vis.immunr_ov_matrix: Repertoire overlap and gene usage visualisations

In immunarch: Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R

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 class 'immunr_ov_matrix'
vis(.data, .plot = c("heatmap", "heatmap2", "circos"), ...)

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;

Value

A ggplot2, pheatmap or circlize object.

Examples

## Not run: 
data(immdata)
ov <- repOverlap(immdata$data)
vis(ov)
vis(ov, "heatmap")
vis(ov, "heatmap2")
vis(ov, "circos")

## End(Not run)

immunarch documentation built on Nov. 5, 2025, 7:21 p.m.