Nothing
#' plotcsSAM
#'
#' Plots the # of genes called significnat at a given false disocvery rate for
#' the SAM (heterogenous tissue) comparison, and for each of the contrasted
#' cell-types using csSAM
#'
#'
#' @param csSAMdata List object output of the fdrCsSAM function
#' @param SAMdata List object output of the fdrSAM function
#' @param alternative Type of test conducted. Will appear in plot title.
#' @param cellID Label for each cell-type
#' @param numcell Number of different cell-types being considered.
#' @param fileName Name of output pdf file.
#' @author Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang
#' @cite Shen-Orr2010
plotCsSAM <-
function(csSAMdata, SAMdata,alternative,cellID,numcell,fileName){
cellnames = cellID
labs=paste("cell type ",as.character(1:numcell),sep="")
pdf(file=fileName, height=11,width=8)
par(mfrow=c(3,3))
plot(SAMdata$ncall.sam,SAMdata$fdr.sam,xlab="## called",ylab="FDR", type="l",log="x",ylim=c(0,1))
title(paste("SAM",alternative))
for(i in 1:numcell) {
plot(csSAMdata$ncall.g[i,],csSAMdata$fdr.g[i,],xlab="# called",ylab="FDR", type="l",log="x",ylim=c(0,1))
title(paste(cellnames[i],alternative))
}
dev.off()
}
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.