abundanceVDJ: Create an abundance graph for clonotype expansion

In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

Create an abundance graph for clonotype expansion

Description

abundanceVDJ creates a dot plot using ggplot that shows the number of reads for each clonotype in each sample and labels the most abundant clonotypes.

Usage

abundanceVDJ(x, ...)

## S4 method for signature 'clonoStats'
abundanceVDJ(x, annotate = 5, title = NULL)

Arguments

x	A matrix created with clonoStats.
...	additional arguments.
annotate	An integer that specifies how many of the most abundant clonotypes should be annotated on the plot.
title	Character vector with an optional title. If FALSE, no title is generated.

Value

Returns a ggplot plot with a dot plot that shows the abundance of the clonotypes in each sample. The most abundant clonotypes are annotated on the plot and ordered from most abundant to least abundant.

Examples

data('contigs')
x <- clonoStats(contigs)
abundanceVDJ(x)

kstreet13/VDJdive documentation built on May 27, 2023, 8:08 a.m.