Function reference • APackOfTheClones

Core functions

vizAPOTC(): Directly visualize clonal expansion of a combined seurat object

RunAPOTC(): Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion

APOTCPlot(): Various variations of visualizations of clonal expansion post-RunAPOTC

AdjustAPOTC(): Adjust the parameters of the APackOfTheClones reduction in a seurat object

Working with RunAPOTC runs

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

containsApotcRun(): Check for the existence of an APackOfTheClones run with its run id

renameApotcRun(): Rename an APackOfTheClones run

deleteApotcData(): Delete the results of an APackOfTheClones run

Further Customization of Clonal Expansion Plots

showCloneHighlight(): Highlight specific clones on an APackOfTheClones ggplot

overlayLegend(): overlay a clone size legend on an APackOfTheClones plot

removeLegend(): Remove current APackOfTheClones legend

Clonal Analysis Utilities

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

mergeCloneSizes(): Merge a list of Clustered Clonotype Frequency Tables

getSharedClones(): Compute a list of clonotypes that are shared between seurat clusters

getReductionCentroids(): Calculate seurat cluster centroids based on a Dimensional reduction

Data

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