## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 7 ) ## ----setup-------------------------------------------------------------------- library(mosbi) ## ----------------------------------------------------------------------------- # Bray-Curtis similarity bray_curtis <- function(s1, s2, overlap) { return(((2 * overlap) / (s1 + s2))) } # Jaccard index jaccard <- function(s1, s2, overlap) { return(((overlap) / (s1 + s2 - overlap))) } # overlap coefficient overlap <- function(s1, s2, overlap) { return((overlap / min(s1, s2))) } # Fowlkes–Mallows index folkes_mallows <- function(s1, s2, overlap) { tp <- choose(overlap, 2) fp <- choose(s1 - overlap, 2) fn <- choose(s2 - overlap, 2) return(sqrt((tp / (tp + fp)) * (tp / (tp + fn)))) } ## ----------------------------------------------------------------------------- # Scenario 1 - two biclusters of the same size size1_1 <- rep(1000, 1000) size2_1 <- rep(1000, 1000) overlap_1 <- seq(1, 1000) # Scenario 2 - two biclusters one of size 500, the other of size 1000 size1_2 <- rep(1000, 500) size2_2 <- rep(500, 500) overlap_2 <- seq(1, 500) ## ----------------------------------------------------------------------------- plot(overlap_1, bray_curtis(size1_1, size2_1, overlap_1), col = "red", type = "l", xlab = "Overlap", ylab = "Similarity", ylim = c(0, 1) ) lines(overlap_1, jaccard(size1_1, size2_1, overlap_1), col = "blue") lines(overlap_1, overlap(size1_1, size2_1, overlap_1), col = "green", lty = 2) lines(overlap_1, folkes_mallows(size1_1, size2_1, overlap_1), col = "orange") legend( x = .8, legend = c("Bray-Curtis", "Jaccard", "Overlap", "Fowlkes–Mallows"), col = c("red", "blue", "green", "orange"), lty = 1, cex = 0.8, title = "Similarity metrics" ) ## ----------------------------------------------------------------------------- plot(overlap_2, bray_curtis(size1_2, size2_2, overlap_2), col = "red", type = "l", xlab = "Overlap", ylab = "Similarity", ylim = c(0, 1) ) lines(overlap_2, jaccard(size1_2, size2_2, overlap_2), col = "blue") lines(overlap_2, overlap(size1_2, size2_2, overlap_2), col = "green") lines(overlap_2, folkes_mallows(size1_2, size2_2, overlap_2), col = "orange") legend( x = .8, legend = c("Bray-Curtis", "Jaccard", "Overlap", "Fowlkes–Mallows"), col = c("red", "blue", "green", "orange"), lty = 1, cex = 0.8, title = "Similarity metrics" ) ## ----------------------------------------------------------------------------- sessionInfo()