inst/app/code/server/s_input.data.R

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

resetUploadedTable = reactive(
    {
        input$usePathways
        print("reset uploaded omics table")
        originalOmicsTable(data.frame())
        uploadedMappingTable(data.frame())
        omicsGlyphIdTable(data.frame())

        originalOmicsTitleText("")
        uploadedMappingTitleText("")
        GlyphIdOmicsTitleText("")
        if(input$usePathways %in% c("UsePrePathways","enrichAnalysis")){
            uploadedMappingTitleText("Using pre-collected pathways. Mapping table is selected internally.")
        }else if(input$usePathways == 'userSBGN'){
            uploadedMappingTitleText("Using uploaded SBGN-ML. Please upload a mapping table.")
        }
        return(NULL)
    }
)
originalOmicsTitleText = reactiveVal("")
output$originalOmicsTitle = renderText({
    originalOmicsTitleText()
})
originalOmicsTable = reactiveVal(data.frame())
output$OriginalOmics <- DT::renderDataTable({
    originalOmicsTable()
})
output$RunLoadOriginalTable = renderText({
    loadOriginalTable()
})
output$RunLoadMappingTable = renderText({
    loadMappingTable()
})
output$RunGenGlyphIdTable = renderText({
    OmicsDataGlyphID()
})
output$RunResetOriginalTable = renderText({
    resetUploadedTable()
})
    # input$file1 will be NULL initially. After the user selects
    # and uploads a file, head of that data file by default,
    # or all rows if selected, will be shown.
loadOriginalTable = reactive({
    req(input$file1)
    # originalOmicsTitleText("Omics data with original molecule IDs")
    originalOmicsTitleText("")
    # when reading semicolon separated files,
    # having a comma separator causes `read.csv` to error
    tryCatch(
        {
            df <- read.table(input$file1$datapath,
                           header = input$header,
                           sep = input$sep,
                           as.is = TRUE,
                           quote = input$quote)
        },
        error = function(e) {
            # return a safeError if a parsing error occurs
            stop(safeError(e))
        }
    )
    print(head(df))
    originalOmicsTable(df)
    return("")
    # if(input$disp == "head") {
    #     return(head(df))
    # }
    # else {
    #     return(df)
    # }
})

GlyphIdOmicsTitleText = reactiveVal("")
output$GlyphIdOmicsTitle = renderText({
    GlyphIdOmicsTitleText()
})
omicsGlyphIdTable = reactiveVal(data.frame())
output$GlyphIdOmics <- DT::renderDataTable({
    # df = OmicsDataGlyphID()
    # return(df)
    omicsGlyphIdTable()
})
SBGN.glyph.id.type = reactiveVal("")

OmicsDataGlyphID = eventReactive(
    input$uploadOmics
    ,{
        # GlyphIdOmicsTitleText("Omics data with SBGN-ML file glyph IDs: Please select the correct parameters on the left panel: 'Omics molecule ID type', 'species' and 'How to map Omics ID to SBGN glyph ID'")
        GlyphIdOmicsTitleText("")
        df <- read.table(input$file1$datapath,
                         header = input$header,
                         sep = input$sep,
                         as.is = TRUE,
                         quote = input$quote)
        cat("\n\n\n uploaded mapping data is\n\n")
        print(head(mapping.data()))
        cat("\n\n\n")
        input.type = input$OmicsIdType
        input.org = input$org
        # if(input$IdMappingSource == "useUserMapping" & ncol(mapping.data())>1){
        if(input$usePathways == 'userSBGN'){
            cat("\n\n\n using user mapping table to change id \n\n")
            output.type = input$uploadedSbgnGlyphIdType
            print(input.type)
            print(output.type)
            if(!all(c(input.type,output.type) %in% colnames(mapping.data()))){
                stop("\n ID mapping table's column names don't match selected 'Omics ID type' and 'SBGN-ML glyph ID types'!\n\n"
                    ,"Your inputs are: \n"
                    ,"SBGN-ML glyph ID type: ", output.type,"\n "
                    ,"Omics molecule ID type: ", input.type,"\n\n"
                    ,"column names of uploaded mapping table are: \n"
                    ,paste(colnames(mapping.data())
                           ,collapse = "   "),"\n\n"
                    ,"If you don't have an ID mapping table for this ID type pair 
                    and if you are using our precollected SBGN-ML file,
                    try to select 'use SBGNview mapping' as 'How to map Omics ID to SBGN glyph ID'."
                     )
            }
            # input.type = input$inputIdUser
            # input.org = input$orgUser
            print(head(mapping.data()))
            id.mapping.table = mapping.data()[,c(input.type,output.type)]
            print(head(id.mapping.table))
            cat("\n\n\n\n printed user mapping parameters \n\n")
        }else if(input$usePathways %in% c("UsePrePathways","enrichAnalysis")){
            cat("\n\n\n changing to pathway commons \n\n")
            # input.type = input$OmicsIdType
            output.type = "pathwayCommons"
            id.mapping.table = NULL
        }
        gene.data <- change.data.id(
            data.input.id = df,
            # input.type = input$OmicsIdType,
            # output.type = "pathwayCommons",
            input.type = input.type,
            output.type = output.type,
            cpd.or.gene = "gene",
            org = input.org,
            sum.method = "sum"
            ,id.mapping.table = id.mapping.table
        )
        SBGN.glyph.id.type(output.type)
        print("converted omics data id to glyph id")
        omicsGlyphIdTable(gene.data)
        return(
            ""
        )
    }
)

# Code to download example data
output$Example <- downloadHandler(
    filename = function() {
        # downloadNameVector[input$preData]
        "test out"
    },
    content = function(file) {
        # file.copy(input$preData, file)
        # if(input$preData == "userSBGN"){
        if(input$usePathways == 'userSBGN'){
            data("gse16873.d")
            out.data = gse16873.d[,1:3]
        # }else if(input$preData == "IFNg"){
        }else if(input$usePathways %in% c("UsePrePathways","enrichAnalysis")){
            print("using sbgnhub")
            count.data <- assays(IFNg)$counts
            wt <- colnames(IFNg)[IFNg$group == "wt"]
            ko <- colnames(IFNg)[IFNg$group == "ko"]
            mean.wt <- apply(count.data[,wt] ,1 ,"mean")
            head(mean.wt)
            mean.ko <- apply(count.data[,ko],1,"mean")
            head(mean.ko)
            ensemble.to.koVsWt <- mean.ko - mean.wt
            out.data = ensemble.to.koVsWt
            out.data = as.matrix(ensemble.to.koVsWt)
            colnames(out.data) = "Fold Change: IFNg-KO v.s. WT"
        }
        write.table(out.data, file = file,sep="\t")
    }
)

DemoOmicsDataTitleText = reactiveVal("")
output$DemoOmicsDataTitle = renderText({
    DemoOmicsDataTitleText()
})


output$demoDataTable <- DT::renderDataTable({
        # if(input$preData == "cancer"){
        if(input$usePathways == 'userSBGN'){
            data("gse16873.d")
            out.data = gse16873.d[,1:3]
            DemoOmicsDataTitleText("Demo Omics Data: breast cancer dataset")
        # }else if(input$preData == "IFNg"){
        }else if(input$usePathways %in% c("UsePrePathways","enrichAnalysis")){
            count.data <- assays(IFNg)$counts
            wt <- colnames(IFNg)[IFNg$group == "wt"]
            ko <- colnames(IFNg)[IFNg$group == "ko"]
            mean.wt <- apply(count.data[,wt] ,1 ,"mean")
            head(mean.wt)
            mean.ko <- apply(count.data[,ko],1,"mean")
            head(mean.ko)
            ensemble.to.koVsWt <- mean.ko - mean.wt
            out.data = as.matrix(ensemble.to.koVsWt)
            colnames(out.data) = "Fold Change: IFNg-KO v.s. WT"
            DemoOmicsDataTitleText("Demo Omics Data: IFNg KO mice dataset")
        }
        return(out.data)
    })


mapping.data = reactiveVal(matrix())

uploadedMappingTitleText = reactiveVal("")


output$uploadedMappingTitle = renderText({
    uploadedMappingTitleText()
})

loadedIdPair = reactiveVal("")
output$loadedMappingPairs <- renderText({
    loadedIdPair()
})
uploadedMappingTable = reactiveVal(data.frame())
output$uploadedMapping <- DT::renderDataTable({
    uploadedMappingTable()
})
loadMappingTable = reactive({
    # or all rows if selected, will be shown.
    req(input$uploadMapping)
    # uploadedMappingTitleText("Uploaded ID mapping table")
    uploadedMappingTitleText("")
    # when reading semicolon separated files,
    # having a comma separator causes `read.csv` to error
    tryCatch(
        {
            df <- read.table(input$uploadMapping$datapath,
                           header = input$headerMapping,
                           sep = input$sepMapping,
                           as.is = TRUE,
                           quote = input$quoteMapping)
        },
        error = function(e) {
            # return a safeError if a parsing error occurs
            stop(safeError(e))
        }
    )
    loadedIdPair(paste0("An ID mapping table has been uploaded: \n\n"
                        ,paste(colnames(df),collapse = "<->")
                        )
                )
    mapping.data(df)
    uploadedMappingTable(df)
    # uploadedMappingTitleText("")
    return("")
    # return(df)
})