percentAA: Examining the relative amino acid composition by position

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

Examining the relative amino acid composition by position

Description

This function the proportion of amino acids along the residues of the CDR3 amino acid sequence.

Usage

percentAA(
  input.data,
  chain = "TRB",
  group.by = NULL,
  order.by = NULL,
  aa.length = 20,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR(), combineBCR(), or combineExpression().
chain	"TRA", "TRB", "TRG", "TRG", "IGH", "IGL".
group.by	The variable to use for grouping.
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order
aa.length	The maximum length of the CDR3 amino acid sequence.
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot of stacked bar graphs of amino acid proportions

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
percentAA(combined, 
          chain = "TRB", 
          aa.length = 20)

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