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

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

circos Quick utility function for circos plot with read depth, junctions, and segments

Description

circos

Quick utility function for circos plot with read depth, junctions, and segments

Usage

circos(
  junctions = jJ(),
  cov = NULL,
  ncov = NULL,
  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

cov	GRanges of scatter points with optional fields $col
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)
jabba_rds	Junction object with optional metadata field $col to specify color
chr.sum	whether to chr.sub everything

Author(s)

Marcin Imielinski

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