plotAbs: Plots for analyzing PureCN solutions

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Plots for analyzing PureCN solutions

Description

This function provides various plots for finding correct purity and ploidy combinations in the results of a runAbsoluteCN call.

Usage

plotAbs(
  res,
  id = 1,
  type = c("hist", "overview", "BAF", "AF", "all"),
  chr = NULL,
  germline.only = TRUE,
  show.contour = FALSE,
  purity = NULL,
  ploidy = NULL,
  alpha = TRUE,
  show.segment.means = c("SNV", "segments", "both"),
  max.mapping.bias = 0.8,
  palette.name = "Paired",
  col.snps = "#2b6391",
  col.chr.shading = "#f0f0f0",
  ...
)

Arguments

res	Return object of the runAbsoluteCN function.
id	Candidate solutions to be plotted. id=1 will draw the plot for the maximum likelihood solution.
type	Different types of plots. hist will plot a histogram, assigning log-ratio peaks to integer values. overview will plot all local optima, sorted by likelihood. BAF plots something like a B-allele frequency plot known from SNP arrays: it plots allele frequencies of germline variants (or most likely germline when status is not available) against copy number. AF plots observed allelic fractions against expected (purity), maximum likelihood (optimal multiplicity) allelic fractions. all plots types BAF and AF for all local optima, and is useful for generating a PDF for manual inspection.
chr	If NULL, show all chromosomes, otherwise only the ones specified (type="BAF" only).
germline.only	If TRUE, show only variants most likely being germline in BAF plot. Useful to set to FALSE (in combination with chr) to study potential artifacts.
show.contour	For type="overview", display contour plot.
purity	Display expected integer copy numbers for purity, defaults to purity of the solution (type="hist" and "AF" only).
ploidy	Display expected integer copy numbers for ploidy, defaults to ploidy of the solution (type="hist" and "AF" only).
alpha	Add transparency to the plot if VCF contains many variants (>2000, type="AF" and type="BAF" only).
show.segment.means	Show segment means in germline allele frequency plot? If both, show SNVs and segment means. If SNV show all SNVs. Only for type="AF".
max.mapping.bias	Exclude variants with high mapping bias from plotting. Note that bias is reported on an inverse scale; a variant with mapping bias of 1 has no bias. (type="AF" and type="BAF" only).
palette.name	The default RColorBrewer palette.
col.snps	The color used for germline SNPs.
col.chr.shading	The color used for shading alternate chromosomes.
...	Additonal parameters passed to the plot function.

Value

Returns NULL.

Author(s)

Markus Riester

See Also

runAbsoluteCN

Examples

data(purecn.example.output)
plotAbs(purecn.example.output, type="overview")
# plot details for the maximum likelihood solution (rank 1)
plotAbs(purecn.example.output, 1, type="hist")
plotAbs(purecn.example.output, 1, type="BAF")
plotAbs(purecn.example.output, 1, type = "BAF", chr="chr2")

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.