vis.immunr_public_repertoire: Public repertoire visualisation

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

Description

Public repertoire visualisation

Usage

## S3 method for class 'immunr_public_repertoire'
vis(.data, .plot = c("freq", "clonotypes"), ...)

Arguments

.data	Public repertoire, an output from pubRep.
.plot	A string specifying the plot type: - "freq" for visualisation of the distribution of occurrences of clonotypes and their frequencies using vis_public_frequencies. - "clonotypes" for visualisation of public clonotype frequenciy correlations between pairs of samples using vis_public_clonotypes
...	Further arguments passed vis_public_frequencies or vis_public_clonotypes, depending on the ".plot" argument.

Examples

## Not run: 
pr = pubRep(immdata$data)
vis(pr, "freq")
vis(pr, "freq", .type="boxplot")
vis(pr, "freq", .type="none")
vis(pr, "freq", .type="mean")
vis(pr, "freq", .by = "Status", .meta=immdata$meta)

vis(pr, "clonotypes", 1, 2)

## End(Not run)

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