trackBTree: trackBTree

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

Description

get the geom_segment location of the BTree track

Usage

trackBTree(.Object, rbd1, rbd2, is.matched = FALSE, min.srcSize = 0.5,
  min.trtSize = 0.1, min.overlap = 1e+05)

## S4 method for signature 'BTreePlotter'
trackBTree(.Object, rbd1, rbd2, is.matched = FALSE,
  min.srcSize = 0.5, min.trtSize = 0.1, min.overlap = 1e+05)

Arguments

.Object	the object
rbd1	rbd one
rbd2	rbd two
is.matched	is it matched
min.srcSize	min src size
min.trtSize	min trt size
min.overlap	min overlap

Value

geom_segment location of BTree track

Examples

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

btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
nn <- "sam2"
rbd1 <- allCall.lst[[nn]]@rbd
rbd2 <- allCall.lst[[nn]]@rbd.adj
arrows <- trackBTree(btreeplotter, rbd1, rbd2, min.srcSize=0.01, 
                     min.trtSize=0.01)
btree <- drawBTree(btreeplotter, rbd1) + 
    drawBubbles(btreeplotter, rbd2, "gray80") + arrows

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