SomatiCA (version 2.2.0)

plotSegment: Plot segmentation.

Description

Plot segmentation.

Usage

plotSegment(segment, input, k = 1, col1 = "orange", col2 = "blue", smooth = FALSE, dev.new = TRUE, cex.point =0.5, ...)

Arguments

segment

A GRanges object, segmentation result.

input

A GRanges object, input for SomatiCA.

k

When there are multiple chromosomes, only kth will be plot each time.

col1

Color for data points.

col2

Color for segments.

smooth

Whether smoothed data is plotted. Default is T.

dev.new

Whether a new device will be opened.

cex.point

Size of data points.

...

Parameters in plot().

Value

A plot.

Examples

#data#
rawLAF <- c(rnorm(300, 0.2, 0.05), rnorm(300, 0.4, 0.05), rnorm(200, 0.3, 0.05), rnorm(200, 0.2, 0.05), rnorm(200, 0.3, 0.05), rnorm(250, 0.4, 0.05)) 
reads <- rep(50, 800+650)
chr <- c(rep("chr1", 800), rep("chr2", 650))
position <- c(c(1:800), c(1:650))
zygo <- rep("het", 800+650)
input <- GRanges(seqnames=chr, 
                 ranges=IRanges(start=position, width=1), 
                 zygosity=zygo, 
                 tCount=reads, 
                 LAF=rawLAF, 
                 tCountN=reads, 
                 gLAF=rawLAF) 
                 
#segment#
chr <- c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2")
start <- c(1, 300, 600, 1, 200, 400) 
end <- c(300, 600, 800, 200, 400, 650)
medLAF <- c(0.2, 0.4, 0.3, 0.2, 0.3, 0.4)
medgermlineLAF <- rep(0.4, 6)
segment <- GRanges(seqnames=chr, 
                   ranges=IRanges(start=start, end=end), 
                   medLAF=medLAF, 
                   medgLAF=medgermlineLAF)

## First chromosome
plotSegment(segment, input, k=1)
## Second chromosome
plotSegment(segment, input, k=2)