# Single-Cell Immune Repertoire and Gene Expression Analysis

## Documentation for package ‘Platypus’ version 3.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GEX_cluster_genes | Differentially expressed genes between clusters or data subsets
GEX_cluster_genes_heatmap | Heatmap of cluster defining genes
GEX_cluster_membership | Cluster membership plots by sample
GEX_coexpression_coefficient | Coexpression of selected genes
GEX_DEgenes | Wrapper for differential gene expression analysis and plotting
GEX_dottile_plot | GEX Dottile plots
GEX_gene_visualization | Visualization of marker expression in a data set or of predefined genes (B cells, CD4 T cells and CD8 T cells).
GEX_GSEA | GEX Gene Set Enrichment Analysis and plotting
GEX_heatmap | Flexible GEX heatmap wrapper
GEX_lineage_trajectories | This is a function to infer single cell trajectories and identifying lineage structures on clustered cells. Using the slingshot library
GEX_pairwise_DEGs | Wrapper for calculating pairwise differentially expressed genes
GEX_phenotype | Assignment of cells to phenotypes based on selected markers
GEX_phenotype_per_clone | Plotting of GEX phenotype by VDJ clone
GEX_proportions_barplot | Plots proportions of a group of cells within a secondary group of cells. E.g. The proportions of samples in seurat clusters, or the proportions of samples in defined cell subtypes
GEX_scatter_coexpression | Scatter plot for coexpression of two selected genes
GEX_volcano | Flexible wrapper for GEX volcano plots
PlatypusDB_AIRR_to_VGM | AIRR to Platypus V3 VGM compatibility function
PlatypusDB_load_from_disk | PlatypusDB utility for import of local datasets
PlatypusDB_VGM_to_AIRR | Platypus V3 VGM to AIRR compatibility function
small_vgm | Small VDJ GEX matrix (VGM) for function testing purposes
VDJ_abundances | Calculate abundances/counts of specific features for a VDJ dataframe
VDJ_alpha_beta_Vgene_circos | Produces a Circos plot from the VDJ_analyze output. Connects the V-alpha with the corresponding V-beta gene for each clonotype.
VDJ_antigen_integrate | Integrates antigen-specific information into the VDJ/VDJ.GEX.matrix[[1]] object
VDJ_assemble_for_PnP | Ab sequence assembly for recombinant PnP expression
VDJ_build | Minimal version of the VDJ building part from VDJ_GEX_matrix() function. Optimized for for Cell Ranger v7 and suitable for older Cell Ranger versions.
VDJ_call_enclone | (Re)clonotype a VDJ object using cellranger's enclone tool
VDJ_circos | Plots a Circos diagram from an adjacency matrix. Uses the Circlize chordDiagram function. Is called by VDJ_clonotype_clusters_circos(), VDJ_alpha_beta_Vgene_circos() and VDJ_VJ_usage_circos() functions or works on its own when supplied with an adjacency matrix.
VDJ_clonal_barplot | Function to create stacked barplots to visualize clonal expansion per repertoire directly from a VDJ matrix (either from the minimal_VDJ() or VDJ_GEX_matrix())
VDJ_clonal_donut | Circular VDJ expansion plots
VDJ_clonal_expansion | Flexible wrapper for clonal expansion barplots by isotype, GEX cluster etc.
VDJ_clonotype | Platypus V3 clonotyping wrapper
VDJ_clonotype_v3_w_enclone | Updated clonotyping function based on implications for cells with different chain numbers than 1 VDJ 1 VJ chains.
VDJ_contigs_to_vgm | Formats "VDJ_contigs_annotations.csv" files from cell ranger to match the VDJ_GEX_matrix output using only cells with 1VDJ and 1VJ chain
VDJ_db_annotate | Wrapper function of VDJ_antigen_integrate function
VDJ_db_load | Load and preprocess a list of antigen-specific databases
VDJ_diversity | Calculates and plots common diversity and overlap measures for repertoires and alike. Requires the vegan package
VDJ_dynamics | Tracks a specific VDJ column across multiple samples/timepoints.
VDJ_expand_aberrants | Expand the aberrant cells in a VDJ dataframe by converting them into additional rows
VDJ_extract_germline_consensus_ref | Making the trimmed reference and concatenating fr1-fr4
VDJ_germline | Infer germline from the desired software/caller
VDJ_get_public | Function to get shared/public elements across multiple repertoires
VDJ_GEX_clonotype_clusters_circos | Makes a Circos plot from the VDJ_GEX_integrate output. Connects the clonotypes with the corresponding clusters.
VDJ_GEX_matrix | VDJ GEX processing and integration wrapper
VDJ_GEX_overlay_clones | Overlay clones on GEX projection
VDJ_GEX_stats | Standalone VDJ and GEX statistics.
VDJ_kmers | Calculates and plots kmers distributions and frequencies.
VDJ_network | Similarity networks based on CDR3 regions
VDJ_ordination | Performs ordination/dimensionality reduction for a species incidence matrix, depending on the species selected in the feature.columns parameter.
VDJ_overlap_heatmap | Wrapper to determine and plot overlap between VDJ features across groups
VDJ_phylogenetic_trees | Creates phylogenetic trees from a VDJ dataframe
VDJ_phylogenetic_trees_plot | Phylogenetic tree plotting
VDJ_plot_SHM | Plotting of somatic hypermutation counts
VDJ_public | Function to get shared/public elements across multiple repertoires
VDJ_rarefaction | Plots rarefaction curves for species denoted in the feature.columns parameter across groups determined by grouping.columns
VDJ_variants_per_clone | Wrapper for variant analysis by clone
VDJ_Vgene_usage | V(D)J gene usage stacked barplots
VDJ_Vgene_usage_barplot | V(D)J gene usage barplots
VDJ_Vgene_usage_stacked_barplot | V(D)J gene usage stacked barplots
VDJ_VJ_usage_circos | Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype.
VGM_build | Function to obtain the VGM object by integrating the VDJ and GEX/Seurat objects
VGM_expanded_clones | VDJ utility for T/F column for clonal expansion
VGM_expand_featurebarcodes | Utility for feature barcode assignment including clonal information
VGM_integrate | Utility for VDJ GEX matrix to integrated VDJ and GEX objects after addition of data to either