barVDJ: Create a bar graph for clonotype expansion

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

Create a bar graph for clonotype expansion

Description

barVDJ creates a barplot using ggplot that shows the number of reads in the sample and colors the sample in accordance to the amount of diversity.

Usage

barVDJ(x, ...)

## S4 method for signature 'Matrix'
barVDJ(x, title = NULL, legend = FALSE)

## S4 method for signature 'matrix'
barVDJ(x, ...)

## S4 method for signature 'clonoStats'
barVDJ(x, ...)

Arguments

x	A matrix created with clonoStats.
...	additional arguments.
title	Character vector with an optional title. If FALSE, no title is generated.
legend	If TRUE, a legend will be included with the plot. If FALSE, no legend is included in the plot.

Value

Returns a ggplot plot with a barplot that shows the abundance of the clonotypes. The coloring indicates the number of cells for each clonotype with darker colors being clonotypes with a single cell (singletons) and lighter colors having more cells with that clonotype (expanded clonotype).

Examples

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

kstreet13/VDJdive documentation built on May 31, 2024, 1:26 p.m.