Highlighting Specific Clones

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

Usage

highlightClones(sc.data, clone.call = NULL, sequence = NULL, cloneCall = NULL)

Arguments

sc.data

The single-cell object to attach after combineExpression()

clone.call

Defines the clonal sequence grouping. Accepted values are: gene (VDJC genes), nt (CDR3 nucleotide sequence), aa (CDR3 amino acid sequence), or strict (VDJC + nt). A custom column header can also be used.

sequence

The specific sequence or sequence to highlight

cloneCall

Use clone.call instead.

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,
                                   clone.call= "aa",
                                   sequence = c("CVVSDNTGGFKTIF_CASSVRRERANTGELFF"))