R: Repertoire overlap and gene usage visualisations

vis.immunr_ov_matrix {immunarch} | R Documentation

## Repertoire overlap and gene usage visualisations

### Description

Visualise matrices with overlap values or gene usage distances among samples. For details see 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")

[Package immunarch version 0.6.5 Index]