highlightClonotypes: Highlighting specific clonotypes in Seurat

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

Description

Use a specific clonotype sequence to highlight on top of the dimensional reduction in seurat object.

Usage

highlightClonotypes(
  sc,
  cloneCall = c("gene", "nt", "aa", "gene+nt"),
  sequence = NULL
)

Arguments

sc	The seurat object to attach
cloneCall	How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
sequence	The specifc sequence or sequence to highlight

Value

DimPlot with highlighted clonotypes

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"))

#Using combineExpresion()
screp_example <- combineExpression(combined, screp_example )

#Using highlightClonotype()
screp_example  <- highlightClonotypes(screp_example, cloneCall= "aa", 
sequence = c("CAVNGGSQGNLIF_CSAEREDTDTQYF"))

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