clonalProportion: Examining the clonal space occupied by specific clonotypes

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

Description

This function calculates the relative clonal space occupied by the clonotypes. The grouping of these clonotypes is based on the parameter split, at default, split will group the clonotypes into bins of 1:10, 11:100, 101:1001, etc. To adjust the clonotypes selected, change the numbers in the variable split. If a matrix output for the data is preferred, set exportTable = TRUE.

Usage

clonalProportion(
  df,
  split = c(10, 100, 1000, 10000, 30000, 1e+05),
  cloneCall = "gene+nt",
  exportTable = FALSE
)

Arguments

df	The product of combineTCR(), combineBCR(), or expression2List().
split	The cutpoints for the specific clonotypes.
cloneCall	How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt) or CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
exportTable	Exports a table of the data into the global environment in addition to the visualization

Value

ggplot of the space occupied by the specific rank of clonotypes

Examples

#Making combined contig data
x <- contig_list
combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")
clonalProportion(combined, cloneCall = "gene")

scRepertoire documentation built on Nov. 8, 2020, 7 p.m.