vis.immunr_public_repertoire: Public repertoire visualisation

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

Public repertoire visualisation

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.

Value

A ggplot2 object.

Examples

data(immdata)
immdata$data <- lapply(immdata$data, head, 300)
pr <- pubRep(immdata$data, .verbose = FALSE)
vis(pr, "freq")
vis(pr, "freq", .type = "none")

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

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