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

In charlotterich/immunarch_code: Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R

Description

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

Usage

## S3 method for class '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 "heatmap3" package; - "circos" - passes arguments to vis_circos and chordDiagram from the "circlize" package.

See Also

geneUsage

Examples

## Not run: 
data(twb)
gu = geneUsage(twb)

# next two plots are similar
vis(gu, .title = "Gene usage on twins")
vis_hist(gu, .title = "Gene usage on twins")

# next two plots are similar as well
vis(gu, "box", .title = "Gene usage on twins")
vis_box(gu, .title = "Gene usage on twins")

## End(Not run)

charlotterich/immunarch_code documentation built on Jan. 24, 2020, 12:08 a.m.