highlightClonotypes {scRepertoire} | R Documentation

## Highlighting specific clonotypes in Seurat

### 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"))

[Package scRepertoire version 1.0.0 Index]