Visualization of Clonal Expansion for Single Cell Immune Profiles

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Documentation for package ‘APackOfTheClones’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

AdjustAPOTC	Adjust the parameters of the APackOfTheClones reduction in a seurat object
APOTCPlot	Various variations of visualizations of clonal expansion post-RunAPOTC
combined_pbmc	Example Multi-sampled T-cell seurat object with integrated TCR library
containsApotcRun	Check for the existence of an APackOfTheClones run with its run id
countCloneSizes	count the number of clonotype sizes in a seurat object combined with a VDJ library overall or by cluster
deleteApotcData	Delete the results of an APackOfTheClones run
getApotcDataIds	Get all run ids of previous RunAPOTC runs on a seurat object
getLastApotcDataId	Get the object id of the most recent RunAPOTC run on a seurat object
getReductionCentroids	Calculate seurat cluster centroids based on a Dimensional reduction
getSharedClones	Compute a list of clonotypes that are shared between seurat clusters
mergeCloneSizes	Merge a list of Clustered Clonotype Frequency Tables
overlayLegend	overlay a clone size legend on an APackOfTheClones plot
removeLegend	Remove current APackOfTheClones legend
renameApotcRun	Rename an APackOfTheClones run
RunAPOTC	Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion
showCloneHighlight	Highlight specific clones on an APackOfTheClones ggplot
vizAPOTC	Directly visualize clonal expansion of a combined seurat object