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Visualization of a repertoire structure through a circular treemap

Source: R/plotFunctions.R
plotIndMap.Rd

This function plots all clones in a single repertoire as a circular treemap, showing the clone distributiion within the repertoire. Each circle represents a unique clone, and the circle size corresponds to the clone count.

Usage

plotIndMap(
  x,
  sampleName = NULL,
  prop = 0.01,
  level = c("aaClone", "ntClone", "V", "J", "VJ", "ntCDR3", "aaCDR3")
)

Arguments

x

an object of class RepSeqExperiment

sampleName

a character specifying the sample_id to analyze. Default is NULL, which plots the first sample in the dataset.

prop

a numeric indicating the proportions of clones to be plotted. It ranges from 0 to 1.

level

a character specifying the level of the repertoire on which the diversity should be estimated. Should be one of "aaClone","ntClone", "V", "J", "VJ", "ntCDR3" or "aaCDR3".

Examples


data(RepSeqData)

sname <- rownames(mData(RepSeqData))[1]

plotIndMap(x=RepSeqData, sampleName=sname, level="aaClone", prop=0.01)