R: Public repertoire visualisation

vis_public_frequencies {immunarch} | R Documentation

## 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)

[Package immunarch version 0.6.5 Index]