clonalOverlap: repertorie analysis functions used for shinyClone modified...

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

repertorie analysis functions used for shinyClone modified based on the functions from Borcherding N's scRepertoire R package Examining the clonal overlap between groups or samples

Description

This functions allows for the calculation and visualizations of the overlap coefficient, morisita, or jaccard index for clonotypes. The overlap coefficient is calculated using the intersection of clonotypes divided by the length of the smallest component.

Usage

clonalOverlap(
  Combined,
  group.by,
  method = c("overlap", "morisita", "jaccard", "raw"),
  exportTable = FALSE
)

Arguments

Combined	The CombinedDataSet object obtained from getCombinedDataSet function.
method	The method to calculate the overlap, either the "overlap" coefficient, "morisita", "jaccard" indices, or "raw" for the base numbers.
exportTable	Returns the data frame used for forming the graph

Value

ggplot of the clonotypic overlap between elements of a list

Examples

Combined <- getCombinedDataSet(TCR,Mice.sub2)
clonalOverlap(combined,method = "overlap",exportTable = FALSE)

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