Examining the clonal overlap between groups or samples

Source: R/clonalOverlap.R

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).

clonalOverlap(
  input.data,
  cloneCall = "strict",
  method = c("overlap", "morisita", "jaccard", "cosine", "raw"),
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  exportTable = FALSE,
  palette = "inferno",
  ...
)

Arguments

input.data

The product of combineTCR(), combineBCR(), or combineExpression()

cloneCall

Defines the clonal sequence grouping. Accepted values are: gene (VDJC genes), nt (CDR3 nucleotide sequence), aa (CDR3 amino acid sequence), or strict (VDJC + nt). A custom column header can also be used.

method

The method to calculate the overlap, morisita, jaccard, cosine indices or raw for the base numbers

chain

The TCR/BCR chain to use. Use both to include both chains (e.g., TRA/TRB). Accepted values: TRA, TRB, TRG, TRD, IGH, IGL (for both light chains), both.

group.by

A column header in the metadata or lists to group the analysis by (e.g., "sample", "treatment"). If NULL, data will be analyzed by list element or active identity in the case of single-cell objects.

order.by

A character vector defining the desired order of elements of the group.by variable. Alternatively, use alphanumeric to sort groups automatically.

exportTable

If TRUE, returns a data frame or matrix of the results instead of a plot.

palette

Colors to use in visualization - input any hcl.pals

...

Additional arguments passed to the ggplot theme

Value

A ggplot object visualizing clonal overlap or a data.frame if exportTable = TRUE.

Details

The formulas for the indices are as follows:

Overlap Coefficient: overlap=∑min(a,b)min(∑a,∑b)

Raw Count Overlap: raw=∑min(a,b)

Morisita Index: morisita=∑ab(∑a)(∑b)

Jaccard Index: jaccard=∑min(a,b)∑a+∑b−∑min(a,b)

Cosine Similarity: cosine=∑ab√(∑a2)(∑b2)

Where:

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

Examples

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

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