pcaInfoPlot <- function (eData, inputType = "hgu133plus2", org = "Hs", groups,
printNames = TRUE, plotCI = TRUE, noProbes = 1365, GOtermsAnnotation = TRUE,
primoAnnotation = TRUE)
{
pcaObj <- pca(eData)
if (!is.na(pcaObj$expressionData[1])) {
chipType <- pcaObj$expressionData[[1]]
if (chipType == "hgu133plus2") {
inputType <- chipType
org <- "Hs"
}
if (chipType == "hugene10st" | chipType == "hugene10stv1") {
inputType <- "hugene10st"
org <- "Hs"
}
if (chipType == "mouse4302") {
inputType <- chipType
org <- "Mm"
}
if (chipType == "mogene10st" | chipType == "mogene10stv1") {
inputType <- "mogene10st"
org <- "Mm"
}
if (chipType == "mogene20st") {
inputType <- "mogene20st"
org <- "Mm"
}
if (chipType == "rat2302") {
inputType <- chipType
org <- "Rn"
}
}
probesPC1pos <- getRankedProbeIds(pcaObj, pc = 1, decreasing = TRUE)[1:noProbes]
probesPC1neg <- getRankedProbeIds(pcaObj, pc = 1, decreasing = FALSE)[1:noProbes]
probesPC2pos <- getRankedProbeIds(pcaObj, pc = 2, decreasing = TRUE)[1:noProbes]
probesPC2neg <- getRankedProbeIds(pcaObj, pc = 2, decreasing = FALSE)[1:noProbes]
if (GOtermsAnnotation) {
GOtreePC1pos <- GOtree(probesPC1pos, inputType = inputType, org = org)
GOtreePC1neg <- GOtree(probesPC1neg, inputType = inputType, org = org)
GOtreePC2pos <- GOtree(probesPC2pos, inputType = inputType, org = org)
GOtreePC2neg <- GOtree(probesPC2neg, inputType = inputType, org = org)
GOtreeObjs <- list(GOtreePC1pos, GOtreePC1neg, GOtreePC2pos, GOtreePC2neg)
}
else {
GOtreeObjs <- NA
}
if (primoAnnotation) {
primoPC1pos <- primo(probesPC1pos, inputType = inputType, org = org)
primoPC1neg <- primo(probesPC1neg, inputType = inputType, org = org)
primoPC2pos <- primo(probesPC2pos, inputType = inputType, org = org)
primoPC2neg <- primo(probesPC2neg, inputType = inputType, org = org)
primoObjs <- list(primoPC1pos, primoPC1neg, primoPC2pos, primoPC2neg)
}
else {
primoObjs <- NA
}
plot(pcaObj, groups = groups, printNames = printNames, plotCI = plotCI,
GOtreeObjs = GOtreeObjs, primoObjs = primoObjs)
}
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