inst/app/server/pathview.R

In TCGAbiolinksGUI: "TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

#----------------------------------------------
#                 DEA Pathview
pathway.data <- function(){
    inFile <- input$pathewayexpfile
    if(class(inFile) != "list") return(NULL)
    file  <- as.character(parseFilePaths(get.volumes(isolate({input$workingDir})), input$pathewayexpfile)$datapath)
    if(tools::file_ext(file)=="csv"){
        se <- read_csv(file)
    } else if(tools::file_ext(file)=="rda"){
        se <- get(load(file))
    }

    return(se)
}
output$deaSE <- DT::renderDataTable({
    data <- pathway.data()
    if(!is.null(data)) createTable(as.data.frame(data))
})

observe({
    shinyFileChoose(input, 'pathewayexpfile',
                    roots=get.volumes(input$workingDir),
                    session=session,
                    restrictions=system.file(package='base'))
})
observeEvent(input$pathwaygraphBt , {
    closeAlert(session,"pathviewAlert")
    data <- pathway.data()
    if(is.null(data)) {
        createAlert(session, "pathviewmessage", "pathviewAlert", title = "Data error", style =  "danger",
                    content = "Please upload results", append = FALSE)
        return(NULL)
    }
    pathway.id <- isolate({input$pathway.id})
    kegg.native <- isolate({input$kegg.native.checkbt})

    # Converting Gene symbol to geneID
    if(all(grepl("ENS", data$Gene_symbol))) {
        fromType <- "ENSEMBL"
    } else {
        fromType <- "SYMBOL"
    }

    eg = as.data.frame(bitr(data$Gene_symbol,
                            fromType=fromType,
                            toType="ENTREZID",
                            OrgDb="org.Hs.eg.db"))
    eg <- eg[!duplicated(eg[,fromType]),]
    colnames(eg) <- c("Gene_symbol","ENTREZID")
    data <- merge(data,eg,by="Gene_symbol")

    data <- subset(data, select = c("ENTREZID", "logFC"))
    genelistDEGs <- as.numeric(data$logFC)
    names(genelistDEGs) <- data$ENTREZID

    withProgress(message = 'Creating pathway graph',
                 detail = 'This may take a while...', value = 0, {
                     # pathway.id: hsa05214 is the glioma pathway
                     # limit: sets the limit for gene expression legend and color
                     tryCatch({
                     hsa05214 <- pathview(gene.data  = genelistDEGs,
                                          pathway.id = pathway.id,
                                          species    = "hsa",
                                          kegg.native = kegg.native,
                                          limit      = list(gene=as.integer(max(abs(genelistDEGs)))))
                     }, error = function(e) {
                         createAlert(session, "pathviewmessage", "pathviewAlert", title = "Error", style =  "warning",
                                     content = "I couldn't convert the pdf to png.", append = FALSE)
                         print(e)
                     })

                     incProgress(1, detail = paste("Done"))
                 })
    getPath <- parseDirPath(get.volumes(isolate({input$workingDir})), input$workingDir)
    if (length(getPath) == 0) getPath <- paste0(Sys.getenv("HOME"),"/TCGAbiolinksGUI")

    if(kegg.native) {
        extension <- ".pathview.png"
    } else {
        extension <- ".pathview.pdf"
    }
    fname <- paste0(pathway.id,extension)
    if(file.path(getwd(),fname) != file.path(getPath,fname)) TCGAbiolinks:::move(fname,file.path(getPath,fname))

    createAlert(session, "pathviewmessage", "pathviewAlert", title = "Pathway graph created", style =  "success",
                content = paste0("Results saved in: ", file.path(getPath,fname)), append = FALSE)
})

observeEvent(input$pathwaygraphBt , {
    updateCollapse(session, "collapsepathview", open = "Pathview plot")
    output$pathviewPlot <- renderUI({
        plotOutput("pathviewImage", height = input$pathwaygraphheigth)
    })
})

observeEvent(input$pathwaygraphBt , {
    output$pathviewImage <- renderImage({
        getPath <- parseDirPath(get.volumes(isolate({input$workingDir})), input$workingDir)
        if (length(getPath) == 0) getPath <- paste0(Sys.getenv("HOME"),"/TCGAbiolinksGUI")
        pathway.id <- isolate({input$pathway.id})
        extension <- ".pathview.png"
        outfile <- file.path(getPath, paste0(pathway.id,extension))

        if(!isolate({input$kegg.native.checkbt})){
            x <- tryCatch({
                conv.extension <- ".pathview.pdf"
                extension <- "aux.pathview.png"
                outfile <- file.path(getPath, paste0(pathway.id,extension))
                animation::ani.options('autobrowse'=FALSE)
                animation::im.convert(file.path(getPath, paste0(pathway.id,conv.extension)), output = outfile, extra.opts="-density 150")
            },  error = function(e) {
                createAlert(session, "pathviewmessage", "pathviewAlert", title = "Error", style =  "warning",
                            content = "I couldn't convert the pdf to png.", append = FALSE)
                print(e)
            })
        }
        # Return a list containing the filename
        list(src = outfile,
             contentType = 'image/png',
             width =  input$pathwaygraphwidth,
             height = input$pathwaygraphheight,
             alt = "File not found")
    }, deleteFile = FALSE)

})