Visualization of Clonal Expansion for Single Cell Immune Profiles

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Documentation for package ‘APackOfTheClones’ version 1.2.0

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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