R/plot.SpliceExprSet.R

In splicegear: splicegear

plot.SpliceExprSet <- function(x, probes.opt = list(),
                               expr.opt = list(col=NA, lty = 1:6),
                               fig.xratio=c(2,1), fig.yratio=c(2,1),
                               probepos.yscale=NULL, ylim = NULL, ...) {
  
  spSites <- x@spliceSites
  probes <- x@probes
  eset <- x@eset

  if (! all(is.list(probes.opt) , is.list(expr.opt)))
    stop("probes.opt and expr.opt should be lists !")
    
  if (all(is.na(expr.opt$col))) {
    expr.opt$col <- rainbow(ncol(exprs(eset)))
  }
  
  layout(matrix(c(1,2), 1, 2), width=fig.xratio, height=fig.yratio) #fig.yratio useless for now
  
  if (is.null(probepos.yscale)) {
    ypos <- 1:nrow(probes@pos)
  } else {
    ypos <- probepos.yscale
  }

  ##ylim <- range(ypos)

  ##plot(probes, spSites, fig.yratio=fig.yratio, probepos.yscale=ypos, ...)
  m.ylim <- plot(probes, spSites, fig.yratio=fig.yratio, probepos.yscale=ypos, ...)
  if (is.null(ylim))
    ylim <- m.ylim
  
#     if (nrow(probes@pos) <= 1)
#     ylim <- c(0,1)
#   else
#     ylim <- c(0,nrow(probes@pos))

  
  if (nrow(exprs(eset)) != nrow(probes@pos))
    stop("length mismatch between number of probes and number of expression values")
  
  opar.mar <- par()$mar
  on.exit(par(mar=opar.mar))
  npar.mar <- opar.mar
  npar.mar[2] <- 1
  par(mar=opar.mar)

  ## useless for now
  ##ylim <- range(ylim, ylim[1] - 1/4 * (ylim[2] - ylim[1]))
  xlim <- c(0, spSites@seq.length)

  do.call(matplot, c(list(exprs(eset), matrix(ypos, ncol=1),
                            ylim=m.ylim,
                            xlab="expression", ylab="probes",
                            type="l"), expr.opt))
  ##overlay typeI
                                        #for (i in 1:nrow(spSites@spsiteIpos))
                                        #  rect(ylim[1], min(spSites@spsiteIpos[i, ]), ylim[2], max(spSites@spsiteIpos[i, ]),
                                        #       col="yellow", border="transparent" )
  ##overlay typeII
                                        #for (i in seq(along=spSites@spsiteIIpos))
                                        #  ##segments(x@spsiteIIpos[i], ylim[1], x@spsiteIIpos[i], ylim[2], col="red")
                                        #  segments(ylim[1], spSites@spsiteIIpos[i], ylim[2], spSites@spsiteIIpos[i], col="red")
  
  ##boxplot(exprs(eset), horizontal=TRUE, add=TRUE)
  
}