cnv_plotDistributionProfile: Plot copy number distribution either by length or chromosome

In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description

Plot copy number distribution either by length or chromosome

Usage

cnv_plotDistributionProfile(data, rm_normal = TRUE, mode = c("ld",
  "cd"), fill = FALSE, scale_chr = TRUE, genome_build = c("hg19",
  "hg38"))

Arguments

data	a data.frame, result of cnv_getLengthFraction function.
rm_normal	logical. Whether removel normal copy (i.e. "segVal" equals 2), default is TRUE.
mode	either "ld" for distribution by CN length or "cd" for distribution by chromosome.
fill	when mode is "cd", if fill is TRUE, plot percentage instead of count.
scale_chr	logical. If TRUE, normalize count to per Megabase unit.
genome_build	genome build version, must be one of 'hg19' or 'hg38'.

Value

a ggplot object

Author(s)

Shixiang Wang [e-mail]

See Also

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_generateSbCMatrix, cnv_getLengthFraction, cnv_pipe, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, cnv_quantifySigExposure, cnv_readprofile

Examples

## Not run: 
cnv_plotLengthSummary(data, mode = "cd")

## End(Not run)

ShixiangWang/VSHunter documentation built on June 27, 2019, 4:56 p.m.