vis_public_clonotypes: Visualisation of public clonotypes

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

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)

immunarch documentation built on Dec. 28, 2022, 2:59 a.m.