getTracks: getTracks

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

Description

get all tracks

Usage

getTracks(p1, p2, title = "")

Arguments

p1	set 1
p2	set 2
title	the title

Value

all of the requested tracks

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "all.somatic.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
ymax <- ifelse(nn %in% c("lung.wgs", "lung.wes"), 9, 4.3)
p1 <- xyTrack(trackplotter,
              result.dat=allCall.lst[[nn]]@result,
              gr2=gr2,
              ymax=ymax) + ggplot2::labs(title=nn)

p2 <- bafTrack(trackplotter,
               result.dat=allCall.lst[[nn]]@result,
               gr2=gr2,
               somatic.gr=all.somatic.lst[[nn]])

t1 <- getTracks(p1, p2)

BubbleTree documentation built on Nov. 8, 2020, 8:22 p.m.