Examining the diversity of amino acids by position

Source: R/positionalEntropy.R

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.

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)