comparison lib.r @ 33:3b2b642542f6 draft

planemo upload commit 896ef116e72008394779322f65137c632af5f4d2

32:23e33e354bb7

# lib.r version="2.2.1"

#@author G. Le Corguille
#The function create a pdf from the different png generated by diffreport
diffreport_png2pdf <- function(filebase, new_file_path) {

    pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")
    pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")

    system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))
    system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))

    file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)
    file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)
}

#@author G. Le Corguille
#This function convert if it is required the Retention Time in minutes
RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

    variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
    return(variableMetadata)
}

#The function annotateDiffreport without the corr function which bugs
annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {
    # Resolve the bug with x11, with the function png
    options(bitmapType='cairo')

    #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
    res=try(is.null(xset@filled))

    # --- Multi condition : diffreport ---
    diffrepOri=NULL
    if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
    #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
    res=try(is.null(xset@filled))
    classes=levels(sampclass(xset))
    x=1:(length(classes)-1)
    for (i in seq(along=x) ) {
        y=1:(length(classes))
        for (n in seq(along=y)){
            if(i+n <= length(classes)){
                filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")

                diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])

                diffrepOri = diffrep

                # renamming of the column rtmed to rt to fit with camera peaklist function output
                colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
                colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"

                # combines results and reorder columns
                diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
                diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])

                diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
                diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])

                if(listArguments[["sortpval"]]){
                    diffrep=diffrep[order(diffrep$pvalue), ]
                }

                write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep=""))

                if (listArguments[["eicmax"]] != 0) {
                    diffreport_png2pdf(filebase, new_file_path)
                }
            }
        }
        }
    }


    # --- variableMetadata ---

    variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
    # if we have 2 conditions, we keep stat of diffrep
    if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
        variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
        if(exists("listArguments[[\"sortpval\"]]")){
          variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
        }
    }

    variableMetadataOri=variableMetadata
    write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)

33:3b2b642542f6

# lib.r

#@author G. Le Corguille
#The function create a pdf from the different png generated by diffreport
diffreport_png2pdf <- function(filebase) {
    dir.create("pdf")

    pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
    pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")

    system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
    system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))

}

#@author G. Le Corguille
#This function convert if it is required the Retention Time in minutes
RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

    variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
    return(variableMetadata)
}

#The function annotateDiffreport without the corr function which bugs
annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") {
    # Resolve the bug with x11, with the function png
    options(bitmapType='cairo')

    #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
    res=try(is.null(xset@filled))

    # --- Multi condition : diffreport ---
    diffrepOri=NULL
    if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
        #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
        res=try(is.null(xset@filled))
        classes=levels(sampclass(xset))
        x=1:(length(classes)-1)
        for (i in seq(along=x) ) {
            y=1:(length(classes))
            for (n in seq(along=y)){
                if(i+n <= length(classes)){
                    filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
                    
                    diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])
                    
                    diffrepOri = diffrep
                    
                    # renamming of the column rtmed to rt to fit with camera peaklist function output
                    colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
                    colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
                    
                    # combines results and reorder columns
                    diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
                    diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
                    
                    diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
                    diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
                    
                    if(listArguments[["sortpval"]]){
                        diffrep=diffrep[order(diffrep$pvalue), ]
                    }
                    
                    dir.create("tabular")
                    write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
                    
                    if (listArguments[["eicmax"]] != 0) {
                        diffreport_png2pdf(filebase)
                    }
                }
            }
        }
    }


    # --- variableMetadata ---

    variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
    # if we have 2 conditions, we keep stat of diffrep
    if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
        variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
        if(exists("listArguments[[\"sortpval\"]]")){
            variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
        }
    }

    variableMetadataOri=variableMetadata
    write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)