Function reference • djvdj

Data Import

import_vdj(): Import V(D)J data

define_clonotypes(): Define clonotypes based on V(D)J data

Clone Frequency

calc_frequency(): Calculate frequency of cell groups present in object

plot_clone_frequency(): Plot clonotype frequency

plot_frequency(): Plot frequency of cell groups present in object

Repertoire Diversity

calc_diversity(): Calculate repertoire diversity

plot_diversity(): Plot repertoire diversity

plot_rarefaction(): Plot rarefaction curves

Repertoire Similarity

calc_similarity(): Calculate repertoire similarity

plot_similarity(): Plot repertoire similarity

calc_mds(): Perform multidimensional scaling

plot_mds(): Create MDS plot

Gene Usage

calc_gene_usage(): Calculate V(D)J segment usage

plot_gene_usage(): Plot V(D)J segment usage

calc_gene_pairs(): Calculate paired usage of V(D)J segments across chains

plot_gene_pairs(): Plot paired usage of V(D)J segments across chains

CDR3 Clustering

cluster_sequences(): Cluster cells based on CDR3 sequences

plot_motifs(): Plot CDR3 sequence motifs

Data Manipulation

fetch_vdj(): Fetch V(D)J data from object

filter_vdj(): Filter V(D)J data in object

summarize_vdj(): Summarize V(D)J data for each cell

mutate_vdj(): Modify V(D)J data in object

mutate_meta(): Modify object meta.data

Plotting

plot_histogram() plot_violin(): Plot numerical single-cell data

plot_scatter(): Create 2D scatter plot

djvdj_theme(): Theme for djvdj plotting functions

Data

tiny_sce: A tiny SingleCellExperiment object

vdj_sce: A tiny SingleCellExperiment object with V(D)J data

mutate_meta(): Modify object meta.data

splen_meta: Meta data for downsampled splenocyte data