Nothing
`plotStringencyGene` <-
function(controlData, lib=NULL, slideIndex=NULL, addLegend=TRUE, logMode=TRUE, ...)
{
if (is(controlData, 'LumiBatch')) {
sampleID <- pData(phenoData(controlData))$sampleID
controlData <- controlData(controlData)
if (nrow(controlData) == 0) stop('Slot controlData is empty!')
} else {
sampleID <- NULL
}
allControlType <- controlData$controlType
allControlProbe <- controlData$ProbeID
uniControlType <- getControlType(controlData)
controlData <- controlData[, -c(1,2)]
if (is.null(slideIndex)) {
if (is.null(sampleID)) sampleID <- colnames(controlData)
sampleIDInfo <- strsplit(sampleID, split="_")
chipID <- sapply(sampleIDInfo, function(x) x[1])
ord <- order(chipID)
chipID <- chipID[ord]
controlData <- controlData[, ord]
chip <- as.numeric(as.factor(chipID))
chipNum <- length(unique(chipID))
} else {
ord <- order(slideIndex)
controlData <- controlData[, ord]
slideIndex <- slideIndex[ord]
chip <- as.numeric(as.factor(slideIndex))
chipNum <- length(unique(slideIndex))
}
# get HOUSEKEEPING
ind <- grep('STRINGENCY', allControlType, ignore.case=TRUE)
if (length(ind) == 0) stop('No STRINGENCY related gene information found!')
strType <- allControlType[ind]
ord <- order(strType)
strType <- strType[ord]
ind <- ind[ord]
hkgene <- allControlProbe[ind]
selControlData <- controlData[ind, ]
if (!is.null(lib)) {
# require(annotate)
require(lib, character.only=TRUE)
hkSymbol <- getSYMBOL(hkgene, lib)
hkSymbol[is.na(hkSymbol)] <- hkgene[is.na(hkSymbol)]
hkgene <- hkSymbol
}
if (logMode) {
if (max(selControlData) > 50) {
selControlData <- selControlData - min(selControlData) + 1
selControlData <- log2(selControlData)
}
ylab <- 'Expression Amplitude (log2)'
} else {
if (max(selControlData) < 50) selControlData <- 2^(selControlData)
ylab <- 'Expression Amplitude'
}
labels <- colnames(selControlData)
if (is.null(labels)) labels <- as.character(1:ncol(selControlData))
## set the margin of the plot
mar <- c(max(nchar(labels))/2 + 4.5, 5, 5, 3)
old.mar <- par('mar')
old.xaxt <- par('xaxt')
par(xaxt='n')
par(mar=mar)
col <- lty <- as.numeric(as.factor(strType))
if (addLegend) {
xlim <- c(1, ncol(selControlData) + 1)
} else {
xlim <- c(1, ncol(selControlData))
}
matplot(t(selControlData), pch = 19, cex=1.2, type='o', col=col, lty=lty, xlim=xlim,
xlab='', ylab=ylab)
title('Expression profile of housekeeping genes')
# plot the vertical lines
if (chipNum > 1) abline(v = 0.5 + which(diff(chip) != 0), lty=2)
if (addLegend) legend('topright', legend=unique(strType), lty=unique(lty), col=unique(col), inset = .02)
par(xaxt='s')
axis(1, at=1:ncol(selControlData), labels=labels, tick=TRUE, las=2)
par(mar=old.mar)
par(xaxt=old.xaxt)
return(invisible(TRUE))
}
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