View source: R/positionalProperty.R
positionalProperty | R Documentation |
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.
positionalProperty(
input.data,
chain = "TRB",
group.by = NULL,
aa.length = 20,
method = "Atchley",
exportTable = FALSE,
palette = "inferno"
)
input.data |
The product of |
chain |
"TRA", "TRB", "TRG", "TRG", "IGH", "IGL". |
group.by |
The variable to use for grouping. |
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. |
More information for the individual methods can be found at the following citations:
Atchley: citation
Kidera: citation
stScales: citation
tScales: citation
VHSE: citation
ggplot of line graph of diversity by position
#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)
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