wgs.circos: wgs.circos Quick utility function for circos plot with read...

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

wgs.circos Quick utility function for circos plot with read depth, junctions, and segments (copied from skitools)

Description

wgs.circos

Quick utility function for circos plot with read depth, junctions, and segments (copied from skitools)

Usage

wgs.circos(
  jabba_rds,
  cov_fn,
  transform = TRUE,
  segs = NULL,
  win = NULL,
  field = "ratio",
  cytoband = NULL,
  y.field = field,
  ylim = NA,
  cytoband.path = "~/DB/UCSC/hg19.cytoband.txt",
  cex.points = 1,
  ideogram.outer = TRUE,
  scatter = TRUE,
  bar = FALSE,
  line = FALSE,
  gap.after = 1,
  labels.cex = 1,
  y.quantile = 0.9999,
  chr.sub = TRUE,
  max.ranges = 10000,
  axis.frac = 0.02,
  palette = "BrBg",
  ...
)

Arguments

jabba_rds	(character) path to jabba
cov_fn	(character) path to coverage
transform	(logical) rel2abs the coverage?
segs	GRanges of segments with optional fields $col and $border
win	GRanges window to limit plot to
cytoband	GRanges of cytoband
y.field	field in cov that specifies the y axis to draw
ylim	ylim on cov (default automatically computed)
cytoband.path	path to UCSC style cytoband path
cex.points	cex for cov points
y.quantile	quantile normalization
max.ranges	max ranges for cov points (1e4)
chr.sum	whether to chr.sub everything

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.