highlightClones: Highlighting specific clones in Seurat

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

Highlighting specific clones in Seurat

Description

Use a specific clonal sequence to highlight on top of the dimensional reduction in single-cell object.

Usage

highlightClones(
  sc.data,
  cloneCall = c("gene", "nt", "aa", "strict"),
  sequence = NULL
)

Arguments

sc.data	The single-cell object to attach after combineExpression()
cloneCall	How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data.
sequence	The specific sequence or sequence to highlight

Value

Single-cell object object with new meta data column for indicated clones

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

#Getting a sample of a Seurat object
scRep_example  <- get(data("scRep_example"))

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

#Using highlightClones()
scRep_example   <- highlightClones(scRep_example, 
                                   cloneCall= "aa", 
                                   sequence = c("CVVSDNTGGFKTIF_CASSVRRERANTGELFF"))

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.