diff chromeister/bin/make-cluster.R @ 0:7fdf47a0bae8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/bin/make-cluster.R	Wed Dec 12 07:18:40 2018 -0500
@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript
+library(ape)
+
+args = commandArgs(trailingOnly=TRUE)
+
+if(length(args) < 1){
+  stop("USE: Rscript --vanilla make-cluster.R <csv>")
+}
+
+
+path = args[1]
+
+inputcsv <- read.csv(path, sep ="-", header=FALSE)
+
+# Make indexing table
+
+indexing_table <- table(inputcsv[,1])
+n_species <- length(indexing_table)
+
+for(i in 1:n_species){
+  indexing_table[i] <- i
+}
+
+
+distmat <- matrix(NA, nrow=n_species, ncol=n_species)
+rownames(distmat) <- rownames(indexing_table)
+colnames(distmat) <- rownames(indexing_table)
+
+for(i in 1:n_species){
+  distmat[i,i] <- 0
+}
+
+
+for(i in 1:length(inputcsv[,1])){
+  redirX <- (as.character(inputcsv[i,1]))
+  redirY <- (as.character(inputcsv[i,2]))
+  
+  distmat[indexing_table[redirX],indexing_table[redirY]] <- as.numeric(inputcsv[i,3])
+  distmat[indexing_table[redirY],indexing_table[redirX]] <- as.numeric(inputcsv[i,3])
+}
+
+cluster <- hclust(dist(distmat), method = "average")
+
+# Rooted hierarchical cluster
+#plot(cluster, main = "Clustering based on automatic scoring", xlab = "Organisms")
+
+# Unrooted
+plot(as.phylo(cluster), type = "unrooted", cex = 0.6, main = "Unrooted clustering based on automatic")
+
+# Fan cluster
+#plot(as.phylo(cluster), type = "fan")
+
+
+