vis_public_frequencies: Public repertoire visualisation

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

Public repertoire visualisation

Description

Visualise public clonotype frequencies.

Usage

vis_public_frequencies(
  .data,
  .by = NA,
  .meta = NA,
  .type = c("boxplot", "none", "mean")
)

Arguments

.data	Public repertoire - an output from the pubRep function.
.by	Pass NA if you want to plot samples without grouping. You can pass a character vector with one or several column names from ".meta" to group your data before plotting. In this case you should provide ".meta". You can pass a character vector that exactly matches the number of samples in your data, each value should correspond to a sample's property. It will be used to group data based on the values provided. Note that in this case you should pass NA to ".meta".
.meta	A metadata object. An R dataframe with sample names and their properties, such as age, serostatus or hla.
.type	Character. Either "boxplot" for plotting distributions of frequencies, "none" for plotting everything, or "mean" for plotting average values only.

Value

A ggplot2 object.

Examples

data(immdata)
immdata$data <- lapply(immdata$data, head, 500)
pr <- pubRep(immdata$data, .verbose = FALSE)
vis(pr, "freq", .type = "boxplot")
vis(pr, "freq", .type = "none")
vis(pr, "freq", .type = "mean")
vis(pr, "freq", .by = "Status", .meta = immdata$meta)

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