getCirclize: Generate data frame to be used with circlize R package to...

In scRepertoire: A toolkit for single-cell immune receptor profiling

Description

This function will take the meta data from the product of combineExpression() and generate a relational data frame to be used for a chord diagram. The output is a measure of relative clonotype overlap between groups and does not reflect exact clonotype matches between groups.

Usage

getCirclize(sc, cloneCall = "gene+nt", groupBy = NULL, proportion = FALSE)

Arguments

sc	object after combineExpression().
cloneCall	How to call the clonotype - CDR3 nucleotide (nt), CDR3 amino acid (aa).
groupBy	The group header for which you would like to analyze the data.
proportion	Binary will calculate relationship as unique clonotypes (proportion = TRUE) or proportion of unique clonotypes (proportion = FALSE)

Value

data frame of shared clonotypes between groups

Author(s)

Dillon Corvino, Nick Borcherding

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

#Getting a sample of a Seurat object
screp_example <- get(data("screp_example"))
screp_example <- combineExpression(combined, screp_example)

#Getting data frame output for Circilize
circles <- getCirclize(screp_example, groupBy = "seurat_clusters")

scRepertoire documentation built on Nov. 8, 2020, 7 p.m.