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

Description Usage Arguments Examples

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.

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

`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()`.

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)
}