plotPropVJ: plot V or J proportion

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function plots V or J proportion in all samples in a RepSeqExperiment object.

Usage

plotPropVJ(
  x,
  level = c("V", "J"),
  sampleName = NULL,
  scale = c("counts", "percent", "cpm")
)

Arguments

x	an object of class RepSeqExperiment.
level	level of repertoire to be used.
sampleName	the name of sample or lib to be plotted, sample name must be existed among x column names. If NULL the first sample name is used.
scale	type of data to be plotted, counts, percentages or counts per million.

Value

a barplot

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeqData)
snames <- rownames(sData(RepSeqData))
# plot percentages of V compared to the library size of in the second sample.
plotPropVJ(x = RepSeqData, level = "V", sampleName = snames[2], scale = "counts")

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.