plot_facets: Plot FACETS output

plot_facetsR Documentation

Plot FACETS output

Description

Generate the following plots:

  • Log-ratio: Copy-number segmentation based on tumor-normal read coverage comparison.

  • Allelic imbalance: Allelic imbalance based on somatic changes in zygosity of heterozygous SNPs in the normal.

  • Integer copy number: Inference of the major and minor copy-number states based on the tumor-normal log ratio and allelic content.

  • Cellular fraction: Estimate of fraction of cells in sample harboring each segment.

Usage

cnlr_plot(facets_data, colors = c("#0080FF", "#4CC4FF"), plotX = FALSE,
  genome = c("hg19", "hg18", "hg38"), highlight_gene = NULL,
  adjust_diplogr = TRUE, subset_snps = NULL, return_object = FALSE)

valor_plot(facets_data, colors = c("#0080FF", "#4CC4FF"),
  plotX = FALSE, genome = c("hg19", "hg18", "hg38"),
  highlight_gene = NULL, subset_snps = NULL, return_object = FALSE)

cf_plot(facets_data, method = c("em", "cncf"), plotX = FALSE,
  genome = c("hg19", "hg18", "hg38"), return_object = FALSE)

icn_plot(facets_data, method = c("em", "cncf"), plotX = FALSE,
  genome = c("hg19", "hg18", "hg38"), highlight_gene = NULL,
  return_object = FALSE)

closeup_plot(facets_data, highlight_gene = NULL, plot_chroms = NULL,
  method = c("em", "cncf"), genome = c("hg19", "hg18", "hg38"),
  return_object = FALSE)

Arguments

facets_data

Output object from run_facets.

colors

Vector of two colors for alternating chromosomes.

plotX

If TRUE, includes chromosome X.

genome

Genome build.

highlight_gene

Highlight gene(s), provide gene symbol or mapped positions (internally).

adjust_diplogr

Normalize by sample dipLogR.

subset_snps

Subset the SNP profile to reduce weight of plotting, supply a factor by which to reduce or TRUE for default.

return_object

If TRUE, returns ggplot2 object instead of printing plot.

method

When available, choose between plotting solution from em or cncf algorithm.

plot_chroms

Chromosomes to plot when using closeup_plot.

Value

ggplot2 objects, see input parameter return_object.


mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.