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APackOfTheClones (version 1.2.4)

Visualization of Clonal Expansion for Single Cell Immune Profiles

Description

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) .

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Install

install.packages('APackOfTheClones')

Monthly Downloads

605

Version

1.2.4

License

MIT + file LICENSE

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Repository

https://github.com/Qile0317/APackOfTheClones

Homepage

https://qile0317.github.io/APackOfTheClones/

Maintainer

Qile Yang

Last Published

November 18th, 2024

Functions in APackOfTheClones (1.2.4)

Directly visualize clonal expansion of a combined seurat object

Remove current APackOfTheClones legend

Example Multi-sampled T-cell seurat object with integrated TCR library

containsApotcRun

Check for the existence of an APackOfTheClones run with its run id

Adjust the parameters of the APackOfTheClones reduction in a seurat object

Various variations of visualizations of clonal expansion post-RunAPOTC

countCloneSizes

count the number of clonotype sizes in a seurat object combined with a VDJ library overall or by cluster

Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion

deleteApotcData

Delete the results of an APackOfTheClones run

mergeCloneSizes

Merge a list of Clustered Clonotype Frequency Tables

getApotcDataIds

Get all run ids of previous RunAPOTC runs on a seurat object

showCloneHighlight

Highlight specific clones on an APackOfTheClones ggplot

clonal_expansion_plot

DEFUNCT: Visualize T cell clonal expansion with a ball-packing plot.

DEFUNCT: Integrate a single TCR library into Seurat object metadata

APackOfTheClones-package

APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

count_clone_sizes

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

overlay a clone size legend on an APackOfTheClones plot

getReductionCentroids

Calculate seurat cluster centroids based on a Dimensional reduction

getLastApotcDataId

Get the object id of the most recent RunAPOTC run on a seurat object

Rename an APackOfTheClones run

getSharedClones

Compute a list of clonotypes that are shared between seurat clusters