Package index

Core functions

vizAPOTC() stable

Directly visualize clonal expansion of a combined seurat object

RunAPOTC() stable

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

APOTCPlot() stable

Various variations of visualizations of clonal expansion post-RunAPOTC

AdjustAPOTC() stable

Adjust the parameters of the APackOfTheClones reduction in a seurat object

Working with RunAPOTC() runs

getApotcDataIds() getApotcRunIds() stable

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

getLastApotcDataId() getLastApotcRunId() stable

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

containsApotcRun() stable

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

renameApotcRun() stable

Rename an APackOfTheClones run

deleteApotcData() stable

Delete the results of an APackOfTheClones run

Further Customization of Clonal Expansion Plots

showCloneHighlight() experimental

Highlight specific clones on an APackOfTheClones ggplot

overlayLegend() stable

overlay a clone size legend on an APackOfTheClones plot

removeLegend() stable

Remove current APackOfTheClones legend

Clonal Analysis Utilities

countCloneSizes() stable

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

mergeCloneSizes() experimental

Merge a list of Clustered Clonotype Frequency Tables

getSharedClones() stable

Compute a list of clonotypes that are shared between seurat clusters

getReductionCentroids() stable

Calculate seurat cluster centroids based on a Dimensional reduction

Updating outputs from previous versions

updateApotc()

Update APackOfTheClones objects to the latest format

Data

combined_pbmc stable

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