Nothing
setMethod("plotVsHkg", signature = "qPCRBatch", definition =
function(qPCRBatch, hkgs, writeToFile = FALSE) {
cts <- exprs(qPCRBatch) # this refers to the actual data
hkgs <- make.names(hkgs)
if(FALSE %in% hkgs %in% featureNames(qPCRBatch)) stop("one or more housekeeper not found in exprs matrix")
plotFrame <- matrix(nrow=length(featureNames(qPCRBatch)),ncol=length(hkgs), dimnames = list(featureNames(qPCRBatch), hkgs))
for (hkg in hkgs) {
cat("housekeeping genes", hkg, "\n\n")
dCts <- deltaCt(qPCRBatch = qPCRBatch, hkgs = hkg, calc="arith")
for(detector in featureNames(qPCRBatch)) {
#cat("\n\n\n")
# print(dCts)
# cat(exprs(qPCRBatch)[detector,],"\t")
plotFrame[detector,hkg] <- mean(exprs(dCts)[detector,],na.rm=TRUE)
#cat(mean(exprs(qPCRBatch)[detector,],na.rm=TRUE),"\t")
#cat(plotFrame[detector,hkg],"\n")
# hkg <- gsub("-.+$", "", hkg) # cut off the stuff from the detector's name after the -
# hkg2ddct <- paste(hkg, "_2^DDCt", sep = "")
# ddct <- cts[, hkg2ddct]
# plotFrame[,hkgs] <- <- data.frame(plotFrame, ddct)
}
#cat("\n")
}
# for (hkg in hkgs[1]) {
# for(detectors in featureNames(qPCRBatch)) {
# cat(plotFrame[detector,hkg])
# }
# }
#stop()
# plotFrame <- plotFrame[, -1] # take off first column of detector names
for (hkg in hkgs) { # now order by each hkg and print
ord.plotFrame <- plotFrame[order(plotFrame[, hkg]), ] # order by 1st column
if (writeToFile) jpeg(file = paste("mean.deltaCt.ordered.by.", hkg, ".jpg", sep = ""))
matplot(ord.plotFrame, type = "l", pch = seq(hkgs), lty = seq(hkgs), main = paste("Ordered By Reference Gene", gsub("\\.+.+","",hkg)),xlab=paste("rank order of",gsub("\\.+.+","",hkg)), ylab="delta Ct")
legend("bottomright", gsub("\\.+.+","",hkgs), lty = seq(hkgs), col = seq(hkgs))
if (writeToFile) {
dev.off()
} else {
# .wait()
}
}
return(plotFrame)
}
)
.wait <- function() {
par(ask=TRUE)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.