R: Histograms and boxplots (general case / gene usage)

vis.immunr_gene_usage {immunarch} | R Documentation

## Histograms and boxplots (general case / gene usage)

### Description

Visualise distributions of genes using heatmaps or other plots.

### Usage

    ## S3 method for class 'immunr_gene_usage'
    vis(.data, .plot = c("hist", "box", "heatmap", "heatmap2", "circos"), ...)

### Arguments

`.data` | Output from the geneUsage function.
`.plot` | String specifying the plot type: - "hist" for histograms using vis_hist; - "heatmap" for heatmaps using vis_heatmap; - "heatmap2" for heatmaps using vis_heatmap2; - "circos" for circos plots using vis_circos.
`...` | Other arguments passed to corresponding functions depending on the plot type: - "hist" - passes arguments to vis_hist; - "box" - passes arguments to vis_box; - "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 object, pheatmap or circlize object.

### See Also

geneUsage

### Examples

    data(immdata)

    gu <- geneUsage(immdata$data[[1]])
    vis(gu)

    gu <- geneUsage(immdata$data)
    vis(gu, .by = "Status", .meta = immdata$meta)
    vis(gu, "box", .by = "Status", .meta = immdata$meta)

[Package immunarch version 0.6.7 Index]