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Plot Relative Amino Acid Composition by Position

Source: R/percentAA.R
percentAA.Rd

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

Usage

percentAA(
  input.data,
  chain = "TRB",
  group.by = NULL,
  order.by = NULL,
  aa.length = 20,
  export.table = NULL,
  palette = "inferno",
  exportTable = NULL,
  ...
)

Arguments

input.data

The product of combineTCR(), combineBCR(), or combineExpression().

chain

The TCR/BCR chain to use. Use both to include both chains (e.g., TRA/TRB). Accepted values: TRA, TRB, TRG, TRD, IGH, IGL, IGK, Light (for both light chains), or both (for TRA/B and Heavy/Light).

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.

export.table

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.

exportTable

[Deprecated] Use export.table instead.

...

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)