gcap.plotCircos: Plot Circos

In ShixiangWang/gcaputils: Utils for Package 'gcap'

Plot Circos

Description

Plot Circos

Usage

gcap.plotCircos(
  fCNA,
  highlights = NULL,
  total_n = NULL,
  clust_distance = 1e+07,
  col = c("#FF000080", "#0000FF80"),
  genome_build = c("hg38", "hg19"),
  chrs = paste0("chr", 1:22),
  ideogram_height = 1,
  only = c(NA_character_, "circular", "noncircular"),
  ...
)

Arguments

fCNA	a fCNA object.
highlights	gene/cytoband list to highlight.
total_n	if not NULL, this is used for calculating percentage.
clust_distance	a distance as cutoff for different clusters. Default is 1e7, i.e. 10Mb. Note 100 Mb is set to genes on different chromosomes, so please don't set value larger than that.
col	length-2 colors for circular and noncircular.
genome_build	genome version.
chrs	chromosome names.
ideogram_height	ideogram height at default.
only	if not NA, only shows a type of amplicon.
...	other parameters passing to ggrepel::geom_label_repel().

Value

Nothing.

Examples

library(gcap)
if (require("circlize") && require("scales")) {
  data("ascn")
  data = ascn

  # Create fake data
  set.seed(1234)
  data$sample = sample(LETTERS[1:10], nrow(data), replace = TRUE)
  rv = gcap.ASCNworkflow(data, outdir = tempdir(), model = "XGB11")

  gcap.plotCircos(rv)

  # Select genes to highlight in plot
  r1 = rv$getGeneSummary()
  gcap.plotCircos(rv, r1[circular == 1]$gene_id[1:10])

  gcap.plotCircos(rv, rv$data[, .(label = .N), by = .(band)][1:10])
  gcap.plotCircos(
    rv,
    rv$data[, .(label = .N, cluster = gsub("(.*):.*", "\\1", band)),
      by = .(band)
    ][1:10]
  )
}

ShixiangWang/gcaputils documentation built on Feb. 14, 2023, 5:58 a.m.