clonalOverlap: Examining the clonal overlap between groups or samples

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

Examining the clonal overlap between groups or samples

Description

This functions allows for the calculation and visualizations of various overlap metrics for clones. The methods include overlap coefficient (overlap), Morisita's overlap index (morisita), Jaccard index (jaccard), cosine similarity (cosine) or the exact number of clonal overlap (raw).

Usage

clonalOverlap(
  input.data,
  cloneCall = "strict",
  method = NULL,
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR(), combineBCR(), or combineExpression()
cloneCall	How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data
method	The method to calculate the "overlap", "morisita", "jaccard", "cosine" indices or "raw" for the base numbers
chain	indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL"
group.by	The variable to use for grouping
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order
exportTable	Returns the data frame used for forming the graph
palette	Colors to use in visualization - input any hcl.pals

Details

The formulas for the indices are as follows:

Overlap Coefficient:

overlap = \frac{\sum \min(a, b)}{\min(\sum a, \sum b)}

Raw Count Overlap:

raw = \sum \min(a, b)

Morisita Index:

morisita = \frac{\sum a b}{(\sum a)(\sum b)}

Jaccard Index:

jaccard = \frac{\sum \min(a, b)}{\sum a + \sum b - \sum \min(a, b)}

Cosine Similarity:

cosine = \frac{\sum a b}{\sqrt{(\sum a^2)(\sum b^2)}}

Where:

• a and b are the abundances of species i in groups A and B, respectively.

Value

ggplot of the overlap of clones by group

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

clonalOverlap(combined, 
              cloneCall = "aa", 
              method = "jaccard")

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.