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APackOfTheClones (version 1.2.1)

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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Version

Install

install.packages('APackOfTheClones')

Monthly Downloads

603

Version

1.2.1

License

MIT + file LICENSE

Maintainer

Qile Yang

Last Published

October 10th, 2024

Functions in APackOfTheClones (1.2.1)

getLastApotcDataId

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

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

Merge a list of Clustered Clonotype Frequency Tables
integrate_tcr

DEFUNCT: Integrate a single TCR library into Seurat object metadata
getSharedClones

Compute a list of clonotypes that are shared between seurat clusters
getReductionCentroids

Calculate seurat cluster centroids based on a Dimensional reduction
overlayLegend

overlay a clone size legend on an APackOfTheClones plot
showCloneHighlight

Highlight specific clones on an APackOfTheClones ggplot
renameApotcRun

Rename an APackOfTheClones run
vizAPOTC

Directly visualize clonal expansion of a combined seurat object
removeLegend

Remove current APackOfTheClones legend
combined_pbmc

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

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

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

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

Delete the results of an APackOfTheClones run
AdjustAPOTC

Adjust the parameters of the APackOfTheClones reduction in a seurat object
APOTCPlot

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
APackOfTheClones-package

APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles
clonal_expansion_plot

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