clonalHomeostasis: Examining the clonal homeostasis

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

Description

This function calculates the space occupied by clonotype proportions. The grouping of these clonotypes is based on the parameter cloneTypes, at default, cloneTypes will group the clonotypes into bins of Rare = 0 to 0.0001, Small = 0.0001 to 0.001, etc. To adjust the proportions, change the number or labeling of the cloneTypes paramter. If a matrix output for the data is preferred, set exportTable = TRUE.

Usage

clonalHomeostasis(
  df,
  cloneTypes = c(Rare = 1e-04, Small = 0.001, Medium = 0.01, Large = 0.1, Hyperexpanded
    = 1),
  cloneCall = "gene+nt",
  exportTable = FALSE
)

Arguments

df	The product of CombineContig() or expression2List()
cloneTypes	The cutpoints of the proportions.
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 propotion 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")
clonalHomeostasis(combined, cloneCall = "gene")

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