immunarch (version 0.9.1)

vis.immunr_public_repertoire: Public repertoire visualisation

Description

Public repertoire visualisation

Usage

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

Value

A ggplot2 object.

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

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)