inst/unitTests/test_xyplot.R

In SNPchip: Visualizations for copy number alterations

##test_coercion <- function(){
##  library(VanillaICE)
##  library(oligoClasses)
##  ##data(hmmResults, package="VanillaICE")
##  data(oligoSetExample, package="oligoClasses")
##  ## coerce from RangedDataHMM
##  dataFrame <- SNPchip:::dataFrameFromRange(hmmResults[1,], object=oligoSet, frame=0)
##  checkEquals(996L, nrow(dataFrame))
##  ## coerce from GRanges
##  ##gr <- oligoClasses:::coerceToGRanges(hmmResults, build="hg19")
##  dataFrame2 <- SNPchip:::dataFrameFromRange(hmmResults[1,], object=oligoSet, frame=0)
##  checkEquals(dataFrame, dataFrame2)
##}

.test_xyplot <- function(){
  library(oligoClasses)
  library(IRanges)
  library(VanillaICE)
  data(oligoSetExample, package="oligoClasses")
  oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
  grl <- hmm(oligoSet, p.hom=0, TAUP=1e10, is.log=FALSE)
  g <- grl[[1]]
  ##data(hmmResults, package="VanillaICE")
  fig <- xyplot2(cn~x | range, data=oligoSet,
                 range=g,
                 frame=2e6, panel=xypanel,
                 cex=2,
                 pch=".",
                 col.het="salmon",
                 fill.het="salmon",
                 col.hom="royalblue",
                 fill.hom="royalblue",
                 state.cex=0.5,
                 border="orange", scales=list(x="free"),
                 par.strip.text=list(cex=0.5),
                 xlab="Mb", ylab=expression(log[2]("copy number")))
  checkTrue(is(fig, "trellis"))
}