getJaccard: Jaccard Similarity

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Jaccard Similarity

Description

Computes Jaccard Similarity between two sets, x1 and x2.

Usage

getJaccard(x1, x2, assert.unique = T)

Arguments

x1	set 1
x2	set 2
assert.unique	Logical flag specifying whether to ensure that x1 and x2 are unique. Default is TRUE.

Value

Jaccard similarity score (numeric)

See Also

pheatmap

Examples

# compute jaccard similarity matrix for (named) list of genesets.
n.sets <- length(gene.sets)
j.mat <- matrix(nrow = n.sets, ncol = n.sets)
for (i in 1:n.sets){
  for (j in 1:n.sets){
    i.name <- names(gene.sets)[i]
    j.name <- names(gene.sets)[j]
    j.mat[i, j] <- getJaccard(gene.sets[[i.name]], gene.sets[[j.name]])
  }
}

# assign row and col names
rownames(j.mat) <- names(gene.sets)
colnames(j.mat) <- names(gene.sets)

# generate heatmap
pheatmap::pheatmap(j.mat, show_colnames = F, main = "Jaccard Similarity")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.