examples/drawBTree-Ex.R

In BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))

# 77 common cancer genes
comm <- btcompare(vol.genes, cancer.genes.minus2)

btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <-new("Annotate")
cc <- allCall.lst[["sam2"]]
z <- drawBTree(btreeplotter, cc@rbd.adj) + 
    ggplot2::labs(title=sprintf("%s (%s)", "sam2", info(cc)))