positionalProperty: Examining the mean property of amino acids by position

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Examining the mean property of amino acids by position

Description

This function calculates the mean selected property for amino acids along the residues of the CDR3 amino acid sequence. The ribbon surrounding the individual line represents the 95% confidence interval.

Usage

positionalProperty(
  input.data,
  chain = "TRB",
  group.by = NULL,
  order.by = NULL,
  aa.length = 20,
  method = "Atchley",
  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.
method	The method to calculate the property - "Atchley", "Kidera", "stScales", "tScales", or "VHSE"
exportTable	Returns the data frame used for forming the graph
palette	Colors to use in visualization - input any hcl.pals

Details

More information for the individual methods can be found at the following citations:

Atchley: citation

Kidera: citation

stScales: citation

tScales: citation

VHSE: citation

Value

ggplot of line graph of diversity by position

Author(s)

Florian Bach, Nick Borcherding

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
positionalProperty(combined, 
                   chain = "TRB",
                   method = "Atchley", 
                   aa.length = 20)

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.