# Visualization of Clonal Expansion for Single Cell Immune Profiles

## Documentation for package ‘APackOfTheClones’ version 1.3.0

- 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
getApotcRunIds | 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
getLastApotcRunId | 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
updateApotc | Update APackOfTheClones objects to the latest format
vizAPOTC | Directly visualize clonal expansion of a combined seurat object