vis.immunr_gene_usage: Histograms and boxplots (general case / gene usage)

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

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)

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