call_MIXCR |
Extracts information on the VDJRegion level using MiXCR. This function assumes the user can run an executable instance of MiXCR and is elgible to use MiXCR as determined by license agreements. The VDJRegion corresponds to the recombined heavy and light chain loci starting from framework region 1 (FR1) and extending to frame work region 4 (FR4). This can be useful for extracting full-length sequences ready to clone and further calculating somatic hypermutation occurances. |
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" |
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_automate |
Automates the transcriptional analysis of the gene expression libraries from cellranger. This function will integrate multiple samples |
GEX_clonotype |
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. |
GEX_cluster_genes |
Extracts the differentially expressed genes between two samples. This function uses the FindMarkers function from the Seurat package. Further parameter control can be accomplished by calling the function directly on the output of automate_GEX or VDJ_GEX_matrix |
GEX_cluster_genes_heatmap |
Produces a heatmap displaying the expression of the top genes that define each cluster in the Seurat object. The output heatmap is derived from DoHeatmap from Seurat and thereby can be edited using typical ggplot interactions. The number of genes per cluster and the nunber of cells to display can be specified by the user. Either the log fold change or the p value can be used to select the top n genes. |
GEX_cluster_membership |
Plots the cluster membership for each of the distinct samples in the Seurat object from the automate_GEX function. The distinct samples are determined by "sample_id" field in the Seurat object. |
GEX_coexpression_coefficient |
Returns eiter a plot or numeric data of coexpression levels of selected genes.Coexpression % is calculated as the quotient of double positive cells (counts \> 0) and the sum of total cells positive for either genes. |
GEX_DEgenes |
Extracts the differentially expressed genes between two groups of cells. These groups are defined as cells having either of two entries (group1, group2) in the grouping.column of the input Seurat object metadata This function uses the FindMarkers function from the Seurat package. |
GEX_DEgenes_persample |
!Only for Platypus version v2. For more flexibility and platypus v3 please refer to GEX_Degenes. Extracts the differentially expressed genes between two samples. This function uses the FindMarkers function from the Seurat package. Further parameter control can be accomplished by calling the function directly on the output of automate_GEX and further extracting sample information from the "sample_id" component of the Seurat object. |
GEX_dottile_plot |
Outputs a dotplot for gene expression, where the color of each dot is scaled by the gene expression level and the size is scaled by the % of cells positive for the gene |
GEX_GOterm |
Runs a GO term analysis on a submitted list of genes. Works with the output of GEX_topN_DE_genes_per_cluster or a custom list of genes to obtain GOterms. |
GEX_GSEA |
Conducts a Gene Set Enrichment Analysis (GSEA) on a set of genes submitted in a data frame with a metric each. Works with the output of GEX_genes_cluster or a custom data frame containing the gene symbols either in a column "symbols" or as rownames and a metric for each gene. The name of the column containing the metric has to be declared via the input metric.colname. |
GEX_heatmap |
Produces a heatmap containing gene expression information at the clonotype level. The rows correspond to different genes that can either be determined by pre-made sets of B or T cell markers, or can be customized by the user. The columns correspond to individual cells and the colors correspond to the different clonotype families. |
GEX_pairwise_DEGs |
Produces and saves a list of volcano plots with each showing differentially expressed genes between pairs groups. If e.g. seurat_clusters used as group.by, a plot will be generated for every pairwise comparison of clusters. For large numbers of this may take longer to run. Only available for platypus v3 |
GEX_phenotype |
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. |
GEX_phenotype_per_clone |
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. ! For platypus.version == "v3" and VDJ_GEX_matrix output the function will iterate over entries in the sample_id column of the GEX by default. |
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 |
Clonal frequency plot displaying clonal expansion for either T and B cells with Platypus v3 input. |
GEX_topN_DE_genes_per_cluster |
Organizes the top N genes that define each Seurat cluster and converts them into a single dataframe. This can be useful for obtaining insight into cluster-specific phenotypes. |
GEX_visualize_clones |
!Only for platypus version v2. For platypus v3 refer to: VDJ_GEX_overlay_clones() Visualize selected clonotypes on the tSNE or UMAP projection. |
GEX_volcano |
Plots a volcano plot from the output of the FindMarkers function from the Seurat package or the GEX_cluster_genes function alternatively. |
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_analyze |
Platypus V2 Processes and organizes the repertoire sequening data from cellranger vdj and returns a list of dataframes, where each dataframe corresponds to an individual repertoire. The function will return split CDR3 sequences, germline gene information, filter out those clones with either incomplete information or doublets (multiple CDR3 sequences for a given chain). This function should be called once for desired integrated repertoire and transcriptome. For example, if there are 3 VDJ libraries and 3 GEX libraries and the goal is to analyze all three GEX libraries together (e.g. one UMAP/tSNE reduction) this then function should be called one time and the three VDJ directories should be provided as input to the single function call. |
VDJ_antigen_integrate |
Integrates antigen-specific information into the VDJ/VDJ.GEX.matrix[[1]] object |
VDJ_assemble_for_PnP |
Assembles sequences from MIXCR output into inserts for expression in PnP cells. For detailes check https://doi.org/10.1038/ncomms12535 ! ALWAYS VALIDATE INDIVIDUAL SEQUENCE IN GENEIOUS OR OTHER SOFTWARE BEFORE ORDERING SEQUENCES FOR EXPRESSION ! Check notes on column content below ! Only cells with 1 VDJ and 1 VJ sequence are considered. Warnings are issued if sequences do not pass necessary checks |
VDJ_call_MIXCR |
Extracts information on the VDJRegion level using MiXCR on WINDOWS, MAC and UNIX systems for input from both Platypus v2 (VDJ.per.clone) or v3 (Output of VDJ_GEX_matrix) This function assumes the user can run an executable instance of MiXCR and is elgible to use MiXCR as determined by license agreements. ! FOR WINDOWS USERS THE EXECUTABLE MIXCR.JAR HAS TO PRESENT IN THE CURRENT WORKING DIRECTORY ! The VDJRegion corresponds to the recombined heavy and light chain loci starting from framework region 1 (FR1) and extending to frame work region 4 (FR4). This can be useful for extracting full-length sequences ready to clone and further calculating somatic hypermutation occurrences. |
VDJ_call_recon |
Calls the Kaplinsky/RECON 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_donut |
Generate circular plots of clonal expansion per repertoire directly from the VDJ matrix of the VDJ_GEX_matrix function |
VDJ_clonal_expansion |
Clonal frequency plot displaying clonal expansion for either T and B cells with Platypus v3 input. Only available for Platypus "v3" available. For v2 plotting of B cell clonotype expansion and isotypes please refer to VDJ_isotypes_per_clone. |
VDJ_clonal_expansion_abundances |
Wrapper function for VDJ_abundances to obtain ranked clonotype barplots |
VDJ_clonal_lineages |
Only Platypus V2 Organizes and extracts full-length sequences for clonal lineage inference. The output sequence can either contain the germline sequence as determined by cellranger or can just contain the sequences contained in each clonal family. |
VDJ_clonotype |
Deprecated function for Platypus V2 with options for Platypus V3. For revised hierarchical clonotyping please use VDJ_clonotype_v3() Returns a list of clonotype dataframes following additional clonotyping. This function works best following filtering to ensure that each clone only has one heavy chain and one light chain. |
VDJ_clonotype_clusters_circos |
Makes a Circos plot from the VDJ_GEX_integrate output. Connects the clonotypes with the corresponding clusters. |
VDJ_clonotype_v3 |
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. Require the vegan package |
VDJ_dublets |
Only Platypus v2 Produces a matrix indicating either the number of cells or clones which contain multiple heavy or light chains (or alpha/beta in the case of T cells). |
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 |
Only Platypus v2 Extracts the full-length germline sequence as determined by cellranger. This function returns an object that now contains the reference germline for each of the clones. If multiple clones (as determined by cellranger) have been merged using the VDJ_clonotype function then these sequences may have distinct germline sequences despite being in the same clonal family (nested list). This is particularly possible when homology thresholds were used to determine the clonotypes. |
VDJ_get_public |
Function to get shared/public elements across multiple repertoires |
VDJ_GEX_clonal_lineage_clusters |
only Platypus v2 Integrates the transcriptional cluster information into the clonal lineages. This requires that automate_GEX, VDJ_clonal_lineages, and VDJ_GEX_integrate have already been ran. The transcriptional cluster will be added to the end of the Name for each sequence. |
VDJ_GEX_expansion |
only Platypus v2 Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object. Output will plot which transcriptional cluster (GEX) that the cells of a given clonotype are found in. |
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 |
Processes both raw VDJ and GEX Cellranger output to compile a single cell level table containing all available information for each cell. If using Feature Barcodes please note the [FB] paragraph in the description and all "FB." parameters |
VDJ_GEX_overlay_clones |
Highlights the cells belonging to any number of top clonotypes or of specifically selected clonotypes from one or more samples or groups in a GEX dimensional reduction. |
VDJ_GEX_stats |
Gives stats on number and quality of reads. |
VDJ_isotypes_per_clone |
Only for Platypus v2 Clonal frequency plot displaying the isotype usage of each clone. ! For platypus v3 use VDJ_clonal_expansion |
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 |
Plots a logoplot of the CDR3 aminoacid region |
VDJ_network |
Creates a similarity network where clones with similar CDR3s are connected. |
VDJ_overlap_heatmap |
Yields overlap heatmap and datatable of features or combined features for different samples or groups |
VDJ_per_clone |
VDJ_per_clone |
VDJ_phylogenetic_trees |
Creates phylogenetic trees from a VDJ dataframe |
VDJ_phylogenetic_trees_plot |
Function to plot phylogenetic trees obtained from VDJ_phylogenetic_trees |
VDJ_plot_SHM |
Plots for SHM based on MIXCR output generated using the VDJ_call_MIXCR function and appended to the VDJ.GEX.matrix.output |
VDJ_reclonotype_list_arrange |
Only Platypus v2 Organizes the top N genes that define each Seurat cluster and converts them into a single dataframe. This can be useful for obtaining insight into cluster-specific phenotypes. |
VDJ_tree |
only Platypus v2 Produces neighbor joining phylogenetic trees from the output of VDJ_clonal_lineages |
VDJ_variants_per_clone |
Returns statistics and plots to examine diversity of any sequence or metadata item within clones on a by sample level or global level |
VDJ_Vgene_usage |
Produces a matrix counting the number of occurences for each VDJ and VJ Vgene combinations for each list enty in VDJ.clonotype.output or for each sample_id in VDJ.matrix |
VDJ_Vgene_usage_barplot |
Produces a barplot with the most frequently used IgH and IgK/L Vgenes. |
VDJ_Vgene_usage_stacked_barplot |
Produces a stacked barplot with the fraction of the most frequently used IgH and IgK/L Vgenes. This function can be used in combination with the VDJ_Vgene_usage_barplot to vizualize V gene usage per sample and among samples. |
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_expand_featurebarcodes |
Replaces the original sample_id column of a vgm object with a pasted version of the original sample_id and the last digits of the feature barcode. |