xyTrack: xyTrack

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

Description

get the xy track

Usage

xyTrack(.Object, result.dat, gr2, min.prev = 0.15, ymax = 4.3)

## S4 method for signature 'TrackPlotter'
xyTrack(.Object, result.dat, gr2, min.prev = 0.15,
  ymax = 4.3)

Arguments

.Object	the object
result.dat	result dataframe
gr2	gr2 object
min.prev	previous min
ymax	the max y

Value

the highlighted xy track

Examples

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

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