R/htmlUtils.R

Defines functions createEGSEAReport generateAllPathwaysPage generateAllHeatmapsPage generateSummaryPage generateAllGOgraphsPage generateAllGOgraphsPage.comparison generateSummaryPage.comparison anyOccur writeEGSEAResultsToHTML writeResultsToHTML

#Ensemble of Gene Set Enrichment Analyses 
# 
# Author: Monther Alhamdoosh, E:[email protected]
###############################################################################

writeResultsToHTML <- function(contrast.name, gsa.results, gs.annot, method, 
file.name){
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using ", method, " (", 
            contrast.name, ")")
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    if (!is.data.frame(gsa.results)){
        rows = row.names(gsa.results)
        gsa.results = data.frame(gsa.results)   
        gsa.results = lapply(gsa.results, as.numeric)
        gsa.results = as.data.frame(gsa.results)
        row.names(gsa.results) = rows
    }   
    annot.frame = gs.annot@anno[match(rownames(gsa.results), 
gs.annot@anno[,"GeneSet"]),]
    if ("BroadUrl" %in% colnames(annot.frame)){
        annot.frame[, "BroadUrl"] = hmakeTag("a", "Go to Broad", 
href=annot.frame[, "BroadUrl"]) 
    }
    if (length(grep("^gsdbgo", gs.annot@label)) == 1){
        annot.frame[, "SourceDB"] = "Go to AmiGO"
        annot.frame[, "SourceURL"] = paste0("http://amigo.geneontology.org/amigo/term/",
                annot.frame[, "GOID"])
    }
    if ("SourceURL" %in% colnames(annot.frame)){
        annot.frame[, "SourceDB"] = hmakeTag("a", annot.frame[, 
"SourceDB"], href=annot.frame[, "SourceURL"])
        annot.frame = annot.frame[, "SourceURL" != 
colnames(annot.frame)]
    }
    table.data = data.frame(annot.frame, gsa.results)   
    if ("Rank"  %in% colnames(table.data) ){
        table.data[, "Rank"] = as.numeric(table.data[, "Rank"])
    }
    if ("p.value" %in% colnames(table.data)){
        table.data[, "p.value"] = as.character(table.data[, "p.value"])
    }
    if ("p.adj" %in% colnames(table.data)){
        table.data[, "p.adj"] = as.character(table.data[, "p.adj"])
    }
    
    capture.output(HTMLsortedTable(table.data, title, title, file=file, path=path))
    
    annot.frame = gs.annot@anno[match(rownames(gsa.results), 
gs.annot@anno[,"GeneSet"]),]
    table.data = data.frame(Rank=as.numeric(seq(1, nrow(gsa.results))), 
            annot.frame,
            gsa.results)
    write.table(table.data,
            file=file.name, 
            sep="\t", 
            quote=FALSE, 
            row.names=FALSE)
}

writeEGSEAResultsToHTML <- function(contrast.name, gsa.results, gs.annot, 
file.name, comparison=FALSE, interactive=TRUE){   
    
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (",
            contrast.name, ")") 
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    if (!is.data.frame(gsa.results)){
        rows = row.names(gsa.results)
        gsa.results = data.frame(gsa.results)   
        gsa.results = lapply(gsa.results, as.numeric)
        gsa.results = as.data.frame(gsa.results)
        row.names(gsa.results) = rows
    }   
    ids = gs.annot@anno[match(rownames(gsa.results), gs.annot@anno[,2]), 
"ID"]
    if (!comparison){
        heatmaps = paste0("../hm-top-gs-", gs.annot@label, "/", 
                sub(" - ", "-", contrast.name), "/", ids, 
".heatmap.pdf")
        csvfiles = paste0("../hm-top-gs-", gs.annot@label, "/", 
                sub(" - ", "-", contrast.name), "/", ids, 
".heatmap.csv")
        
    }
    else{
        heatmaps = paste0("../hm-top-gs-", gs.annot@label, "/", ids, 
".heatmap.multi.pdf")       
        csvfiles = paste0("../hm-top-gs-", gs.annot@label, "/", ids, 
".heatmap.multi.csv")       
    }
    
    heatmaps = hmakeTag("a", "Show Map", href=heatmaps)     
    csvfiles = hmakeTag("a", "Interpret Results", href=csvfiles)
    heatmaps = paste(heatmaps, csvfiles)
    
    if (length(grep("^kegg", gs.annot@label)) == 0){
        table.data = data.frame(Rank=as.numeric(seq(1, 
nrow(gsa.results))), 
                Heatmaps=heatmaps, 
                gs.annot@anno[match(rownames(gsa.results), 
gs.annot@anno[,"GeneSet"]),],
                gsa.results)
        
        write.table(table.data[, -c(which(colnames(table.data) == 
"Heatmaps"))],
                file=file.name, 
                sep="\t", 
                quote=FALSE, 
                row.names=FALSE)
        
    }
    else{
        if (!comparison){
            pathways = paste0("../pv-top-gs-", gs.annot@label, "/", 
                    sub(" - ", "-", contrast.name), "/", 
ids, ".pathview.png")           
        } else{
            pathways = paste0("../pv-top-gs-", gs.annot@label, "/",
                    ids, ".pathview.multi.png")
        }
        pathways = hmakeTag("a", "Show Pathway", href=pathways)
        pathways = paste(pathways, csvfiles)
        table.data = data.frame(Rank=as.numeric(seq(1, 
nrow(gsa.results))),
                Heatmaps=heatmaps,
                Pathways=pathways,
                gs.annot@anno[match(rownames(gsa.results), 
gs.annot@anno[,"GeneSet"]),],
                gsa.results)
        write.table(table.data[, -c(which(colnames(table.data) == 
"Heatmaps"), which(colnames(table.data) == "Pathways"))],
                file=file.name, 
                sep="\t", 
                quote=FALSE, 
                row.names=FALSE)
    }
    for (i in 1:ncol(table.data)){
        if (is.numeric(table.data[, i])){
            if (!anyOccur(colnames(table.data)[i], c("p.value", 
"p.adj", "min.pvalue")))
                table.data[, i] = round(table.data[,i], 2)
            else if (! interactive)
                table.data[, i] = round(table.data[,i], 6)
        }
    }

    if ("BroadUrl" %in% colnames(table.data)){
        table.data[, "BroadUrl"] = hmakeTag("a", "Go to Broad", 
                href=table.data[, "BroadUrl"], 
'target'='_blank')  
    }
    if (length(grep("^gsdbgo", gs.annot@label)) == 1){
        table.data[, "SourceDB"] = "Go to AmiGO"
        table.data[, "SourceURL"] = paste0("http://amigo.geneontology.org/amigo/term/",
                table.data[, "GOID"])
    }
    if ("SourceURL" %in% colnames(table.data)){
        table.data[, "SourceDB"] = hmakeTag("a", table.data[, 
"SourceDB"], href=table.data[, "SourceURL"])
        table.data = table.data[, "SourceURL" != colnames(table.data)]
    }
    if ("GeneSet" %in% colnames(table.data)){
        table.data[, "GeneSet"] = gsub("_", " ", table.data[, 
"GeneSet"]) 
    }
    if ("Description" %in% colnames(table.data)){
        
        desc = c()
        for ( t in table.data[, "Description"]){
            l = stri_length(t)
            if (is.na(l) || l <= 50)
                desc = c(desc, t)
            else
                desc = c(desc, paste0("<span title='", t,"'>", 
substr(t, 1, 50), " ... </span>"))
        }
        table.data[, "Description"] = desc
    }
    if ("direction" %in% colnames(table.data)){
   
        table.data[, "direction"] = 
as.character(lapply(as.numeric(table.data[, "direction"]), 
                function(x) if (x > 0) "Up" else if (x < 0) 
"Down" else "Neutral"))

    }
    if ("Rank"  %in% colnames(table.data) ){
        table.data[, "Rank"] = as.numeric(table.data[, "Rank"])
    }
    if ("p.value" %in% colnames(table.data)){
        table.data[, "p.value"] = as.character(table.data[, "p.value"])
    }
    if ("p.adj" %in% colnames(table.data)){
        table.data[, "p.adj"] = as.character(table.data[, "p.adj"])
    }
    
    capture.output(HTMLsortedTable(table.data, title, title, file=file, path=path))
    if(interactive){
      saveWidget(widget=datatable(table.data,escape = FALSE), 
                 selfcontained=FALSE, libdir=file.path(path,"lib"), 
                 file=file.path(path,file)) # DT::datatable 
    }else{
      capture.output(HTMLsortedTable(table.data, title, title, file=file, path=path))
    }
    
    
}

anyOccur <- function(string, list){
    occur = FALSE
    for (x in list){
        if (length(grep(x, string)) > 0){
            occur = TRUE
            break
        }           
    }
    return(occur)
}

generateSummaryPage.comparison <- function(contrast.names, gs.annot, 
        sum.plot.axis, sort.by, file.name, interactive=TRUE){
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (Comparison Analysis)")
    if (length(contrast.names) == 2 ){
        img.files = paste0("./", gs.annot@label, "-summary-",
                sum.plot.axis, c("-rank", "-dir"),".png")
        plot.titles = c("Summary plot based on gene set rank and size", 
        "Summary plot based on regulation direction and significance")
    }
    else if (length(contrast.names) > 2){
        img.files = c()
        plot.titles = c()
        anchor.names = c()
        anchors.table = matrix("-", length(contrast.names), 
length(contrast.names))
        colnames(anchors.table) = contrast.names
        rownames(anchors.table) = contrast.names
        for (i in 1:(length(contrast.names)-1)){
            for (j in (i+1):length(contrast.names)){
                anchor.names = c(anchor.names, c(paste0('anch', 
                        i,j),paste0('anch', i,j)))
                anchors.table[i, j] = hmakeTag("a", "View", 
                        style="text-decoration: none",
                        href=paste0("#", 'anch', i,j))
                anchors.table[j, i] = hmakeTag("a", "View", 
                        style="text-decoration: none",
                        href=paste0("#", 'anch', i,j))
                img.files = c(img.files, paste0("./", 
                        gs.annot@label, paste0('-', 
                        i,j), "-summary-",
                        sum.plot.axis, c("-rank", "-dir"),
                        ".png"))
                titles = c("Summary plot based on gene set rank 
and size <br/>", 
                        "Summary plot based on 
regulation direction and significance <br/>")
                titles = paste0(titles, contrast.names[i]," | 
", contrast.names[j])
                plot.titles = c(plot.titles, titles)
                
            }
        }
    }
    else{
        img.files = c()
        plot.titles = c()
    }
    # add summary heatmaps if more than 2 contrasts to the comparison analysis page
    if (length(contrast.names) >= 2){
        file.name = paste0("./",gs.annot@label, 
                "-summary-heatmap-", sort.by,".png")
        img.files = c(img.files, file.name)
        fig.title = paste0("Summary heatmap of the top gene sets (",
            hmakeTag("a", "Interpret Results", 
                    href=sub(".png", ".csv", file.name)), ")")
        plot.titles = c(plot.titles, fig.title)
    }
    if(interactive){
      html.img.files = sub(".png", ".html", img.files)
      pdfs = hmakeTag("a", "Open interactive plot", href=html.img.files) 
      # actually they are html files. but for convention we still call it pdf
      pdf.files = html.img.files
    }else{
      pdf.img.files = sub(".png", ".pdf", img.files)
      pdfs = hmakeTag("a", "Download pdf file", href=pdf.img.files) 
      pdf.files = pdf.img.files
    }
    file.name.bar = paste0("./",                    
            "comparison-", gs.annot@label, "-bar-plot-", 
            sort.by ,".png")
    img.files = c(img.files, file.name.bar)
    plot.titles = c(plot.titles, "Bar plot of the top gene sets")
    pdf.files = c(pdf.files, sub(".png", ".pdf", file.name.bar))
    images = hmakeTag("a", hmakeTag("img", src=img.files, width=500), 
href=pdf.files)
    content = paste(images, plot.titles, pdfs, sep="<br/>")
    if (length(contrast.names) > 2){
        anchors = hmakeTag("a", "", name=anchor.names)
        content = paste(anchors, content, sep="")
    }   
    if (length(content) %% 2 != 0){     
        content = c(content, "")# to make sure there are multiple of 2s
    }   
    content = matrix(content, ncol=2, byrow = TRUE) 

    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    if (length(contrast.names) > 2){
        hwrite(anchors.table, align="center", border=1, width="1000px", 
                cellspacing=0, row.bgcolor='#ffffaa',
                row.style=list('font-weight:bold'),
                col.bgcolor='#ffffaa',
                col.style=list('font-weight:bold'),
                page=p)
    }
    hwrite(content, align="center", border=0, page=p)
    closePage(p)    
}

generateAllGOgraphsPage.comparison <- function(contrast.names, gs.annot, 
        sort.by, file.name){
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (Comparison Analysis)")   
    check.files = file.exists(paste0(path, 
                    "comparison-", gs.annot@label, "-top-", 
            sort.by, "-",  c("BP", "MF", "CC"), ".png"))
    if (sum(check.files) == 0 )
        content = hmakeTag("h3", "GO graphs could not be generated!")
    else{
        img.files = paste0("./comparison-", gs.annot@label, "-top-", 
                sort.by, "-",  c("BP", "MF", "CC"), ".png")[check.files]
        plot.titles =c("Top GO Biological Processes ", "Top GO Molecular Functions", 
            "Top GO Cellular Components ")[check.files]
        
        pdf.files = sub(".png", ".pdf", img.files)
        
        images = hmakeTag("a", hmakeTag("img", src=img.files, width=500), 
            href=pdf.files)
        pdfs = hmakeTag("a", "Download pdf file", href=pdf.files)
            
        content = paste(images, plot.titles, pdfs, sep="<br/>")
        if (length(content) %% 2 != 0){     
            content = c(content, "")# to make sure there are multiple of 2s
        }   
        content = matrix(content, ncol=2, byrow = TRUE)
    }
    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    hwrite(content, align="center", border=0, page=p)
    closePage(p)
}

generateAllGOgraphsPage <- function(contrast.name, gs.annot, sort.by,
        file.name){
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (",
            contrast.name, ")") 
    
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(normalizePath(paste(path[1:length(path) -1], collapse = 
"/")), "/")
    
    tmp = c("BP", "MF", "CC")
    img.files = c()
    plot.titles = c()
    cat.names = c("Top GO Biological Process.", "Top GO Molecular 
Functions.", 
            "Top GO Cellular Components.")
    names(cat.names) = tmp
    for (cat in tmp){
        f= paste0(sub(" - ", "-", contrast.name), "-", gs.annot@label, 
                "-top-", sort.by, "-", cat, ".png")
        if (file.exists(paste0(path, f))){
            img.files = c(img.files, f)
            plot.titles = c(plot.titles, cat.names[cat])
        }
    }
    if (length(img.files) > 0){
        img.files = paste0("./", img.files)
        pdf.files = sub(".png", ".pdf", img.files)
        
        images = hmakeTag("a", hmakeTag("img", src=img.files, 
width=600), href=pdf.files)
        pdfs = hmakeTag("a", "Download pdf file", href=pdf.files)
        
        content = paste(images, plot.titles, pdfs, sep="<br/>")
        if (length(content) %% 2 != 0){     
            content = c(content, "")# to make sure there are 
# multiple of 2s
        }   
        content = matrix(content, ncol=2, byrow = TRUE)
    }
    else
        content = hmakeTag("h3", "GO graphs could not be generated!")
    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    hwrite(content, align="center", border=0, page=p)
    closePage(p)
}

generateSummaryPage <- function(contrast.name, gs.annot, sum.plot.axis, 
        sort.by, contr.num, file.name, interactive=TRUE){
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (",
            contrast.name, ")") 
    img.files = paste0("./", sub(" - ", "-", contrast.name), "-", 
gs.annot@label, "-summary-", sum.plot.axis ,"-rank.png")
    img.files = c(img.files, paste0("./", sub(" - ", "-", contrast.name), 
"-", gs.annot@label, "-summary-", sum.plot.axis,"-dir.png"))
    path = strsplit(file.name, "/")[[1]]    
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    mds.file = paste0(sub(" - ", "-", contrast.name), "-", gs.annot@label, 
"-methods.png")
    if(interactive){
      pdf.files = sub(".png", ".html", img.files)
      pdfs = hmakeTag("a", "Open interactive plot", href=pdf.files)
    }else{
      pdf.files = sub(".png", ".pdf", img.files)
      pdfs = hmakeTag("a", "Download pdf file", href=pdf.files)
    }
    if (file.exists(paste0(path, mds.file))){
      img.files = c(img.files, paste0("./", mds.file))
      ta = hmakeTag("a", "Download pdf file", href=sub(".png", ".pdf", paste0("./", mds.file)))
      pdfs = c(pdfs, ta)
      pdf.files = c(pdf.files, sub(".png", ".pdf", paste0("./", mds.file)))
      
    }
    # add summary heatmap to the contrast summary page if no. contrasts = 1
    if (contr.num == 1){
        file.name.sum = paste0("./", gs.annot@label, 
                "-summary-heatmap-", sort.by,".png")
        img.files = c(img.files, file.name.sum)  
        ta = hmakeTag("a", "Download pdf file", href=sub(".png", ".pdf", file.name.sum))
        pdfs = c(pdfs, ta)
        pdf.files =  c(pdf.files, sub(".png", ".pdf", file.name.sum))
    }
    file.name.bar = paste0("./",contrast.name,                    
            "-", gs.annot@label, "-bar-plot-", 
            sort.by,".png")
    img.files = c(img.files, file.name.bar)
    pdf.files = c(pdf.files, sub(".png", ".pdf", file.name.bar))
    
    images = hmakeTag("a", hmakeTag("img", src=img.files, width=500), 
href=pdf.files)
    pdfs = c(pdfs, hmakeTag("a", "Download pdf file", href=sub(".png", ".pdf", file.name.bar)))
    plot.titles = c("Summary plot based on gene set rank and size", 
            "Summary plot based on regulation direction and significance")
    if (file.exists(paste0(path, mds.file)))
        plot.titles = c(plot.titles,
                "MDS plot for the gene set ranking in different base methods.")
    if (contr.num == 1) {
        fig.title = paste0("Summary heatmap of the top gene sets (",
                hmakeTag("a", "Interpret Results", 
                        href=sub(".png", ".csv", file.name.sum)), ")")
        plot.titles = c(plot.titles, fig.title)
    }
        
    content = paste(images, plot.titles, pdfs, sep="<br/>")
    if (length(content) %% 2 != 0){     
        content = c(content, "")# to make sure there are multiple of 2s
    }   
    content = matrix(content, ncol=2, byrow = TRUE)
    
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    
    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    hwrite(content, align="center", border=0, page=p)
    closePage(p)    
}

generateAllHeatmapsPage <- function(contrast.name, gsa.results, gs.annot, 
file.name, comparison=FALSE){
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (",
            contrast.name, ")") 
    ids = gs.annot@anno[match(rownames(gsa.results), gs.annot@anno[,2]), 
"ID"]
    names = gs.annot@anno[match(rownames(gsa.results), gs.annot@anno[,2]), 
"GeneSet"]
    if(!comparison){
        heatmaps.img = paste0("./", sub(" - ", "-", contrast.name), 
"/", ids, ".heatmap.png")
        heatmaps = paste0("./", sub(" - ", "-", contrast.name), "/", 
ids, ".heatmap.pdf")
        csvfiles = paste0("./", sub(" - ", "-", contrast.name), "/", 
ids, ".heatmap.csv")
    } else{
        heatmaps.img = paste0("./", ids, ".heatmap.multi.png")
        heatmaps = paste0("./", ids, ".heatmap.multi.pdf")
        csvfiles = paste0("./", ids, ".heatmap.multi.csv")
    }
    heatmaps.img = hmakeTag("a", hmakeTag("img", src=heatmaps.img, 
width=300, center=TRUE), href=heatmaps) 
    heatmaps = hmakeTag("a", "Large Map", href=heatmaps)    
    csvfiles = hmakeTag("a", "Interpret Results", href=csvfiles)
    heatmaps = paste(heatmaps, csvfiles)
    heatmaps = paste(heatmaps.img, ids, substr(names, 1, 30), heatmaps, 
sep="<br />")   
#   head(heatmaps)
    if (length(heatmaps) %% 5 != 0)
        heatmaps = c(heatmaps, rep("", 5 - (length(heatmaps) %% 5 )))
    hm.table = matrix(heatmaps, ncol=5, byrow = TRUE)
            
            
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    
    
    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    hwrite(hm.table, col.width = 200, page=p)
    closePage(p)        
    
}

generateAllPathwaysPage <- function(contrast.name, gsa.results, gs.annot, 
file.name, comparison=FALSE){
    title = paste0("Gene Set Enrichment Analysis on ", gs.annot@name, " 
using EGSEA (",
            contrast.name, ")") 
    ids = gs.annot@anno[match(rownames(gsa.results), gs.annot@anno[,2]), 
"ID"]
    names = gs.annot@anno[match(rownames(gsa.results), gs.annot@anno[,2]), 
"GeneSet"]
    if (!comparison){
        pathways.img = paste0("./", sub(" - ", "-", contrast.name), 
"/", ids, ".pathview.png")
        csvfiles = paste0("../hm-top-gs-",gs.annot@label, "/", sub(" - 
", "-", contrast.name), "/", ids, ".heatmap.csv")
        pathways = paste0("./", sub(" - ", "-", contrast.name), "/", 
ids, ".pathview.png")
    } else{
        pathways.img = paste0("./", ids, ".pathview.multi.png")
        csvfiles = paste0("../hm-top-gs-",gs.annot@label, "/", ids, 
".heatmap.multi.csv")
        pathways = paste0("./", ids, ".pathview.multi.png")
    }   
    pathways.img = hmakeTag("a", hmakeTag("img", src=pathways.img, 
width=300, center=TRUE), href=pathways)     
    csvfiles = hmakeTag("a", "Interpret Results", href=csvfiles)  
    pathways = hmakeTag("a", "Large Pathway", href=pathways)
    pathways = paste(pathways, csvfiles)
    pathways = paste(pathways.img,ids, substr(names, 1, 30), pathways, 
sep="<br />")   
#   head(heatmaps)
    if (length(pathways) %% 5 != 0)
        pathways = c(pathways, rep("", 5 - (length(pathways) %% 5 )))
    hm.table = matrix(pathways, ncol=5, byrow = TRUE)
    
    
    path = strsplit(file.name, "/")[[1]]    
    file = path[length(path)]
    file = gsub(".txt", ".html", file)
    path = paste0(paste(path[1:length(path) -1], collapse = "/"), "/")
    
    
    p = openPage(file, dirname=path, title=title)
    hwrite(title, heading=1, br=TRUE, page=p)
    hwrite(hm.table, col.width = 200, page=p)
    closePage(p)
}

createEGSEAReport <- function(sampleSize, contr.names, gs.annots, baseInfo, 
combineMethod, 
        sort.by,  report.dir, 
        logFC.cal, symbolsMap,
        egsea.ver,
        egseadata.ver){ 
    contr.num = length(contr.names)    
    gs.labels = sapply(gs.annots, function(x) x$label)
    gs.names =  sapply(gs.annots, function(x) x$name)
    gs.versions = sapply(gs.annots, function(x) x$version)
    gs.dates = sapply(gs.annots, function(x) x$date)
    ranked.gs.dir = "./ranked-gene-sets-base"    
    pv.dir = paste0("./pv-top-gs-", gs.labels[grep("^kegg", gs.labels)], 
"/")
    hm.dir = paste0("./hm-top-gs-", gs.labels, "/")
    summary.dir = "./summary/"
    go.dir = "./go-graphs/"
    
    
    p = openPage("index.html", dirname=report.dir, title="Ensemble of Gene 
Set Enrichment Analyses (EGSEA) - Report")    
    logo.file = system.file("logo", "EGSEA_logo.png", package="EGSEA")
    if (file.exists(logo.file)){
        file.copy(logo.file, report.dir)
        img = hmakeTag("img", src="EGSEA_logo.png", width="150", 
                style="float:left;")
        title = hmakeTag("h1", "Gene Set Testing Report",
                style="color:#0f284f; position:relative; top:18px; left:10px;")
        tmp = hmakeTag("div", paste0(img, title))
        hwrite(tmp, div=TRUE, heading=1, br=TRUE, page=p)
    }else
        hwrite("EGSEA Gene Set Testing Report", style="color:#0f284f",
                heading=1, br=TRUE, page=p) 
    
    hwrite("Analysis Parameters", style="color:#22519b", 
            heading=2, page=p)
    #### write analysis parameters
    hwrite(paste0(hmakeTag("b", "Total number of genes: ") ,
                    length(gs.annots[[1]]$featureIDs)), 
        br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b", "Total number of samples: " ),
                    sampleSize), br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b", "Number of contrasts: ") ,contr.num), 
            br=TRUE, page=p)
    base.names = names(baseInfo)
    base.vers = sapply(base.names, function(x) as.character(baseInfo[[x]]$version))
    base.pkgs = sapply(base.names, function(x) baseInfo[[x]]$package)
    baseMethods = paste0(base.names, " (", base.pkgs, ":", base.vers, ")")
    hwrite(paste0(hmakeTag("b","Base GSEA methods: ") ,paste(baseMethods, 
            collapse=", ")), br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b","P-value combine method: " ), 
            combineMethod), br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b","Sorting statistic: " ),sort.by), br=TRUE, 
            page=p)
    hwrite(paste0(hmakeTag("b","Fold changes calculated: " ),logFC.cal), 
            br=TRUE, page=p)    
    hwrite(paste0(hmakeTag("b","Gene IDs - Symbols mapping used: " ), 
            ifelse(nrow(symbolsMap) > 0, "Yes", 
            "No")), br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b","Organism: " ), gs.annots[[1]]$species), 
            br=TRUE, page=p)
    gs.cols = paste0(gs.names, " (", gs.versions, ", ", gs.dates, ")")
    hwrite(paste0(hmakeTag("b","Gene set collections: " ), paste(gs.cols, collapse=", ")), 
        br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b","EGSEA version: " ), egsea.ver), 
        br=TRUE, page=p)
    hwrite(paste0(hmakeTag("b","EGSEAdata version: " ), egseadata.ver), 
        br=TRUE, page=p)    
 
    hwrite(hmakeTag("br"), br=TRUE)
    hwrite("Analysis Results", style="color:#22519b",
            heading=2, page=p)
    main = ""
    ## Main Page Generation 
    for (i in 1:contr.num){        
        
        file.name = paste0(ranked.gs.dir, "/ranked-", gs.labels, 
"-gene-sets-", 
                sub(" - ", "-", contr.names[i]), 
'.html')        
        temp = paste0(gs.names, " (", hmakeTag("a", "Stats Table", 
href=file.name))
            
        file.name = paste0(hm.dir,  
                sub(" - ", "-", contr.names[i]), 
'-allHeatmaps.html')
        temp = paste0(temp, ", ", hmakeTag("a", "Heatmaps" , 
href=file.name))
                    
        kegg.idx =  grep("^kegg", gs.labels)
        if (length(kegg.idx) != 0){
            file.name = paste0(pv.dir, 
                    sub(" - ", "-", contr.names[i]), 
'-allPathways.html')    
            temp[kegg.idx] = paste0(temp[kegg.idx], ", ", 
hmakeTag("a", "Pathways" , href=file.name))
        }
        
        go.idx = c(grep("^c5", gs.labels), grep("^gsdbgo", gs.labels))
        if (length(go.idx) !=0 ){
            file.name = paste0(go.dir, 
                    sub(" - ", "-", contr.names[i]), 
                    "-", gs.labels[go.idx], '-allGOgraphs.html')    
            temp[go.idx] = paste0(temp[go.idx], ", ", hmakeTag("a", 
"GO Graphs" , href=file.name))
        }
        
        file.name = paste0(summary.dir, sub(" - ", "-", 
contr.names[i]), "-", gs.labels, 
                "-summary.html")
        temp = paste0(temp, ", ", hmakeTag("a", "Summary Plots", 
href=file.name))
        
        file.name = paste0(ranked.gs.dir, "/ranked-", gs.labels, 
"-gene-sets-", 
                sub(" - ", "-", contr.names[i]), '.txt')
        temp = paste0(temp, ", ", hmakeTag("a", "Download 
Stats",target="_blank", href=file.name))
            
        
        temp = paste0(temp, ")")
        
        temp = hmakeTag("il", paste(hmakeTag("b", 
contr.names[i]), hmakeTag("ul", paste(hmakeTag("li", temp), 
collapse="\n")), sep="\n"))
        main = paste(main, temp, sep="\n")
    }
    
    if (contr.num > 1){
        file.name = paste0(ranked.gs.dir, "/ranked-", gs.labels, 
"-gene-sets-compare.html")      
        
        temp = paste0(gs.names, " (", hmakeTag("a", "Stats Table", 
href=file.name))
        
        file.name = paste0(hm.dir, 'allHeatmaps.html')
        temp = paste0(temp, ", ", hmakeTag("a", "Heatmaps" , 
href=file.name))
        
        kegg.idx =  grep("^kegg", gs.labels)
        if (length(kegg.idx) != 0){
            file.name = paste0(pv.dir, 'allPathways.html')
            temp[kegg.idx] = paste0(temp[kegg.idx], ", ", 
hmakeTag("a", "Pathways" , href=file.name))
        }
        
        go.idx = c(grep("^c5", gs.labels), grep("^gsdbgo", gs.labels))
        if (length(go.idx) !=0 ){
            file.name = paste0(go.dir, gs.labels[go.idx], '-allGOgraphs.html')  
            temp[go.idx] = paste0(temp[go.idx], ", ", hmakeTag("a", 
                "GO Graphs" , href=file.name))
        }
        
        file.name = paste0(summary.dir, gs.labels, "-summary.html")
        temp = paste0(temp, ", ", hmakeTag("a", "Summary Plots", 
href=file.name))
        
        file.name = paste0(ranked.gs.dir, "/ranked-", gs.labels, 
"-gene-sets-compare.txt")
        temp = paste0(temp, ", ", hmakeTag("a", "Download Stats" , 
target="_blank", href=file.name))
        
        temp = paste0(temp, ")")
        
        temp = hmakeTag("il", paste(hmakeTag("b", "Comparison 
Analysis"), hmakeTag("ul", paste(hmakeTag("li", temp), collapse="\n")), 
sep="\n"))
        main = paste(main, temp, sep="\n")
    }

    hwrite(hmakeTag("ul", main, style="list-style-type:square"), page=p)
    hwrite(hmakeTag("footer", "Report generated by EGSEA package. For any 
inquiry, please contact the authors."))
    closePage(p)
    
}

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EGSEA documentation built on May 2, 2018, 2:43 a.m.