Plot Relative Amino Acid Composition by Position

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: The TCR/BCR chain to use. Accepted values: TRA, TRB, TRG, TRD, IGH, or IGL (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 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.
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 visualizing amino acid by proportion or a data.frame if exportTable = TRUE.

Examples

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

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