vis.immunr_ov_matrix: Repertoire overlap and gene usage visualisations

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

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 chordDiagram from the "circlize" package;

Value

A ggplot2, pheatmap or circlize object.

Examples

data(immdata)
ov <- repOverlap(immdata$data)
vis(ov)
vis(ov, "heatmap")
vis(ov, "heatmap2")
vis(ov, "circos")

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.