <- "TRUE"
dispbetaAsso <- "FALSE"
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
dispbetaAsso <- "TRUE"
dispReg <- "FALSE"
if( !is.null(input$dispReg) & (input$defineParm) & input$dispReg)
dispReg <- "TRUE"
datalab <- NULL
if(!is.null(input$datalabel) & (input$defineParm))
datalab <- input$datalabel
datasymb <- NULL
if(!is.null(input$datasymb) & (input$defineParm))
datasymb <- input$datasymb
datacolor <- "red"
if(!is.null(input$datacolor) & (input$defineParm))
datacolor <- input$datacolor
datalargeformat <- NULL
if(!is.null(input$datalargeformat) & (input$defineextraParm))
datalargeformat <-input$datalargeformat
displargeAsso <- "FALSE"
if(!is.null(input$dispAssolarge) & (input$defineextraParm) & input$dispAssolarge)
displargeAsso <- "TRUE"
dispbetaAssolarge <- "FALSE"
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & input$dispbetaAssolarge)
dispbetaAssolarge <- "TRUE"
dispReglarge <- "FALSE"
if( !is.null(input$dispReglarge) & (input$defineextraParm) & input$dispReglarge)
dispReglarge <- "TRUE"
disReglarge <- as.character(dispReglarge)
datalablarge <- NULL
if(!is.null(input$datalargelabel) & (input$defineextraParm))
datalablarge <- input$datalargelabel
datalargesymb <- NULL
if(!is.null(input$datalargesymb) & (input$defineextraParm))
datalargesymb <- input$datalargesymb
datalargecolor <- "green"
if(!is.null(input$datalargecolor) & (input$defineextraParm))
datalargecolor <- input$datalargecolor
cormethod <- "spearman"
if(!is.null(input$cormethod) & (input$definecorParm))
cormethod <- input$cormethod
corformat <- "raw"
if(!is.null(input$corformat) & (input$definecorParm))
corformat <- input$corformat
coralphaCI <- 0.05
if(!is.null(input$coralphaCI) & (input$definecorParm))
coralphaCI <- input$coralphaCI
copvalThres <- 0.05
if(!is.null(input$corpvalThres) & (input$definecorParm))
corpvalThres <- input$corpvalThres
coradjmethod <- "none"
if(!is.null(input$coradjmethod) & (input$definecorParm))
coradjmethod <- input$coradjmethod
corcolor <- "bluewhitered"
if(!is.null(input$corcolor) & (input$definecorParm))
corcolor <- input$corcolor
genomeCpG <- "hg19"
if(!is.null(input$genome) & (input$defineplotParm))
genomeCpG <- input$genome
startCpG <- NULL
if(!is.null(input$startCpG) & (input$defineplotParm))
startCpG <- input$startCpG
stopCpG <- NULL
if(!is.null(input$stopCpG) & (input$defineplotParm))
stopCpG <- input$stopCpG
myrefCpG <- NULL
if(!is.null(input$reflistCpG) & (!(input$reflistCpG == "" )) & (input$defineplotParm) & input$refCpG)
myrefCpG <- as.character(input$reflistCpG)
dispCpG <- "FALSE"
if(!is.null(input$refCpGcolor) & (input$defineplotParm) & input$refCpGcolor)
dispCpG <- "TRUE"
if(!is.null(input$refCpGcolor) & (!input$defineplotParm))
dispCpG <- "TRUE"
pvalThres <- 0.0000001
if(!is.null(input$pvalThres) & (input$defineParm))
pvalThres <- input$pvalThres
pvalThres2 <- 0.00001
if(!is.null(input$pvalThres2) & (input$defineParm))
pvalThres2 <- input$pvalThres2
fontfactorGviz <- 5
if(!is.null(input$fontfactorGviz) & (input$defineParm))
fontfactorGviz <- input$fontfactorGviz
annotformat <- NULL
if(!is.null(input$annotformat) & input$annotformat != "NULL"
&(input$defineTrack))
annotformat <- as.character(input$annotformat)
annotplot <- NULL
if(!is.null(input$annotplot) & input$annotplot != "NULL"
& (input$defineTrack))
annotplot <- as.character(input$annotplot)
imagetitle <- "coMET plot"
if(!is.null(input$imagetitle))
imagetitle <- as.character(input$imagetitle)
if (is.null(configdatainFile)) {
cat(file=stderr(), "Run coMET.web from values added by hand \n")
cat(file=stderr(), " config ",configdatainFile$datapath,"\n")
cat(file=stderr(), " data ",datainFile$datapath,"\n")
cat(file=stderr(), " cormatrix ",cordatainFile$datapath,"\n")
#plot(1,2)
#comet.web(mydata.file=datainFile$datapath,mydata.format=as.character(input$dataformat))
if(is.null(annotdatainFilepath)){
if(is.null(largedatainFilepath)){
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}
}else{
cat(file=stderr(), " Annotation data ",annotdatainFilepath,"\n")
if(is.null(largedatainFilepath)){
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz, list.tracks=listTrack, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(mydata.file=datainFile$datapath,mydata.format=dataformat,disp.association=dispAsso,
disp.beta.association=dispbetaAsso,
disp.region=dispReg, sample.labels=datalab, symbols=datasymb, color.list=datacolor,
cormatrix.file=cordatainFile$datapath,cormatrix.method=cormethod,
cormatrix.format=corformat, cormatrix.adjust=coradjmethod,
cormatrix.conf.level=coralphaCI, cormatrix.sig.level=corpvalThres,
cormatrix.color.scheme=corcolor,mydata.large.file=largedatainFilepath,
mydata.large.format=datalargeformat,disp.association.large=displargeAsso,
disp.beta.association.large=dispbetaAssolarge,
disp.region.large=dispReglarge, sample.labels.large=datalablarge,
symbols.large=datalargesymb, color.list.large=datalargecolor,genome=genomeCpG,
start=startCpG,end=stopCpG,mydata.ref=myrefCpG,disp.color.ref=dispCpG,
pval.threshold=pvalThres, pval.threshold.2=pvalThres2, factor.beta=factorbeta,
font.factor=fontfactorGviz,
list.tracks=listTrack, biofeat.user.file=annotdatainFilepath,
biofeat.user.type=annotformat, biofeat.user.type.plot=annotplot, image.title=imagetitle,
print.image=FALSE, verbose=TRUE)
}
}
} else {
cat(file=stderr(), "Run plotprintInput with configuration files\n")
cat(file=stderr(), " config ",configdatainFile$datapath,"\n")
cat(file=stderr(), " data ",datainFile$datapath,"\n")
cat(file=stderr(), " cormatrix ",cordatainFile$datapath,"\n")
#plot(1,2)
#mydata.large.file=largedatainFilepath,
#configFile="/home/tmartin/git_iop/comet/Rpackage/comet/data/smoking/config_cyp1b1_zoom_local.txt"
#comet.web(config.file=configFile,mydata.file=datainFile$datapath,cormatrix.file=cordatainFile$datapath, print.image=FALSE)
if(is.null(annotdatainFilepath)){
if(is.null(largedatainFilepath)){
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, mydata.large.file=largedatainFilepath,
print.image=FALSE, verbose=TRUE)
}
}else{
cat(file=stderr(), " Annotation data ",annotdatainFilepath,"\n")
if(is.null(largedatainFilepath)){
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, biofeat.user.file=annotdatainFilepath,
print.image=FALSE, verbose=TRUE)
}else{
cat(file=stderr(), " large data ",largedatainFilepath,"\n")
comet.web(config.file=configdatainFile$datapath, mydata.file=datainFile$datapath,
cormatrix.file=cordatainFile$datapath, mydata.large.file=largedatainFilepath,
biofeat.user.file=annotdatainFilepath,print.image=FALSE, verbose=TRUE)
}
}
}
# cat(file=stderr(), "comet.web has finished !\n")
}
output$downloadPlot <- downloadHandler(
filename = function() { paste(input$plotfilename, input$imageformat, sep='.') },
content = function(file) {
if(input$imageformat == "pdf"){
cat(file=stderr(), "in pdf \n")
pdf(encoding = "ISOLatin1.enc",
file = file,
onefile=FALSE,
width=as.numeric(input$imagesize),
height=as.numeric(input$imagesize),
paper="special")
}
if(input$imageformat == "eps"){
cat(file=stderr(), "in eps \n")
postscript(encoding = "ISOLatin1.enc",
file = file,
horizontal=FALSE,
onefile=FALSE,
width=as.numeric(input$imagesize),
height=as.numeric(input$imagesize),
paper="special",
pagecentre=TRUE,
fonts=c("sans"))
}
if(input$imageformat == "png"){
cat(file=stderr(), "png \n")
pngsize <- as.numeric(input$imagesize) * 1000
png(file = file,
width=pngsize,
height=pngsize,
fonts=c("sans"))
par(mar=c(1,1,1,1))
}
#lena = readImage(filenameImage)
#display(lena)
cometplotPrint()
# cat(file=stderr(), "finished to do the plot\n")
dev.off()
cat(file=stderr(), "finished to create files \n")
}
)
observe({
if(input$goPlot) {
# cat(file=stderr(), "Ask to run plot in the page \n")
if(is.null(input$datafile)){
output$cometplotUI <- renderUI({
h5("Need to upload data file",style = "color:red")
})
} else if (is.null(input$corfile)) {
output$cometplotUI <- renderUI({
h5("Need to upload correlation file",style = "color:red")
})
} else if (is.null(input$configfile) && ((input$defineParm == FALSE) || (input$definecorParm == FALSE) || (input$defineplotParm == FALSE))) {
output$cometplotUI <- renderUI({
h5("Need to upload configuration file to define parameters of data file, of correlation file and of plot or define from the website",style = "color:red")
})
} else {
cat(file=stderr(), "Run the creation plot \n")
output$cometplotUI <- renderUI({
tagList(
p('your plot is running, please wait....'),
p('Connexion to UCSC and Ensembl'),
hr(),
imageOutput("cometplotImage"),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
hr(),
h5("Download your image",style = "color:red"),
p('Click on the image and save the image in png or redo in pdf or eps'),
p('It is going to take time because it need to rerun coMET and need to connect to UCSC and ENSEMBL'),
downloadButton('downloadPlot', 'Download')
)
})
}
}else { output$cometplotUI <- renderUI({
h5("Need to upload different files, parameters, and to click on button that launch the plot",style = "color:red")
})
}
})
#### PARAMETERS of coMET PLOT
output$configtableUI <- renderUI({
tagList(
h1('Parameters used in coMET plot'),
h3('Parameters from web interface :'),
#### List of parameters
h4('Info file :'),
p("Info File :",input$datafile),
if(!is.null(input$dataformat) & (input$defineParm))
p('Format of info file:',input$dataformat),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
p('Show association of info file:',input$dispbetaAsso),
if(!is.null(input$dispAsso) & (input$defineParm) & input$dispAsso)
p('Show association of info file:',input$dispAsso),
if(!is.null(input$dispAsso) & (input$defineParm) & !input$dispAsso)
p('Show association of info file: FALSE'),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & input$dispbetaAsso)
p('Show association of info file:',input$dispbetaAsso),
if(!is.null(input$dispbetaAsso) & (input$defineParm) & !input$dispbetaAsso)
p('Show beta of association of info file: FALSE'),
if( !is.null(input$dispReg) & (input$defineParm) & input$dispReg)
p('Show region of info file:',TRUE),
if( !is.null(input$dispReg) & (input$defineParm) & !input$dispReg)
p('Show region of info file:',FALSE),
if(!is.null(input$datalabel) & (input$defineParm))
p('Label of info file:',input$datalabel),
if(!is.null(input$datasymb) & (input$defineParm))
p('Symbol of info file:', input$datasymb),
if(!is.null(input$datacolor) & (input$defineParm))
p('Color of info file:', input$datacolor),
##Correlation
h4('Info file :'),
p('Correlation File :', input$corfile),
if(!is.null(input$cormethod) & (input$definecorParm))
p('Method of Correlation File:',input$cormethod),
if(!is.null(input$corformat) & (input$definecorParm))
p('Format of Correlation File:',input$corformat),
if(!is.null(input$corcolor) & (input$definecorParm))
p('Color Correlation File:',input$corcolor),
#Supplementary file
h4('Supplementary file :'),
if (!is.null(input$datalargefile))
p('Supplementary File :',input$datalargefile),
if(!is.null(input$datalargeformat) & (input$defineextraParm))
p('Format of supplementary file:',input$datalargeformat),
if(!is.null(input$dispAssolarge) & (input$defineextraParm) & input$dispAssolarge)
p('Show association of supplementary file:',input$dispAssolarge),
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & input$dispbetaAssolarge)
p('Show association of supplementary file:',input$dispbetaAssolarge),
if(!is.null(input$dispbetaAssolarge) & (input$defineParm) & !input$dispbetaAssolarge)
p('Show beta of association of supplementary file: FALSE'),
if( !is.null(input$dispReglarge) & (input$defineextraParm) & input$dispReglarge)
p('Show region of supplementary file:',input$dispReglarge),
if(!is.null(input$datalargelabel) & (input$defineextraParm))
p('Label of supplementary file:',input$datalargelabel),
if(!is.null(input$datalargesymb) & (input$defineextraParm))
p('Symbole of supplementary file:',input$datalargesymb),
if(!is.null(input$datalargecolor) & (input$defineextraParm))
p('Color of supplementary file:',input$datalargecolor),
#Configuration
h4('Configuration file :'),
p('Configuration File :',input$configfile),
if (is.null(input$trackAnnot))
p('list of tracks:geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP'),
if(!is.null(input$trackAnnot) & input$defineTrack)
p('list of tracks:',paste(input$trackAnnot,collapse=',')),
if(!is.null(input$startCpG) & (input$defineplotParm))
p('Start of genomic region :',input$startCpG),
if(!is.null(input$stopCpG) & (input$defineplotParm))
p('Stop of genomic region :',input$stopCpG),
if(!is.null(input$reflistCpG) & (!(input$reflistCpG == "" )) & (input$defineplotParm) & input$refCpG)
p('Name of reference element:',as.character(input$reflistCpG)),
if(!is.null(input$refCpGcolor) & (input$defineplotParm) & input$refCpGcolor)
p('Show reference element:',input$refCpGcolor),
if(!is.null(input$refCpGcolor) & (!input$defineplotParm))
p('Show reference element:',input$refCpGcolor),
#Annotation
h4('user file for annotation :'),
if (!is.null(input$annotfile))
p('Annotation File :',input$annotfile),
if(!is.null(input$annotformat) & (input$defineTrack))
p('Format of annotation file :',as.character(input$annotformat)),
if(!is.null(input$annotplot) & (input$defineTrack))
p('Type of plot :',as.character(input$annotplot)),
if(!is.null(input$imagetitle))
p('Title of plot :',as.character(input$imagetitle)),
####
h3('Parametres from configuration file'),
tableOutput("configtable")
)
})
##### EXPLANATIONS ABOUT COMET
output$home <- renderUI({
tagList(
h1('Welcome to coMET'),
h3('Overview'),
p('The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest.',
'coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation).',
'The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on such as the ',
a(href = 'http://genome.ucsc.edu/ENCODE/', 'Encode'),' and annotation tracks from', a(href = 'https://genome.ucsc.edu/', 'UCSC Genome Browser website'),
'project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data, e.g. gene expression array data.'
),
h3('coMET webservice'),
p('The webservice is the pre-formated web service of coMET with a reduction of parameters availlable.'),
p('Only 100 omic features can be visualised in the correlation matrix.'),
p('If the region is large or ENSEMBL and UCSC is busy, the creation of plot can take time.'),
h3('Developpers'),
p('coMET is developed by Tiphaine C. Martin in collaboration with Tom Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T.Bell, Department of Twin Research, Kings College London.'),
h3('Cite'),
p('Martin, T.C., Yet, I., Tsai, P-C., Bell and J.T. (2015).',
a(href='http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0568-2','“coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.”'),
' BMC Bioinformatics.'),
p('Martin, T.C, Erte, I, Tsai, P-C, Bell, J.T.,coMET: an R plotting package to visualize regional plots of epigenome-wide association scan results,',
a(href='http://quantgen.soc.srcf.net/qg14/', 'QG14'),
', 2014.'),
h3('Example of coMET plot'),
img(src='http://comet.epigen.kcl.ac.uk:3838/minimal-cometwebPlot.jpeg'),
h3('Contacts'),
p('For any question, you can send an email to',
a(href='mailto:tiphaine.martin@kcl.ac.uk;jordana.bell@kcl.ac.uk?Subject=CoMET', 'Tiphaine Martin and Jordana Bell')),
h3('More information'),
p('Go to the website',
a(href='http://epigen.kcl.ac.uk/comet', ' Department of Twin Research')),
h3('Download'),
p('Want to download the R package :',
a(href='https://github.com/TiphaineCMartin/coMET', ' Department of Twin Research'))
)
})
output$help <- renderUI({
tagList(
h1('Welcome to coMET help'),
h3('Format of info file (mandatory)'),
p('It is mandatory and has to be a file in tabular format with an header.'),
p('The info file can be a list of CpG sites with/without Beta (or direction sign). If it is a CpG-site file then it is mandatory to have 4 columns as shown below with headers in the same order. The beta or direction can be included in the 5th column (optional).'),
tableOutput("infoHelp"),
p('Alternatively, the info file can be region-based and if so, the region-based info file must have the 5 columns (see below) with headers in this order. The beta or direction can be included in the 6th column (optional).'),
tableOutput("inforegionHelp"),
p('There are 4 different options for mydata.format: site (4 columns), region (5 columns), site_asso (5 columns), region_asso (6 columns).'),
h3('Format of correlation matrix (mandatory)'),
p('It is mandatory and has to be a file in tabular format with an header.'),
p('The correlation matrix dataset can either be a pre-calculated correlation matrix or the raw data. There are two format for raw data. The format called RAW is put if the CpG sites/regions are by column and the samples are by row whereas the format called raw_rev is put if the CpG sites/regions are by row and the samples are by column. If it is a raw data then you can select the type of correlation method (spearman, kendall or pearson).'),
p('Example of data at RAW format:'),
tableOutput("corHelp"),
h3('Format of extra info file'),
p('It is optional file or list of files separatated by comma. Files should be in tabular format with an header'),
p('This can be another type of info file (e.g Expression data or replication data) and it follows the same rules than the info file.'),
h3('Format of annotation file'),
p('format accepted by GViz such as BED, GTF, and GFF3 format. It is optional file.'),
h3('Option of config.file'),
p('If you would like to make your own changes to the plot you can download the configuration file from this site. After you make the relative changes you can upload it to the server again and plot.'),
p('It is a file where each line is one option. The name of option is in capital and is separated to its value by "=". If there are multiple values such as for the option list.tracks or the options for exta data.'),
tableOutput("configFileHelp"),
hr(),
h3('Option of comet.web'),
p('Info: ', ?comet.web)
)
})
})
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