Objective 3

Installing Necessary Packages

#install.packages("philentropy")
library(philentropy)
#install.packages("RColorBrewer")
library(RColorBrewer)
#install.packages("pheatmap")
library(pheatmap)

Establishing a Color Palette

colpal <- RColorBrewer::brewer.pal(9,"YlGnBu")

Bhattacharyya Distance:

calcbhatdist <- function(p,q) {
  #p and q are the clusters
  dist <- bhattacharyya(p,q,testNA = T, 
                        unit = "log2", epsilon = 0.00001)
  return(dist)
}

bhatdist <- function(mat) {
  #create empty matrix: it'll be the result matrix
  #it's dimensions are nrow(mat)xnrow(mat)
  final_bhdist <- matrix(, nrow= ncol(mat), ncol=ncol(mat))
  #need 2 loop
  #1st: to select P 
  #2nd: make Bhat. calc with with q 
  
  for (i in 1:ncol(mat)) {
    #select the cluster and calculate it's distance with the rest of the clusters
    p <- c(mat[,i])
    for (j in 1:ncol(mat)) {
      #Perform the calculation 
      q <- c(mat[,j])
      final_bhdist[i,j] <- calcbhatdist(p,q)
    }
    
  }
  rownames(final_bhdist) <- colnames(mat)
  colnames(final_bhdist) <- colnames(mat)
  return(final_bhdist)

} 

Plot the Heatmap:

#pheatmap(bhatdist(), display_numbers=T, color = colpal)

Example

GeneB <- c(0.1000,0.1001,1500)
GeneM<- c(0.2000,0.2500,500)
GeneG <- c(0.800,0.81,300)
GeneL<- c(0.5,0.510,2000)
matr <- matrix(c(GeneB,GeneM,GeneG,GeneL), nrow = 4, ncol=3, byrow=T)
rownames(matr) <- c("GeneB","GeneM","GeneG","GeneL")
colnames(matr) <- c("c1","c2","c3")
matr

##        c1     c2   c3
## GeneB 0.1 0.1001 1500
## GeneM 0.2 0.2500  500
## GeneG 0.8 0.8100  300
## GeneL 0.5 0.5100 2000

bhatdist(matr)

##            c1         c2         c3
## c1 -0.6780719 -0.7080693  -6.116077
## c2 -0.7080693 -0.7399345  -6.148930
## c3 -6.1160769 -6.1489302 -12.070121

#bhatdist(clu_me)

pheatmap(bhatdist(matr), display_numbers=F, color = colpal, show_rownames= T, cluster_col=F)

pheatmap(bhatdist(matr), display_numbers=T, color = colpal)