plot_cnv: Plot Copy Number Variations

Description Usage Arguments Examples

View source: R/plot.R

Description

Plots copy number variations in a grid to allow for comparisons between individuals. Deletions and duplications are represented in red and green, respectively.

Usage

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plot_cnv(dat, lwd = 1, col = grDevices::rgb(0, 0, 0, 0.5), x.cex = 1,
  y.cex = 1, ...)

Arguments

dat

List object, containing vectors samples, pos and chr and matrix cnv.

lwd

Line width for raster.

col

Color of raster lines.

x.cex

Character size in x-axis.

y.cex

Character size in y-axis.

...

are forwarded to the image() command.

Examples

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## Not run: 
if(require(brassicaData)){
data(raw_napus, package = "brassicaData", envir = environment())
raw_napus <- filt_samp(raw_napus, raw_napus$samples[-(1:10)])
raw_napus <- filt_snps(raw_napus, raw_napus$snps[-(1:100)][-(30000:30100)])
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)
plot_cnv(dat)
}

## End(Not run)

grafab/gsrc documentation built on May 14, 2017, 3 p.m.