Nothing
R/htmlUtils.R
In EGSEA: Ensemble of Gene Set Enrichment Analyses
Defines functions
createEGSEAReport
generateAllPathwaysPage
generateAllHeatmapsPage
generateSummaryPage
generateAllGOgraphsPage
generateAllGOgraphsPage.comparison
generateSummaryPage.comparison
anyOccur
writeEGSEAResultsToHTML
writeResultsToHTML
#Ensemble of Gene Set Enrichment Analyses
#
# Author: Monther Alhamdoosh, E:m.hamdoosh@gmail.com
###############################################################################
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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Defines functions createEGSEAReport generateAllPathwaysPage generateAllHeatmapsPage generateSummaryPage generateAllGOgraphsPage generateAllGOgraphsPage.comparison generateSummaryPage.comparison anyOccur writeEGSEAResultsToHTML writeResultsToHTML
#Ensemble of Gene Set Enrichment Analyses
#
# Author: Monther Alhamdoosh, E:m.hamdoosh@gmail.com
###############################################################################
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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