pieVDJ: Create a pie chart for clonotype expansion

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

Create a pie chart for clonotype expansion

Description

pieVDJ creates a list of pie charts created using ggplot that shows the the level of expansion in each clonotype.

Usage

pieVDJ(x, ...)

## S4 method for signature 'Matrix'
pieVDJ(x, legend = "bottom")

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

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

Arguments

x	A matrix created with summarizeClonotypes.
...	additional arguments.
legend	Can take on the values use in the legend.position command in ggplot ("left","top", "right", "bottom", or a numeric vector) to indicate where the legend should be placed. If left NULL, no legend will be created.

Value

If x contains more than one sample, a list of pie charts will be returned. If x contains only one sample, the pie chart will be returned. 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)
pieVDJ(x)

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