positionalEntropy: Examining the diversity of amino acids by position

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

Examining the diversity of amino acids by position

Description

This function the diversity amino acids along the residues of the CDR3 amino acid sequence. Please see clonalDiversity() for more information on the underlying methods for diversity/entropy calculations. Positions without variance will have a value reported as 0 for the purposes of comparison.

Usage

positionalEntropy(
  input.data,
  chain = "TRB",
  group.by = NULL,
  order.by = NULL,
  aa.length = 20,
  method = "norm.entropy",
  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.
method	The method to calculate the entropy/diversity - "shannon", "inv.simpson", "norm.entropy"
exportTable	Returns the data frame used for forming the graph
palette	Colors to use in visualization - input any hcl.pals

Value

ggplot of line graph of diversity by position

Examples

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

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