plotAbs: Plots for analyzing PureCN solutions

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotAbs.R

Description

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

Usage

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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

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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")

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.