gsrc (version 1.1)

plot_global: Plot all chromosomes of a population

Description

Plot all chromosomes of a sample. The one subgenome is plotted on top, the other at the bottom. If available, the synteny plots can be plotted between them. Deletions and duplications are indicated by different colors.

Usage

plot_global(dat, sb = NULL, baf = FALSE, cex = 0.2, ...)

Arguments

dat

List object, containing at least two matrices "baf" and "rratio" and two vectors "chr" and "pos".

sb

Synteny blocks. Data frame with columns start1, start2, end1, end2, chr1 and chr2.

baf

Logical, if B-Allele frequency should be plotted.

cex

Size of dots.

...

arguments are forwarded to plot().

Examples

if(require(brassicaData)){
data("raw_napus", package = "brassicaData", envir = environment())

dat <- intens_theta(raw_napus)
dat <- remove_suffix(dat, "_Grn")
dat <- geno_baf_rratio(dat, delthresh = 11)
dat <- segm(dat)
dat <- cnv(dat, dup = 0.03, del = -0.06)
data("synteny_blocks", package = "brassicaData", envir = environment())
plot_global(dat, sb = synteny_blocks)
}