plot_facets: Plot FACETS output
In mskcc/facets-suite: Functions to run and parse output from FACETS

plot_facets

R 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`.