Single-Cell Immune Repertoire and Gene Expression Analysis


[Up] [Top]

Documentation for package ‘Platypus’ version 3.3.5

Help Pages

A B C E G H I M N O P S T U V

-- A --

AbForests_AntibodyForest Infer and draw B cell evolutionary networks
AbForests_CompareForests Comparison of distinct B cell repertoires
AbForests_ConvertStructure Extract transcriptome/isotype information and B cell receptor sequences from single cell immune repertoire formatted as list of data.frames
AbForests_CsvToDf Convert list of csvs, to nested list of data.frames
AbForests_ForestMetrics Calculate metrics for networks
AbForests_PlotGraphs Plot igraph and ggplot objects
AbForests_PlyloToMatrix Conversion of phylogenetic tree to distance matrix
AbForests_RemoveNets Filter sub-repertoires with less than N unique sequences or with less than C unique cells
AbForests_SubRepertoiresByCells Split single cell immune repertoire into sub-repertoires by isotype based on number of B cells
AbForests_SubRepertoiresByUniqueSeq Split single cell immune repertoire into sub-repertoires by isotype based on number of unique sequences
AbForests_UniqueAntibodyVariants Count the number of unique antibody variants per clonal lineage
automate_GEX GEX processing wrapper in Platypus V2

-- B --

Bcell_sequences_example_tree Example csv file 1
Bcell_tree_2 Example csv file 2

-- C --

call_MIXCR Calls MiXCR VDJ object of Platypus V2
class_switch_prob_hum class_switch_prob_hum The probability matrix of class switching for human b cells. The row names of the matrix are the isotypes the cell is switching from, the column names are the isotypes the cell is switching to. All B cells start from IGHM, and switch to one of the other isotypes or remain the same.
class_switch_prob_mus class_switch_prob_mus The probability matrix of class switching for mouse b cells. The row names of the matrix are the isotypes the cell is switching from, the column names are the isotypes the cell is switching to. All B cells start from IGHM, and switch to one of the other isotypes or remain the same.
clonofreq Plot clonal frequency barplot of the outout simulated data
clonofreq.isotype.data Get information about the clonotype counts grouped by isotype.
clonofreq.isotype.plot Get information about the clonotype counts grouped by isotype.
clonofreq.trans.data Get information about the clonotype counts grouped by transcriptome state(cell type).
clonofreq.trans.plot Get information about the clonotype counts grouped by transcriptome state(cell type).
cluster.id.igraph Get clone network igraphs colored by seurat cluster id.
colors colors A vector of characters specifying colors used in igraph phylogenetic tree. Default colors: "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3" ,"#A6D854"

-- E --

Echidna_simulate_repertoire Simulate immune repertoire and transcriptome data
Echidna_vae_generate Simulate B or T cell receptor sequences by variational autoencodes(VAEs) trained with experimental data.

-- G --

get.avr.mut.data Get information about somatic hypermutation in the simulation. This function return a barplot showing the average mutation.
get.avr.mut.plot Get information about somatic hypermutation in the simulation. This function return a barplot showing the average mutation.
get.barplot.errorbar Return a barplot of mean and standard error bar of certain value of each clone.
get.elbow Get the seurat object from simulated transciptome output.
get.n.node.data Get the number of unique variants in each clone in a vector. The output is the vector representing the numbers of unique variants.
get.n.node.plot Get the number of unique variants in each clone in a vector and the barplot. The first item in the output is the vector representing the numbers of unique variants, the second item is the barplot.
get.seq.distance Computing sequence distance according to the number of unmatched bases.
get.umap Further process the seurat object from simulated transciptome output and make UMAP ready for plotting.
get.vgu.matrix Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.
GEX_clonotype Platypus V2 GEX and VDJ integration for clonotypes
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_DEgenes_persample Platypus V2 Differentially expressed genes
GEX_dottile_plot GEX Dottile plots
GEX_GOterm GEX GO-Term analysis and plotting
GEX_GSEA GEX Gene Set Enrichment Analysis and plotting
GEX_heatmap Flexible GEX heatmap wrapper
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_topN_DE_genes_per_cluster Platypus V2 GEX DE genes helper
GEX_visualize_clones Platypus V2 GEX and VDJ integration for visualizing clone clustering
GEX_volcano Flexible wrapper for GEX volcano plots

-- H --

hotspot_df hotspot_df Hotspot mutations taken from Yaari et al., Frontiers in Immunology, 2013. This contains transition probabilities for all 5mer combinations based on high throughput sequencing data. The transition probabilities are for the middle nucleotide in each 5mer set. This can be customized by changing the genes and sequences. Custom mutation hotspots can be supplied by modifying this dataframe. Repeating particular hotspot entries allows for the hotspot to mutate more than one time per SHM event.
hum_b_h hum_b_h
hum_b_l hum_b_l
hum_t_h hum_t_h
hum_t_l hum_t_l

-- I --

iso_SHM_prob iso_SHM_prob A probability dataframe specifying SHM.nuc.prob for cells of different isotypes. The first column is the names of isotypes, while the second column is the SHM.nuc.prob of cell of that isotype. user can define different SHM.nuc.prob for isotypes.

-- M --

mus_b_h mus_b_h
mus_b_l mus_b_l
mus_b_trans mus_b_trans A data frame contains mouse B cell average gene expression for multiple cell types, with the rows representing the gene names, column names representing the cell type names. The original single cell sequencing data is retrieved from 10xgenomics and combined with experimental data from.#? The expression level for different cell types are obtained by calculating the average expression after sorting the original data by markers as shown below. NaiveBcell Cd19+;Cd27-;Cd38- GerminalcenterBcell Fas+;Cd19+ Plasmacell Sdc1+ MemoryBcell Cd38+;Fas-
mus_t_h mus_t_h
mus_t_l mus_t_l

-- N --

no.empty.node Get clone network igraphs without empty mode. Empty node represents the 'extincted' sequences, that are not in any living cell but once existed.

-- O --

one_spot_df one_spot_df

-- P --

pheno_SHM_prob pheno_SHM_prob A probability dataframe specifying SHM.nuc.prob for cells of different phenotypes. The first column is the names of phenotypes, while the second column is the SHM.nuc.prob of cell of that phenotype. user can define different SHM.nuc.prob for phenotypes.
PlatypusDB_AIRR_to_VGM AIRR to Platypus V3 VGM compatibility function
PlatypusDB_fetch Loads and saves RData objects from the PlatypusDB
PlatypusDB_find_CDR3s CDR3 query function for PlatypusDB
PlatypusDB_list_projects Metadata download by project for PlatypusDB
PlatypusDB_load_from_disk PlatypusDB utility for import of local datasets
PlatypusDB_VGM_to_AIRR Platypus V3 VGM to AIRR compatibility function

-- S --

select.top.clone Get the index of top ranking clones.
small_vgm Small VDJ GEX matrix (VGM) for function testing purposes
special_v special_v a dataframe, of heavy and light chain v gene combination and their probability to be selected for expansion.

-- T --

trans_switch_prob_b trans_switch_prob_b The probability for B cell transcriptome states switching. The row names of the matrix are the cell states the cell is switching from, the column names are the cells states the cell is switching to.
trans_switch_prob_t trans_switch_prob_t The probability for T cell transcriptome states switching. The row names of the matrix are the cell states the cell is switching from, the column names are the cells states the cell is switching to.

-- U --

umap.top.highlight Set idents for top abundant clones in Seurat object, get ready for highlight the top abundant clones in UMAP.

-- V --

VDJ_abundances Calculate abundances/counts of specific features for a VDJ dataframe
VDJ_alpha_beta_Vgene_circos Circos plot for VDJ and VJ pairings
VDJ_analyze Platypus V2 VDJ processing wrapper.
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_bulk_to_vgm Utility function for bulk data to standard Platypus format conversion
VDJ_call_MIXCR MiXCR wrapper for Platypus V3 VDJ object
VDJ_call_recon Calls the Kaplinsky/RECON tool
VDJ_circos Internal utility for circos functions
VDJ_clonal_donut Circular VDJ expansion plots
VDJ_clonal_expansion Flexible wrapper for clonal expansion barplots by isotype, GEX cluster etc.
VDJ_clonal_expansion_abundances Wrapper function for VDJ_abundances to obtain ranked clonotype barplots
VDJ_clonal_lineages Platypus V2 lineage utility
VDJ_clonotype Deprecated Platypus V2 clonotyping wrapper
VDJ_clonotype_clusters_circos Circos plot for clonotype - GEX cluster pairings
VDJ_clonotype_v3 Platypus V3 clonotyping wrapper
VDJ_contigs_to_vgm Local VDJ dataframe to VDJ.GEX.matrix format utility
VDJ_db_annotate Wrapper function of VDJ_antigen_integrate function
VDJ_db_load Load and preprocess a list of antigen-specific databases
VDJ_diversity Diversity metrics for VDJ
VDJ_dublets Platypus V2 annotation utility
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 Platypus V2 utility for full germline sequence via MiXCR
VDJ_get_public Function to get shared/public elements across multiple repertoires
VDJ_GEX_clonal_lineage_clusters Platypus V2 lineage - GEX integration utility
VDJ_GEX_expansion Platypus V2 utility
VDJ_GEX_integrate only Platypus v2 Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object and the index of the cell in the Seurat RNA-seq object.
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_isotypes_per_clone Platypus V2 clonal utility
vdj_length_prob vdj_length_prob A list dataframe specifying lengths and probabilities of bases deleted or inserted at each junction site of VDJ recombination event. v3_deletion length and probability of deleted bases at 3' end of V segment d5_deletion length and probability of deleted bases at 5' end of D segment d3_deletion length and probability of deleted bases at 3' end of D segment j5_deletion length and probability of deleted bases at 5' end of J segment dj_insertion length and probability of inserted bases between D-J segment vj_insertion length and probability of inserted bases between V-J segment for light or alpha chains
VDJ_logoplot_vector Flexible logoplot wrapper
VDJ_network Similarity networks based on CDR3 regions
VDJ_overlap_heatmap Wrapper to determine and plot overlap between VDJ features across groups
VDJ_per_clone VDJ_per_clone
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_reclonotype_list_arrange Platypus V2 dataframe utility
VDJ_tree Platypus V2 phylogenetic trees.
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_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