Plot Positional Physicochemical Property Analysis

This function analyzes the physicochemical properties of amino acids at each position along the CDR3 sequence. It calculates the mean property value and the 95% confidence interval for each position across one or more groups, visualizing the results as a line plot with a confidence ribbon.

Usage

positionalProperty(
  input.data,
  chain = "TRB",
  group.by = NULL,
  order.by = NULL,
  aa.length = 20,
  method = "atchleyFactors",
  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.

method

Character string (one of the supported names) Defaults to "atchleyFactors", but includes: "crucianiProperties", "FASGAI", "kideraFactors", "MSWHIM", "ProtFP", "stScales", "tScales", "VHSE", "zScales"

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

Use export.table instead.

...

Additional arguments passed to the ggplot theme

Value

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

Details

The function uses one of several established physicochemical property scales to convert amino acid sequences into numerical vectors. More information for the individual methods can be found at the following citations:

atchleyFactors: citation

crucianiProperties: citation

FASGAI: citation

kideraFactors: citation

MSWHIM: citation

ProtFP: citation

stScales: citation

tScales: citation

VHSE: citation

zScales: citation

Author

Florian Bach, Nick Borcherding

Examples

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

# Using positionalProperty()
positionalProperty(combined, 
                   chain = "TRB",
                   method = "atchleyFactors", 
                   aa.length = 20)