count_clone_sizes

<a href="https://lifecycle.r-lib.org/articles/stages.html#defunct"><img src="figures/lifecycle-defunct.svg?package=APackOfTheClones&version=1.2.1" alt="[Defunct]"></a>
ALL v0.1.x functions are deprecated, and the workflow has been completely revamped - now depending on the scRepertoire v2 package - which allows for the processing of multi-sampled single cell data. Please read the vignettes with <code>browseVignettes("APackOfTheClones")</code>or visit https://qile0317.github.io/APackOfTheClones/

internal

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Qile Yang

APackOfTheClones

Visualization of Clonal Expansion for Single Cell Immune
Profiles

count_clone_sizes function

<dl><dt>...</dt>
<dd>arbitrary arguments</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#defunct'><img src='figures/lifecycle-defunct.svg' alt='[Defunct]' /></a>
ALL v0.1.x functions are deprecated, and the workflow has been completely revamped - now depending on the scRepertoire v2 package - which allows for the processing of multi-sampled single cell data. Please read the vignettes with <code>browseVignettes("APackOfTheClones")</code>or visit https://qile0317.github.io/APackOfTheClones/

DEFUNCT: count the number of clonotype sizes per cell cluster in a seurat
object integrated with a TCR library — count_clone_sizes

<dl>

<dt>...</dt>
<dd>arbitrary arguments</dd>

</dl>

count_clone_sizes: DEFUNCT: count the number of clonotype sizes per cell cluster in a seurat object integrated with a TCR library

Description

Usage

Value

Arguments