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`geneAnswersConcepts` <-
function(x, centroidSize=c('geneNum', 'pvalue', 'foldChange', 'oddsRatio', 'correctedPvalue'), output=c('fixed','interactive'), showCats=c(1:5), catTerm=FALSE, catID=FALSE) {
centroidSize <- match.arg(centroidSize)
if ((centroidSize == 'correctedPvalue') & !('fdr p value' %in% colnames(x@enrichmentInfo))) stop('input geneAnswer class does not contain fdr p value!!!')
if (is.numeric(showCats)) {
if (!(all(showCats %in% c(1:dim(x@enrichmentInfo)[1])))) print('Some specified categories might not be statistical significant! Only show significant categories.')
showCats <- intersect(showCats, c(1:dim(x@enrichmentInfo)[1]))
} else {
if (is.character(showCats)) {
showCats <- intersect(showCats, rownames(x@enrichmentInfo))
if (length(showCats) < 1) stop('specified categories can not be recognized!')
} else stop('specified categories can not be recognized!')
}
orderby <- switch(centroidSize,
'geneNum'= c('genes in Category', 'TRUE', 'Normal'),
'pvalue' = c('p value', 'FALSE', '-Log10'),
'foldChange' = c('fold of overrepresents', 'TRUE', 'Normal'),
'oddsRatio' = c('odds ratio', 'FALSE', '-Log'),
'correctedPvalue' = c('fdr p value', 'FALSE', '-Log10'))
x@enrichmentInfo <- x@enrichmentInfo[order(x@enrichmentInfo[, orderby[1]], decreasing=as.logical(orderby[2])), ]
centroidSize <- x@enrichmentInfo[, orderby[1]]
names(centroidSize) <- rownames(x@enrichmentInfo)
temp <- centroidSize[showCats]
scaledTemp <- switch(orderby[3],
'Normal'=temp,
'-Log'=-log(temp),
'-Log10'= -log10(temp))
newList <- x@genesInCategory[showCats]
if (catTerm) {
if (x@categoryType %in% c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH', 'CABIO.PATH')) {
if (catID) {
names(newList) <- paste(getCategoryTerms(names(newList), x@categoryType, missing='name'), '::', names(newList), sep='')
names(scaledTemp) <- paste(getCategoryTerms(names(scaledTemp), x@categoryType, missing='name'), '::', names(scaledTemp), sep='')
} else {
names(newList) <- getCategoryTerms(names(newList), x@categoryType, missing='name')
names(scaledTemp) <- getCategoryTerms(names(scaledTemp), x@categoryType, missing='name')
}
} else {
print('Slot categoryType is not recognized! No mapping ...')
}
}
names(newList) <- paste(names(newList), '::', sapply(newList, length), sep='')
categoryNet(newList, centroidSize=scaledTemp, output=output)
return(invisible(x))
}
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