getCirclize {scRepertoire} | R Documentation |
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.
getCirclize(sc, cloneCall = "gene+nt", groupBy = NULL, proportion = FALSE)
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) |
data frame of shared clonotypes between groups
Dillon Corvino, Nick Borcherding
#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")