gsrc (version 1.1)

plot_gsr: Plot all chromosomes of a sample

Description

Plot all chromosomes of a sample. One subgenome is plotted on top, the other at the bottom. If available, the synteny plots can be plotted between them. Genome structure rearrangements (gsr) (e.g.g deletions or duplications) are highlighted by different colors.

Usage

plot_gsr(dat, samp, sb = NULL, ncol = NULL, baf = FALSE, tl = FALSE, tlcoord = c(1.1, 0.68, 0.32, -0.1), ...)

Arguments

dat

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

samp

Integer, which sample should be plotted.

sb

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

ncol

Number of columns.

baf

Logical, if B-Allele frequency should be plotted.

tl

Logical, if translocations should be highlighted.

tlcoord

Numeric vector of length four. The y-coordinates used to highlight translocations. Top and bottom of top translocation and top and bottom of bottom translocation.

...

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_gsr(dat, samp = 1, sb = synteny_blocks)
}