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

The TCR/BCR chain to use. Accepted values: TRA, TRB, TRG, TRD, IGH, or IGL (for both light chains).

group.by

A column header in the metadata or lists to group the analysis by (e.g., "sample", "treatment"). If NULL, data will be analyzed as by list element or active identity in the case of single-cell objects.

order.by

A character vector defining the desired order of elements of the group.by variable. Alternatively, use alphanumeric to sort groups automatically.

aa.length

The maximum length of the CDR3 amino acid sequence.

method

The method to calculate the entropy/diversity - "shannon", "inv.simpson", "gini.simpson", "norm.entropy", "pielou", "hill0", "hill1", "hill2"

exportTable

If TRUE, returns a data frame or matrix of the results instead of a plot.

palette

Colors to use in visualization - input any hcl.pals

...

Additional arguments passed to the ggplot theme

Value

A ggplot object displaying entropy or diversity by amino acid position. If exportTable = TRUE, a matrix of the raw data is returned.

Examples

# Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

# Using positionalEntropy()
positionalEntropy(combined, 
                  chain = "TRB", 
                  aa.length = 20)