highlightClonotypes {scRepertoire} | R Documentation |
Use a specific clonotype sequence to highlight on top of the dimensional reduction in seurat object.
highlightClonotypes( sc, cloneCall = c("gene", "nt", "aa", "gene+nt"), sequence = NULL )
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 |
DimPlot with highlighted clonotypes
#' #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"))