gsrc (version 1.1)

plot_cnv: Plot Copy Number Variations

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

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

## 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)