Nothing
R/groupReport.R
In GeneAnswers: Integrated Interpretation of Genes
Defines functions
`groupReport`
`groupReport` <-
function(dataMatrix, gAList, topCat=10, methodOfCluster=c('mds', 'sort'), matrixOfHeatmap=NULL, clusterTable=c('geneNum', 'pvalue', NULL), catTerm=TRUE,
fileName = "multiConceptsGenes.html", title='Multigroup Genes Concepts Analysis', catType=c('GO', 'KEGG', 'DOLITE', 'REACTOME.PATH', 'CABIO.PATH', 'Unknown'), reverseOfCluster=FALSE, colorValueColumn = NULL,
annLib=c('org.Hs.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db', 'org.Dm.eg.db'), nameLength=94, addID=TRUE, interactive=FALSE, bgColor='#ffffff', keepCytoscapeFiles=TRUE, wordleOn=FALSE, ...) {
catType <-match.arg(catType)
annLib <- match.arg(annLib)
showCats <- c(1:topCat)
k <- 0
while (TRUE) {
if ((all(!file.exists(c(paste(fileName, '_', k, '.html', sep=''), paste(paste(fileName, '_', k, '.html', sep=''), 'files', sep='.'), paste(paste(fileName, '_', k, '.html', sep=''), 'cytoscapeWebFiles', sep='.')))) & (k > 0)) |
(all(!file.exists(c(fileName, paste(fileName, 'files', sep='.'), paste(fileName, 'cytoscapeWebFiles', sep='.')))) & (k == 0))) {
if (k > 0) {
fileName <- paste(fileName, '_', k, '.html', sep='')
print(paste('New file is', fileName))
}
break;
} else {
if (k > 0) print(paste(paste(c(paste(fileName, '_', k, '.html', sep=''), paste(paste(fileName, '_', k, '.html', sep=''), 'files', sep='.'), paste(paste(fileName, '_', k, '.html', sep=''), 'cytoscapeWebFiles', sep='.')),
collapse=' and/or '), 'are in current location, they will not be overwritten.'))
else print(paste(paste(c(fileName, paste(fileName, 'files', sep='.'), paste(fileName, 'cytoscapeWebFiles', sep='.')), collapse=' and/or '), 'are in the current location, they will not be overwritten.'))
}
k <- k + 1
}
if (!is.null(colorValueColumn) & (length(colorValueColumn) > 1) & (length(colorValueColumn) != length(gAList))) stop('Specified colorValueColumns can not match the given gAList! Aborting ...')
if (length(colorValueColumn) == 1) colorValueColumn <- rep(colorValueColumn, length(gAList))
if (!is.null(colorValueColumn)) {
allColNames <- lapply(gAList, function(x) return(colnames(getGeneInput(x))))
validColNames <- c()
for (i in 1:length(colorValueColumn)) validColNames <- c(validColNames, colorValueColumn[i] %in% allColNames[[i]])
if (!(all(validColNames))) stop(paste("The given colorValueColumn(s)[position ", paste(which(!validColNames), sep="", collapse=" "), "] might not be the column names of geneInput slots of the given gAList! Aborting ...", sep=''))
}
if (is.matrix(dataMatrix) | is.data.frame(dataMatrix) | is.vector(dataMatrix)) {
dataMatrix <- as.matrix(dataMatrix)
if ((NA %in% rownames(dataMatrix)) | is.null(rownames(dataMatrix))) print('Warning: NA or NULL might be in rownames of dataMatrix!')
if ((NA %in% colnames(dataMatrix)) | is.null(colnames(dataMatrix))) print('Warning: NA or NULL might be in colnames of dataMatrix!')
} else stop('Input is not a valid matrix!')
HTwrap <- function(x, tag = "TD", scripts=NULL) {
if (is.null(scripts)) return(paste("<", tag, ">", x, "</", tag, ">", sep = ""))
else return(paste("<", tag, ' ', scripts, ">", x, "</", tag, ">", sep = ""))
}
if (!is.null(clusterTable) & !is.null(matrixOfHeatmap)) {
if (clusterTable == 'geneNum') {
if (is.numeric(dataMatrix)) {
baseM <- dataMatrix[1:(dim(dataMatrix)[1]-1),]
}
else stop('The input Matrix is not numeric!')
} else {
baseM <- matrixOfHeatmap
}
if (methodOfCluster == 'mds') {
distBaseM <- as.matrix(dist(baseM, method = "euclidean", upper=TRUE))
distBaseM[distBaseM < 1e-6] <- 1e-6
diag(distBaseM) <- 0
clusterResult <- isoMDS(distBaseM, k=1)$points
clusterOrder <- rownames(clusterResult)[order(clusterResult, decreasing=reverseOfCluster)]
originalIndexMatrix <- originalIndexMatrix[clusterOrder,]
matrixOfHeatmap <- matrixOfHeatmap[clusterOrder,]
tempM <- dataMatrix[c(clusterOrder, rownames(dataMatrix)[dim(dataMatrix)[1]]),]
dataMatrix <- tempM
} else {
clusterOrder <- sort(rownames(baseM), ...)
tempM <- dataMatrix[c(clusterOrder, rownames(dataMatrix)[dim(dataMatrix)[1]]),]
dataMatrix <- tempM
}
}
indexM <- which((is.numeric(dataMatrix) & (dataMatrix > 0)) | (is.character(dataMatrix) & (dataMatrix != "0 (1)")), arr.ind = TRUE)
if (catType != 'Unknown') {
indexNames <- rownames(indexM)[1:dim(indexM)[1]]
indexTerms <- getCategoryTerms(indexNames[which(!indexNames %in% "Genes / Group")], catType = catType, missing = "keep")
trueTerms <- paste('Genes in', names(indexTerms), '::', indexTerms, 'and Group', colnames(dataMatrix)[indexM[1:(dim(indexM)[1]),2][which(!(names(indexM[1:(dim(indexM)[1]),2]) %in% "Genes / Group"))]])
names(trueTerms) <- names(indexTerms)
pseudoTerms <- paste('Genes in Group', colnames(dataMatrix))
names(pseudoTerms) <- rep('Genes / Group', length(pseudoTerms))
finalTerms <- rep('', length(indexNames))
finalTerms[which(!indexNames %in% "Genes / Group")] <- trueTerms
finalTerms[which(indexNames %in% "Genes / Group")] <- pseudoTerms
names(finalTerms) <- NULL
tableNames <- c('Concepts-Genes Table', 'Concepts Relation', paste('Group', colnames(dataMatrix), 'Concepts-Gene network'), finalTerms)
#gsub('Genes / Group :: NA and ', replacement='', paste('Genes in', rownames(indexM)[1:dim(indexM)[1]], '::', getCategoryTerms(rownames(indexM)[1:dim(indexM)[1]], catType=catType, missing='keep'), 'and Group', colnames(dataMatrix)[indexM[1:dim(indexM)[1],2]]))
} else {
tableNames <- c('Concepts-Genes Table', 'Concepts Relation', paste('Group', colnames(dataMatrix), 'Concepts-Gene network'), gsub('Genes / Group and ', replacement='',
paste('Genes in', rownames(indexM)[1:dim(indexM)[1]], 'and Group', colnames(dataMatrix)[indexM[1:dim(indexM)[1],2]])))
}
attr <- c(catType, rep('Pictures', (1+dim(dataMatrix)[2])), rep('Entrez', dim(indexM)[1]))
outFile <- file(fileName, "w")
cat('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">', file = outFile, sep = "\n")
if (dir.create(paste(fileName, '.files', sep=''), showWarnings=FALSE) | file.exists(paste(fileName, '.files', sep=''))) {
if (interactive) {
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/js', sep=''), paste(fileName, '.files', sep=''), recursive=TRUE)) print(paste('Copy js to', paste(fileName, '.files', sep='')))
else { close(outFile); stop('js subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/swf', sep=''), paste(fileName, '.files', sep=''), recursive=TRUE)) print(paste('Copy swf to', paste(fileName, '.files', sep='')))
else { close(outFile); stop('swf subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/NetworkTransformer.jar', sep=''), '.', overwrite=TRUE)) {
Sys.chmod('NetworkTransformer.jar', mode='0777')
print(paste('Copy NetworkTransformer.jar to', paste(fileName, '.files', sep='')))
}
else { close(outFile); stop('NetworkTransformer.jar subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
headInfo <- paste(HTwrap(title, tag = "title"), '\n\t', HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/json2.min.js"', sep='')), '\n\t',
HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/AC_OETags.min.js"', sep='')), '\n\t',
HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/cytoscapeweb.min.js"', sep='')), '\n', sep='')
headInfo <- paste(headInfo, paste('\t', HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/edges_', c(1:length(gAList)), '.js"', sep='')),'\n', sep='', collapse=''),
'\t\t<script type="text/javascript">\n\t\twindow.onload=function() {\n', sep='')
headInfo <- paste(headInfo, paste('\t\t\tvar div_id', c(1:length(gAList)), ' = "cytoscapeweb', c(1:length(gAList)), '";\n', sep='', collapse=''),
'\t\t\tvar options = {\n\t\t\t\tswfPath: "', paste(fileName, '.files', sep=''), '/swf/CytoscapeWeb",\n\t\t\t\tflashInstallerPath: "', paste(fileName, '.files', sep=''), '/swf/playerProductInstall"\n\t\t\t};\n', sep='')
headInfo <- paste(headInfo, paste('\t\t\tvar vis', c(1:length(gAList)), ' = new org.cytoscapeweb.Visualization(div_id', c(1:length(gAList)), ', options);\n\t\t\tvis', c(1:length(gAList)), '.draw({ network: xml',c(1:length(gAList)), ' });\n', sep='', collapse=''),
'\t\t};</script>\n\t', HTwrap(' html, body { height: 100%; width: 100%; padding: 0; margin: 10; }\n\t#cytoscapeweb { width: 100%; height: 100%; }', tag='style'), sep='')
cat("<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>", HTwrap(headInfo, tag = "head"), '<body bgcolor="', bgColor, '">', file = outFile, sep = "\n")
} else {
cat("<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>", HTwrap(HTwrap(title, tag = "title"), tag = "head"), '<body bgcolor="', bgColor, '">', file = outFile, sep = "\n")
}
} else {
close(outFile)
stop(paste('Failure to create', paste(fileName, '.files', sep=''), 'subdirectory! Aborting ...'))
}
if (!missing(title)) cat("<center><H1 align=\"center\">", title, " </H1></center>\n", file = outFile, sep = "\n")
cat('</body>', "</html>", sep = "\n", file = outFile)
cat('<H1><font face="courier" size="4"><a name="h-0">Multigroup Genes Concepts Analysis</a></font></H1>\n<font face="courier" size="1">Generated by Bioconductor package <a HREF="http://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html">GeneAnswers</a> at ', format(Sys.Date(), "%a, %b %d %Y"), '</font>\n<p> </p>',file = outFile, sep = "")
for (i in 1:(2+dim(dataMatrix)[2])) {
cat(paste('<li><font face="courier" size="2"><a href="', paste('#h-', i, sep=''), '">', sep=''), tableNames[i], '</a></font>\n<p></p>\n',file = outFile, sep = "")
}
for (i in 1:length(tableNames)) {
if (attr[i] != 'Pictures') {
if (attr[i] == 'Entrez') {
a <- i - 2 - dim(dataMatrix)[2]
tempGeneInput <- getGeneInput(gAList[[indexM[a,2]]])
if (indexM[a,1] == dim(dataMatrix)[1]){
# generate all genes table
temp <- as.matrix(tempGeneInput)
colnames(temp) <- colnames(tempGeneInput)
rownames(temp) <- temp[,1]
if (dim(temp)[2] > 1) {
if (dim(temp)[1] > 1) {
tempColNames <- colnames(temp)
temp <- temp[!duplicated(temp),]
if (!is.matrix(temp)) {
temp <- matrix(temp, ncol=length(tempColNames))
rownames(temp) <- temp[,1]
colnames(temp) <- tempColNames
}
}
if (dim(temp)[2] > 1) {
tempColNames <- colnames(temp)[2:dim(temp)[2]]
tempRowNames <- rownames(temp)
temp <- as.matrix(temp[,2:dim(temp)[2]])
colnames(temp) <- tempColNames
rownames(temp) <- tempRowNames
}
}
.drawHTMLtable(temp, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=getAnnLib(gAList[[1]]), lastRowLink=TRUE, highlightLastRow=FALSE, topCat=0, IDCols=2)
} else {
#generate genes in concept table
tempGenes <- unlist(getGenesInCategory(gAList[[indexM[a,2]]])[rownames(dataMatrix)[indexM[a,1]]])
temp <- as.matrix(tempGeneInput[tempGeneInput[,1] %in% tempGenes,])
rownames(temp) <- temp[,1]
colnames(temp) <- colnames(tempGeneInput)
if (dim(temp)[2] > 1) {
if (dim(temp)[1] > 1) {
tempColNames <- colnames(temp)
temp <- temp[!duplicated(temp),]
if (!is.matrix(temp)) {
temp <- matrix(temp, ncol=length(tempColNames))
rownames(temp) <- temp[,1]
colnames(temp) <- tempColNames
}
}
if (dim(temp)[2] > 1) {
tempColNames <- colnames(temp)[2:dim(temp)[2]]
tempRowNames <- rownames(temp)
temp <- matrix(temp[,2:dim(temp)[2]], ncol=length(tempColNames))
colnames(temp) <- tempColNames
rownames(temp) <- tempRowNames
}
}
#### generate a hyperlink by table name based on catType
.drawHTMLtable(temp, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=getAnnLib(gAList[[1]]), lastRowLink=TRUE, highlightLastRow=FALSE, topCat=0, IDCols=2)
}
} else {
.drawHTMLtable(dataMatrix, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=annLib, matrixOfHeatmap=matrixOfHeatmap, topCat=max(showCats), displayText=TRUE)
}
} else {
if (i == 2) {
if (catType == 'GO') tempConceptsRelationFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-1]]), '.png', sep='')
else tempConceptsRelationFileName <- paste(tableNames[i], '_', catType, '.png', sep='')
setwd(paste(fileName, '.files', sep=''))
png(filename=tempConceptsRelationFileName, width=1000, height=1000, bg=bgColor)
if (is.matrix(dataMatrix[c(1:(dim(dataMatrix)[1]-1)),])) {
.catsCluster(dataMatrix[c(1:(dim(dataMatrix)[1]-1)),], gAList, catType=catType, nameLength=nameLength, addID=addID)
} else {
newTempM <- dataMatrix[c(1:(dim(dataMatrix)[1]-1)),]
.catsCluster(matrix(newTempM, ncol=1, dimnames=list(c(names(newTempM)), c(names(gAList)))), gAList, catType=catType, nameLength=nameLength, addID=addID)
}
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempConceptsRelationFileName, '"></center>\n', file = outFile, sep="")
} else {
if (!is.null(matrixOfHeatmap) & is.numeric(showCats)) {
temp <- matrixOfHeatmap[,(i-2)]
drawCats <- names(sort(temp))[showCats]
} else drawCats <- showCats
if (is.character(drawCats)) drawCats <- drawCats[drawCats %in% rownames(getEnrichmentInfo(gAList[[i-2]]))]
else drawCats <- rownames(getEnrichmentInfo(gAList[[i-2]]))[intersect(showCats, c(1:dim(getEnrichmentInfo(gAList[[i-2]]))[1]))]
if (!is.null(drawCats)) {
##if (catType == 'GO') tempConceptFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '.png', sep='')
##else tempConceptFileName <- paste(tableNames[i], '_', catType, '.png', sep='')
tempCrossTableFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '_CrossTable.png', sep='')
tempWordleFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '_Wordle.png', sep='')
if (interactive) {
g <- geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn[i-2], output='none', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, colorMap=NULL, bgColor=bgColor, symmetry=FALSE)
graphInfo <- c('vertex.attributes'=list(as.data.frame(cbind('NODES'=V(g)$label, 'NODE_FILL_COLOR'=V(g)$color, 'NODE_SIZE'=3*V(g)$size,
'NODE_LABEL_COLOR'=rep('#666666', vcount(g)), 'NODE_BORDER_COLOR'=V(g)$color), stringsAsFactors =FALSE)),
'edge.attributes'=list(as.data.frame(cbind(get.edgelist(g), 'EDGE_COLOR'=E(g)$color, 'EDGE_LINE_WIDTH'=E(g)$width), stringsAsFactors =FALSE)))
colnames(graphInfo[['edge.attributes']])[1:2] <- c('NODES1', 'NODES2')
.convertCytoscapeWeb(graphInfo, htmlName=fileName, fileSuffix=(i-2), verbose=TRUE, destination=paste('../',fileName, '.files', sep=''), bgColor=bgColor)
setwd(paste(fileName, '.files', sep=''))
if (wordleOn) {
geneSymbols <- unique(unlist(lookUp(getGeneInput(gAList[[i-2]])[,1], gsub("\\.db$", "", getAnnLib(gAList[[i-2]])), "SYMBOL")))
geneSymbols <- geneSymbols[!is.na(geneSymbols)]
getListGIF(glist=geneSymbols, output=tempWordleFileName)
}
png(filename=tempCrossTableFileName, width=1000, height=1500, bg=bgColor)
if (is.null(getGeneExprProfile(gAList[[i-2]]))) geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='column',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
else geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='both',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
if (wordleOn) cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempWordleFileName, '"></center>\n<p></p>\n<p></p>\n', file = outFile, sep="")
cat('<body><center><div id="cytoscapeweb',(i-2), '" style="width:1000px;height:1000px;">Cytoscape Web will replace the contents of this div with your graph.</div></center></body>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempCrossTableFileName, '"></center>\n', file = outFile, sep="")
} else {
tempConceptFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '.png', sep='')
setwd(paste(fileName, '.files', sep=''))
if (wordleOn) {
geneSymbols <- unique(unlist(lookUp(getGeneInput(gAList[[i-2]])[,1], gsub("\\.db$", "", getAnnLib(gAList[[i-2]])), "SYMBOL")))
geneSymbols <- geneSymbols[!is.na(geneSymbols)]
getListGIF(glist=geneSymbols, output=tempWordleFileName)
}
png(filename=tempConceptFileName, width=1000, height=1000, bg=bgColor)
geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn[i-2], output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, bgColor=bgColor, symmetry=FALSE)
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
png(filename=tempCrossTableFileName, width=1000, height=1500, bg=bgColor)
if (is.null(getGeneExprProfile(gAList[[i-2]]))) geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='column',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
else geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='both',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
if (wordleOn) cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempWordleFileName, '"></center>\n<p></p>\n<p></p>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempConceptFileName, '"></center>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempCrossTableFileName, '"></center>\n', file = outFile, sep="")
}
} else {
print('Given categories are not statistical significant!!! No category is selected!')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
cat('<p style="font-family:courier;text-align:center;color:red">Given categories are not statistical significant!!!!</p>', file = outFile, sep = "\n")
}
}
}
cat('<a HREF="#h-1"><p style="font-family:courier;text-align:right;font-size:11px">To Concepts-Genes Table</p></a>\n<br> <br /><br> <br />\n',file = outFile, sep = "")
}
cat('</body>', "</html>", sep = "\n", file = outFile)
if (interactive) {
file.remove('NetworkTransformer.jar')
if (!keepCytoscapeFiles) {
if (file.remove(paste(fileName, 'cytoscapeWebFiles', sep='.'))) print(paste(paste(fileName, 'cytoscapeWebFiles', sep='.'), 'is removed.'))
else print(paste('Warning:', paste(getwd(), '', fileName, 'cytoscapeWebFiles', sep='.'), 'can not be removed.'))
}
}
close(outFile)
print(paste(fileName, 'is generated at', getwd()))
}
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Defines functions `groupReport`
`groupReport` <-
function(dataMatrix, gAList, topCat=10, methodOfCluster=c('mds', 'sort'), matrixOfHeatmap=NULL, clusterTable=c('geneNum', 'pvalue', NULL), catTerm=TRUE,
fileName = "multiConceptsGenes.html", title='Multigroup Genes Concepts Analysis', catType=c('GO', 'KEGG', 'DOLITE', 'REACTOME.PATH', 'CABIO.PATH', 'Unknown'), reverseOfCluster=FALSE, colorValueColumn = NULL,
annLib=c('org.Hs.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db', 'org.Dm.eg.db'), nameLength=94, addID=TRUE, interactive=FALSE, bgColor='#ffffff', keepCytoscapeFiles=TRUE, wordleOn=FALSE, ...) {
catType <-match.arg(catType)
annLib <- match.arg(annLib)
showCats <- c(1:topCat)
k <- 0
while (TRUE) {
if ((all(!file.exists(c(paste(fileName, '_', k, '.html', sep=''), paste(paste(fileName, '_', k, '.html', sep=''), 'files', sep='.'), paste(paste(fileName, '_', k, '.html', sep=''), 'cytoscapeWebFiles', sep='.')))) & (k > 0)) |
(all(!file.exists(c(fileName, paste(fileName, 'files', sep='.'), paste(fileName, 'cytoscapeWebFiles', sep='.')))) & (k == 0))) {
if (k > 0) {
fileName <- paste(fileName, '_', k, '.html', sep='')
print(paste('New file is', fileName))
}
break;
} else {
if (k > 0) print(paste(paste(c(paste(fileName, '_', k, '.html', sep=''), paste(paste(fileName, '_', k, '.html', sep=''), 'files', sep='.'), paste(paste(fileName, '_', k, '.html', sep=''), 'cytoscapeWebFiles', sep='.')),
collapse=' and/or '), 'are in current location, they will not be overwritten.'))
else print(paste(paste(c(fileName, paste(fileName, 'files', sep='.'), paste(fileName, 'cytoscapeWebFiles', sep='.')), collapse=' and/or '), 'are in the current location, they will not be overwritten.'))
}
k <- k + 1
}
if (!is.null(colorValueColumn) & (length(colorValueColumn) > 1) & (length(colorValueColumn) != length(gAList))) stop('Specified colorValueColumns can not match the given gAList! Aborting ...')
if (length(colorValueColumn) == 1) colorValueColumn <- rep(colorValueColumn, length(gAList))
if (!is.null(colorValueColumn)) {
allColNames <- lapply(gAList, function(x) return(colnames(getGeneInput(x))))
validColNames <- c()
for (i in 1:length(colorValueColumn)) validColNames <- c(validColNames, colorValueColumn[i] %in% allColNames[[i]])
if (!(all(validColNames))) stop(paste("The given colorValueColumn(s)[position ", paste(which(!validColNames), sep="", collapse=" "), "] might not be the column names of geneInput slots of the given gAList! Aborting ...", sep=''))
}
if (is.matrix(dataMatrix) | is.data.frame(dataMatrix) | is.vector(dataMatrix)) {
dataMatrix <- as.matrix(dataMatrix)
if ((NA %in% rownames(dataMatrix)) | is.null(rownames(dataMatrix))) print('Warning: NA or NULL might be in rownames of dataMatrix!')
if ((NA %in% colnames(dataMatrix)) | is.null(colnames(dataMatrix))) print('Warning: NA or NULL might be in colnames of dataMatrix!')
} else stop('Input is not a valid matrix!')
HTwrap <- function(x, tag = "TD", scripts=NULL) {
if (is.null(scripts)) return(paste("<", tag, ">", x, "</", tag, ">", sep = ""))
else return(paste("<", tag, ' ', scripts, ">", x, "</", tag, ">", sep = ""))
}
if (!is.null(clusterTable) & !is.null(matrixOfHeatmap)) {
if (clusterTable == 'geneNum') {
if (is.numeric(dataMatrix)) {
baseM <- dataMatrix[1:(dim(dataMatrix)[1]-1),]
}
else stop('The input Matrix is not numeric!')
} else {
baseM <- matrixOfHeatmap
}
if (methodOfCluster == 'mds') {
distBaseM <- as.matrix(dist(baseM, method = "euclidean", upper=TRUE))
distBaseM[distBaseM < 1e-6] <- 1e-6
diag(distBaseM) <- 0
clusterResult <- isoMDS(distBaseM, k=1)$points
clusterOrder <- rownames(clusterResult)[order(clusterResult, decreasing=reverseOfCluster)]
originalIndexMatrix <- originalIndexMatrix[clusterOrder,]
matrixOfHeatmap <- matrixOfHeatmap[clusterOrder,]
tempM <- dataMatrix[c(clusterOrder, rownames(dataMatrix)[dim(dataMatrix)[1]]),]
dataMatrix <- tempM
} else {
clusterOrder <- sort(rownames(baseM), ...)
tempM <- dataMatrix[c(clusterOrder, rownames(dataMatrix)[dim(dataMatrix)[1]]),]
dataMatrix <- tempM
}
}
indexM <- which((is.numeric(dataMatrix) & (dataMatrix > 0)) | (is.character(dataMatrix) & (dataMatrix != "0 (1)")), arr.ind = TRUE)
if (catType != 'Unknown') {
indexNames <- rownames(indexM)[1:dim(indexM)[1]]
indexTerms <- getCategoryTerms(indexNames[which(!indexNames %in% "Genes / Group")], catType = catType, missing = "keep")
trueTerms <- paste('Genes in', names(indexTerms), '::', indexTerms, 'and Group', colnames(dataMatrix)[indexM[1:(dim(indexM)[1]),2][which(!(names(indexM[1:(dim(indexM)[1]),2]) %in% "Genes / Group"))]])
names(trueTerms) <- names(indexTerms)
pseudoTerms <- paste('Genes in Group', colnames(dataMatrix))
names(pseudoTerms) <- rep('Genes / Group', length(pseudoTerms))
finalTerms <- rep('', length(indexNames))
finalTerms[which(!indexNames %in% "Genes / Group")] <- trueTerms
finalTerms[which(indexNames %in% "Genes / Group")] <- pseudoTerms
names(finalTerms) <- NULL
tableNames <- c('Concepts-Genes Table', 'Concepts Relation', paste('Group', colnames(dataMatrix), 'Concepts-Gene network'), finalTerms)
#gsub('Genes / Group :: NA and ', replacement='', paste('Genes in', rownames(indexM)[1:dim(indexM)[1]], '::', getCategoryTerms(rownames(indexM)[1:dim(indexM)[1]], catType=catType, missing='keep'), 'and Group', colnames(dataMatrix)[indexM[1:dim(indexM)[1],2]]))
} else {
tableNames <- c('Concepts-Genes Table', 'Concepts Relation', paste('Group', colnames(dataMatrix), 'Concepts-Gene network'), gsub('Genes / Group and ', replacement='',
paste('Genes in', rownames(indexM)[1:dim(indexM)[1]], 'and Group', colnames(dataMatrix)[indexM[1:dim(indexM)[1],2]])))
}
attr <- c(catType, rep('Pictures', (1+dim(dataMatrix)[2])), rep('Entrez', dim(indexM)[1]))
outFile <- file(fileName, "w")
cat('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">', file = outFile, sep = "\n")
if (dir.create(paste(fileName, '.files', sep=''), showWarnings=FALSE) | file.exists(paste(fileName, '.files', sep=''))) {
if (interactive) {
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/js', sep=''), paste(fileName, '.files', sep=''), recursive=TRUE)) print(paste('Copy js to', paste(fileName, '.files', sep='')))
else { close(outFile); stop('js subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/swf', sep=''), paste(fileName, '.files', sep=''), recursive=TRUE)) print(paste('Copy swf to', paste(fileName, '.files', sep='')))
else { close(outFile); stop('swf subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
if (file.copy(paste(system.file('External', package='GeneAnswers'), '/NetworkTransformer.jar', sep=''), '.', overwrite=TRUE)) {
Sys.chmod('NetworkTransformer.jar', mode='0777')
print(paste('Copy NetworkTransformer.jar to', paste(fileName, '.files', sep='')))
}
else { close(outFile); stop('NetworkTransformer.jar subdirectory can not be copied to ', paste(fileName, '.files', sep=''), '. Aborting ...') }
headInfo <- paste(HTwrap(title, tag = "title"), '\n\t', HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/json2.min.js"', sep='')), '\n\t',
HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/AC_OETags.min.js"', sep='')), '\n\t',
HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/js/cytoscape_web/cytoscapeweb.min.js"', sep='')), '\n', sep='')
headInfo <- paste(headInfo, paste('\t', HTwrap('', tag='script', scripts=paste('type="text/javascript" src="', paste(fileName, '.files', sep=''), '/edges_', c(1:length(gAList)), '.js"', sep='')),'\n', sep='', collapse=''),
'\t\t<script type="text/javascript">\n\t\twindow.onload=function() {\n', sep='')
headInfo <- paste(headInfo, paste('\t\t\tvar div_id', c(1:length(gAList)), ' = "cytoscapeweb', c(1:length(gAList)), '";\n', sep='', collapse=''),
'\t\t\tvar options = {\n\t\t\t\tswfPath: "', paste(fileName, '.files', sep=''), '/swf/CytoscapeWeb",\n\t\t\t\tflashInstallerPath: "', paste(fileName, '.files', sep=''), '/swf/playerProductInstall"\n\t\t\t};\n', sep='')
headInfo <- paste(headInfo, paste('\t\t\tvar vis', c(1:length(gAList)), ' = new org.cytoscapeweb.Visualization(div_id', c(1:length(gAList)), ', options);\n\t\t\tvis', c(1:length(gAList)), '.draw({ network: xml',c(1:length(gAList)), ' });\n', sep='', collapse=''),
'\t\t};</script>\n\t', HTwrap(' html, body { height: 100%; width: 100%; padding: 0; margin: 10; }\n\t#cytoscapeweb { width: 100%; height: 100%; }', tag='style'), sep='')
cat("<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>", HTwrap(headInfo, tag = "head"), '<body bgcolor="', bgColor, '">', file = outFile, sep = "\n")
} else {
cat("<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>", HTwrap(HTwrap(title, tag = "title"), tag = "head"), '<body bgcolor="', bgColor, '">', file = outFile, sep = "\n")
}
} else {
close(outFile)
stop(paste('Failure to create', paste(fileName, '.files', sep=''), 'subdirectory! Aborting ...'))
}
if (!missing(title)) cat("<center><H1 align=\"center\">", title, " </H1></center>\n", file = outFile, sep = "\n")
cat('</body>', "</html>", sep = "\n", file = outFile)
cat('<H1><font face="courier" size="4"><a name="h-0">Multigroup Genes Concepts Analysis</a></font></H1>\n<font face="courier" size="1">Generated by Bioconductor package <a HREF="http://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html">GeneAnswers</a> at ', format(Sys.Date(), "%a, %b %d %Y"), '</font>\n<p> </p>',file = outFile, sep = "")
for (i in 1:(2+dim(dataMatrix)[2])) {
cat(paste('<li><font face="courier" size="2"><a href="', paste('#h-', i, sep=''), '">', sep=''), tableNames[i], '</a></font>\n<p></p>\n',file = outFile, sep = "")
}
for (i in 1:length(tableNames)) {
if (attr[i] != 'Pictures') {
if (attr[i] == 'Entrez') {
a <- i - 2 - dim(dataMatrix)[2]
tempGeneInput <- getGeneInput(gAList[[indexM[a,2]]])
if (indexM[a,1] == dim(dataMatrix)[1]){
# generate all genes table
temp <- as.matrix(tempGeneInput)
colnames(temp) <- colnames(tempGeneInput)
rownames(temp) <- temp[,1]
if (dim(temp)[2] > 1) {
if (dim(temp)[1] > 1) {
tempColNames <- colnames(temp)
temp <- temp[!duplicated(temp),]
if (!is.matrix(temp)) {
temp <- matrix(temp, ncol=length(tempColNames))
rownames(temp) <- temp[,1]
colnames(temp) <- tempColNames
}
}
if (dim(temp)[2] > 1) {
tempColNames <- colnames(temp)[2:dim(temp)[2]]
tempRowNames <- rownames(temp)
temp <- as.matrix(temp[,2:dim(temp)[2]])
colnames(temp) <- tempColNames
rownames(temp) <- tempRowNames
}
}
.drawHTMLtable(temp, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=getAnnLib(gAList[[1]]), lastRowLink=TRUE, highlightLastRow=FALSE, topCat=0, IDCols=2)
} else {
#generate genes in concept table
tempGenes <- unlist(getGenesInCategory(gAList[[indexM[a,2]]])[rownames(dataMatrix)[indexM[a,1]]])
temp <- as.matrix(tempGeneInput[tempGeneInput[,1] %in% tempGenes,])
rownames(temp) <- temp[,1]
colnames(temp) <- colnames(tempGeneInput)
if (dim(temp)[2] > 1) {
if (dim(temp)[1] > 1) {
tempColNames <- colnames(temp)
temp <- temp[!duplicated(temp),]
if (!is.matrix(temp)) {
temp <- matrix(temp, ncol=length(tempColNames))
rownames(temp) <- temp[,1]
colnames(temp) <- tempColNames
}
}
if (dim(temp)[2] > 1) {
tempColNames <- colnames(temp)[2:dim(temp)[2]]
tempRowNames <- rownames(temp)
temp <- matrix(temp[,2:dim(temp)[2]], ncol=length(tempColNames))
colnames(temp) <- tempColNames
rownames(temp) <- tempRowNames
}
}
#### generate a hyperlink by table name based on catType
.drawHTMLtable(temp, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=getAnnLib(gAList[[1]]), lastRowLink=TRUE, highlightLastRow=FALSE, topCat=0, IDCols=2)
}
} else {
.drawHTMLtable(dataMatrix, outFile, tableName=tableNames[i], tableLink=paste('h-', i, sep=''), catType=attr[i], species=annLib, matrixOfHeatmap=matrixOfHeatmap, topCat=max(showCats), displayText=TRUE)
}
} else {
if (i == 2) {
if (catType == 'GO') tempConceptsRelationFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-1]]), '.png', sep='')
else tempConceptsRelationFileName <- paste(tableNames[i], '_', catType, '.png', sep='')
setwd(paste(fileName, '.files', sep=''))
png(filename=tempConceptsRelationFileName, width=1000, height=1000, bg=bgColor)
if (is.matrix(dataMatrix[c(1:(dim(dataMatrix)[1]-1)),])) {
.catsCluster(dataMatrix[c(1:(dim(dataMatrix)[1]-1)),], gAList, catType=catType, nameLength=nameLength, addID=addID)
} else {
newTempM <- dataMatrix[c(1:(dim(dataMatrix)[1]-1)),]
.catsCluster(matrix(newTempM, ncol=1, dimnames=list(c(names(newTempM)), c(names(gAList)))), gAList, catType=catType, nameLength=nameLength, addID=addID)
}
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempConceptsRelationFileName, '"></center>\n', file = outFile, sep="")
} else {
if (!is.null(matrixOfHeatmap) & is.numeric(showCats)) {
temp <- matrixOfHeatmap[,(i-2)]
drawCats <- names(sort(temp))[showCats]
} else drawCats <- showCats
if (is.character(drawCats)) drawCats <- drawCats[drawCats %in% rownames(getEnrichmentInfo(gAList[[i-2]]))]
else drawCats <- rownames(getEnrichmentInfo(gAList[[i-2]]))[intersect(showCats, c(1:dim(getEnrichmentInfo(gAList[[i-2]]))[1]))]
if (!is.null(drawCats)) {
##if (catType == 'GO') tempConceptFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '.png', sep='')
##else tempConceptFileName <- paste(tableNames[i], '_', catType, '.png', sep='')
tempCrossTableFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '_CrossTable.png', sep='')
tempWordleFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '_Wordle.png', sep='')
if (interactive) {
g <- geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn[i-2], output='none', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, colorMap=NULL, bgColor=bgColor, symmetry=FALSE)
graphInfo <- c('vertex.attributes'=list(as.data.frame(cbind('NODES'=V(g)$label, 'NODE_FILL_COLOR'=V(g)$color, 'NODE_SIZE'=3*V(g)$size,
'NODE_LABEL_COLOR'=rep('#666666', vcount(g)), 'NODE_BORDER_COLOR'=V(g)$color), stringsAsFactors =FALSE)),
'edge.attributes'=list(as.data.frame(cbind(get.edgelist(g), 'EDGE_COLOR'=E(g)$color, 'EDGE_LINE_WIDTH'=E(g)$width), stringsAsFactors =FALSE)))
colnames(graphInfo[['edge.attributes']])[1:2] <- c('NODES1', 'NODES2')
.convertCytoscapeWeb(graphInfo, htmlName=fileName, fileSuffix=(i-2), verbose=TRUE, destination=paste('../',fileName, '.files', sep=''), bgColor=bgColor)
setwd(paste(fileName, '.files', sep=''))
if (wordleOn) {
geneSymbols <- unique(unlist(lookUp(getGeneInput(gAList[[i-2]])[,1], gsub("\\.db$", "", getAnnLib(gAList[[i-2]])), "SYMBOL")))
geneSymbols <- geneSymbols[!is.na(geneSymbols)]
getListGIF(glist=geneSymbols, output=tempWordleFileName)
}
png(filename=tempCrossTableFileName, width=1000, height=1500, bg=bgColor)
if (is.null(getGeneExprProfile(gAList[[i-2]]))) geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='column',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
else geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='both',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
if (wordleOn) cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempWordleFileName, '"></center>\n<p></p>\n<p></p>\n', file = outFile, sep="")
cat('<body><center><div id="cytoscapeweb',(i-2), '" style="width:1000px;height:1000px;">Cytoscape Web will replace the contents of this div with your graph.</div></center></body>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempCrossTableFileName, '"></center>\n', file = outFile, sep="")
} else {
tempConceptFileName <- paste(tableNames[i], '_', getCategoryType(gAList[[i-2]]), '.png', sep='')
setwd(paste(fileName, '.files', sep=''))
if (wordleOn) {
geneSymbols <- unique(unlist(lookUp(getGeneInput(gAList[[i-2]])[,1], gsub("\\.db$", "", getAnnLib(gAList[[i-2]])), "SYMBOL")))
geneSymbols <- geneSymbols[!is.na(geneSymbols)]
getListGIF(glist=geneSymbols, output=tempWordleFileName)
}
png(filename=tempConceptFileName, width=1000, height=1000, bg=bgColor)
geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn[i-2], output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, bgColor=bgColor, symmetry=FALSE)
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
png(filename=tempCrossTableFileName, width=1000, height=1500, bg=bgColor)
if (is.null(getGeneExprProfile(gAList[[i-2]]))) geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='column',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
else geneAnswersHeatmap(gAList[[i-2]], showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE, nameLength=nameLength, catID=TRUE, sortBy='both',
colorMap=c(rgb(255-col2rgb(bgColor)[1], 255-col2rgb(bgColor)[2], 255-col2rgb(bgColor)[3], maxColorValue=255), bgColor), mapType='heatmap')
#else geneAnswersConceptNet(gAList[[i-2]], centroidSize='pvalue', colorValueColumn = colorValueColumn, output='fixed', showCats=drawCats, catTerm=catTerm, geneSymbol=TRUE)
dev.off()
setwd('..')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
if (wordleOn) cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempWordleFileName, '"></center>\n<p></p>\n<p></p>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempConceptFileName, '"></center>\n', file = outFile, sep="")
cat('<center><IMG src="', paste(fileName, '.files', sep=''), '/', tempCrossTableFileName, '"></center>\n', file = outFile, sep="")
}
} else {
print('Given categories are not statistical significant!!! No category is selected!')
cat(paste('<H2 align=center><font face="courier" size="2"><A name="', paste('h-', i, sep=''), '">', tableNames[i], "</a></font></H2>", sep=''), file = outFile, sep = "\n")
cat('<p style="font-family:courier;text-align:center;color:red">Given categories are not statistical significant!!!!</p>', file = outFile, sep = "\n")
}
}
}
cat('<a HREF="#h-1"><p style="font-family:courier;text-align:right;font-size:11px">To Concepts-Genes Table</p></a>\n<br> <br /><br> <br />\n',file = outFile, sep = "")
}
cat('</body>', "</html>", sep = "\n", file = outFile)
if (interactive) {
file.remove('NetworkTransformer.jar')
if (!keepCytoscapeFiles) {
if (file.remove(paste(fileName, 'cytoscapeWebFiles', sep='.'))) print(paste(paste(fileName, 'cytoscapeWebFiles', sep='.'), 'is removed.'))
else print(paste('Warning:', paste(getwd(), '', fileName, 'cytoscapeWebFiles', sep='.'), 'can not be removed.'))
}
}
close(outFile)
print(paste(fileName, 'is generated at', getwd()))
}
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