Examining the relative amino acid composition by position

Source: R/percentAA.R

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

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)