Nothing
plotPi0<-function(est,ui,li,samples,labels=NULL,xlab="Segment",ylab=expression(pi[0]),pchFac=rep(1,length(est)),
whHighlight=NULL,nMut=NULL,xorder=NULL,...){
#require(gplots)
if(requireNamespace("gplots", quietly = TRUE) ){
samples<-factor(samples)
indToPlot<-tapply(1:length(est),samples, function(ii){
p<-est[ii]
whNA<-ii[which(is.na(p))]
return(setdiff(ii[order(p)],c(whNA)))
#whL20<-ii[which(df$N[ii]<20)]
#return(setdiff(ii[order(p)],c(whNA,whL20)))
})
if(is.null(xorder)) xord<-unlist(indToPlot)
else xord<-xorder
nPerSamp<-sapply(indToPlot,length)
plotCI(est[xord],ui=ui[xord],li=li[xord],xlab=xlab,
ylab=ylab,xaxt="n",pch=c(1:5)[pchFac[xord]],sfrac=0.001,cex=.7,...)
n<-length(xord)
#separate the samples
segments(x0=cumsum(nPerSamp)+.5,y1=par("usr")[4]+.2,y0=par("usr")[3]-.1,xpd=NA,lty=2)
mids<-(c(1,head(cumsum(nPerSamp)+.5,-1))+cumsum(nPerSamp)+.5)/2
axis(3,mids,levels(samples),tick=FALSE)
#label the segments
axis(1,1:n,labels[xord],las=2,cex.axis=0.7)
if(!is.null(nMut)){
axis(3,1:n,nMut[xord],line=-1,tick=FALSE,cex.axis=.7)
mtext("N=",side=3,at=par("usr")[1])
}
#
if(!is.null(whHighlight)){
wh<-which(xord%in%whHighlight)
plotCI((1:n)[wh],est[xord][wh],ui=ui[xord][wh],li=li[xord][wh],
pch=c(1:5)[pchFac[xord][wh]],col="red",sfrac=0.001,cex=.7,add=TRUE,lwd=1.7)
}
invisible(xord)
}
else{stop("This function requires the package 'gplots' to be installed.")}
}
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