clonalProportion: Examining the clonal space occupied by specific clonotypes

In JuanXie19/LRT: LRT (Lineage estimation by integrative analysis of single-cell RNA-seq and TCR-seq data)

Examining the clonal space occupied by specific clonotypes

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(
  Combined,
  group.by,
  split = c(10, 100, 1000, 10000, 30000, 1e+05),
  exportTable = FALSE
)

Arguments

split	The cutpoints for the specific clonotypes.
exportTable	Exports a table of the data into the global environment in addition to the visualization
df	The product of combineTCR(), combineBCR(), expression2List(), or combineExpression().
cloneCall	How to call the clonotype - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or VDJC gene + CDR3 nucleotide (strict).
chain	indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL"

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")

JuanXie19/LRT documentation built on April 14, 2025, 7:09 p.m.