Man pages for APackOfTheClones
Visualization of Clonal Expansion for Single Cell Immune Profiles
| AdjustAPOTC | Adjust the parameters of the APackOfTheClones reduction in a... |
| APackOfTheClones-package | APackOfTheClones: Visualization of Clonal Expansion for... |
| APOTCPlot | Various variations of visualizations of clonal expansion... |
| clonal_expansion_plot | DEFUNCT: Visualize T cell clonal expansion with a... |
| combined_pbmc | Example Multi-sampled T-cell seurat object with integrated... |
| containsApotcRun | Check for the existence of an APackOfTheClones run with its... |
| count_clone_sizes | DEFUNCT: count the number of clonotype sizes per cell cluster... |
| countCloneSizes | count the number of clonotype sizes in a seurat object... |
| 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... |
| getReductionCentroids | Calculate seurat cluster centroids based on a Dimensional... |
| getSharedClones | Compute a list of clonotypes that are shared between seurat... |
| integrate_tcr | DEFUNCT: Integrate a single TCR library into Seurat object... |
| 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... |
| 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... |
