plot_global: Plot all chromosomes of a population

In gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

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)
}

Example output

Loading required package: brassicaData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'brassicaData'

gsrc documentation built on May 30, 2017, 4:16 a.m.