plot_gsr: Plot all chromosomes of a sample
In grafab/gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Description Usage Arguments Examples

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.

1 2	plot_gsr(dat, samp, sb = NULL, ncol = NULL, baf = FALSE, tl = FALSE, tlcoord = c(1.1, 0.68, 0.32, -0.1), ...)

`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()`.

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)
}