immunarch (version 0.6.4)

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

Description

Visualise distributions of genes using heatmaps, treemaps or other plots.

Usage

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

Arguments

.data

Output from the geneUsage function.

.plot

String specifying the plot type:

- "hist" for histograms using vis_hist;

- "tree" for histograms using vis_treemap;

- "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;

- "tree" - passes arguments to vis_treemap and treemap from the treemap package;

- "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, circlize or treemap object.

See Also

geneUsage

Examples

# NOT RUN {
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)
# }