APackOfTheClones: Visualization of clonal expansionwith circle packing

T and B lymphocytes exhibit diverse surface receptor repertoires that interact with antigens to communicate and protect the body from foreign invaders.(Haan et al., 2014) Modern methods allows the experimental characterization of the collective identity of the immune cells in tissue samples by sequencing RNA transcripts and cell receptors with scRNA-seq and scTCR-seq / scBCR-seq.Such methods generate high-dimensional data which are analyzed with the aid of dimensional reduction techniques to allow annotation of cell subsets.(Huang et al., 2022) The R (R Core Team, 2023) package APackOfTheClones implements and extends a novel method to visualize clonal expansion (abbreviated as CE) at a single-cell (abbreviated as SC) resolution using circle packing, along with many clonal analysis utilities.Clonotype frequencies for each cell subset is counted and the values are used as radii and packed into one circular cluster with the largest circles near the center, and overlaid onto a the centroids of each cell subset on the corresponding 2D dimensional reduction plot.The package easily integrates into existing analysis pipelines using the Seurat (Hao et al., 2023) and scRepertoire (Borcherding & Bormann, 2020) packages.The original implementation was created in the Julia language