#' Plot RNA-seq curves
#' @export
RNAcurve = function(datmat,exonset,indlist=NULL,colmat=NULL,
plot.title="data",title.cex=1.5,
yaxis.logcount=NULL,same.yaxis=TRUE,
mean.plot=TRUE,
xlab=NULL,ylab=NULL,xlim=NULL,ylim=NULL,
ep.col=NULL,...) {
if (is.null(colmat)) {
x.mda <- svd(datmat) ;
projmat <- diag(x.mda$d)%*%t(x.mda$v) ;
projmat[1,] <- -projmat[1,] ;
colmat <- rainbow(n=length(projmat[1,]), start=0, end=0.756)[rank(-projmat[1,])]
}
if (is.null(indlist)) {
case=1
RNAcurveOne(datmat=datmat,exonset=exonset,indlist=case,colmat=colmat,
plot.title=plot.title,title.cex=title.cex,
mean.plot=mean.plot,yaxis.logcount=yaxis.logcount,
same.yaxis=same.yaxis,xlim=xlim,ylim=ylim,
xlab=xlab,ylab=ylab,ep.col=ep.col,...)
for (case in 2:ncol(datmat)) {
points(datmat[,case],type='l', lty=1, col=colmat[case], ...)
}
} else {
RNAcurveOne(datmat=datmat,exonset=exonset,indlist=indlist[1],colmat=colmat,
plot.title=plot.title,title.cex=title.cex,
mean.plot=mean.plot,yaxis.logcount=yaxis.logcount,
same.yaxis=same.yaxis,xlim=xlim,ylim=ylim,
xlab=xlab,ylab=ylab,ep.col=ep.col,...)
for (case in indlist[2:length(indlist)]) {
points(datmat[,case],type='l', lty=1, col=colmat[case], ...)
}
}
}
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