pca.segments: Perform PCA on segments frequency data.

In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description

Perform PCA on gene segments frequency data for V- and J-segments and either return pca object or plot the results.

Usage

pca.segments(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)

pca.segments.2D(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)

Arguments

.data	Either data.frame or a list of data.frame or a result obtained from the geneUsage function.
.cast.freq.seg	if T then apply codegeneUsage to the supplied data.
...	Further arguments passed to prcomp or geneUsage.
.text	If T then plot sample names in the resulting plot.
.do.plot	if T then plot a graphic, else return a pca object.

Value

If .do.plot is T than ggplot object; else pca object.

Examples

## Not run: 
# Load the twins data.
data(twb)
# Plot a plot of results of PCA on V-segments usage.
pca.segments(twb, T, scale. = T)

## End(Not run)

imminfo/tcr documentation built on June 13, 2020, 7:01 a.m.