immunarch (version 0.10.3)

vis.immunr_ov_matrix: Repertoire overlap and gene usage visualisations

Description

Visualises matrices with overlap values or gene usage distances among samples. For details see the links below.

Usage

# S3 method for immunr_ov_matrix
vis(.data, .plot = c("heatmap", "heatmap2", "circos"), ...)

Value

A ggplot2, pheatmap or circlize object.

Arguments

.data

Output from repOverlap or geneUsageAnalysis.

.plot

A string specifying the plot type:

• "heatmap" for heatmaps using vis_heatmap;

• "heatmap2" for heatmaps using vis_heatmap2;

• "circos" for circos plots using vis_circos;

...

Other arguments are passed through to the underlying plotting function:

• "heatmap" - passes arguments to vis_heatmap;

• "heatmap2" - passes arguments to vis_heatmap2 and heatmap from the "pheatmap" package;

• "circos" - passes arguments to vis_circos and circlize::chordDiagram from the "circlize" package;

Examples

if (FALSE) {
data(immdata)
ov <- repOverlap(immdata$data)
vis(ov)
vis(ov, "heatmap")
vis(ov, "heatmap2")
vis(ov, "circos")
}