R: Visualisation of public clonotypes

vis_public_clonotypes {immunarch} | R Documentation

## Visualisation of public clonotypes

### Description

Visualise correlation of public clonotype frequencies in pairs of repertoires.

### Usage

    vis_public_clonotypes(
      .data,
      .x.rep = NA,
      .y.rep = NA,
      .title = NA,
      .ncol = 3,
      .point.size.modif = 1,
      .cut.axes = TRUE,
      .density = TRUE,
      .lm = TRUE,
      .radj.size = 3.5
    )

### Arguments

`.data` | Public repertoire data - an output from the pubRep function.
`.x.rep` | Either indices of samples or character vector of sample names for the x-axis. Must be of the same length as ".y.rep".
`.y.rep` | Either indices of samples or character vector of sample names for the y-axis. Must be of the same length as ".x.rep".
`.title` | The text for the title of the plot.
`.ncol` | An integer number of columns to print in the grid of pairs of repertoires.
`.point.size.modif` | An integer value that is a modifier of the point size. The larger the number, the larger the points.
`.cut.axes` | If TRUE then axes limits become shorter.
`.density` | If TRUE then displays density plot for distributions of clonotypes for each sample. If FALSE then removes density plot from the visualisation.
`.lm` | If TRUE then fit a linear model and displays an R adjusted coefficient that shows how similar samples are in terms of shared clonotypes.
`.radj.size` | An integer value, that defines the size of the The text for the R adjusted coefficient.

### Value

A ggplot2 object.

### See Also

pubRep, vis.immunr_public_repertoire

### Examples

    data(immdata)
    pr <- pubRep(immdata$data, .verbose = FALSE)
    vis(pr, "clonotypes", 1, 2)

[Package immunarch version 0.6.5 Index]