Mercurial > repos > bitlab > bitlab
comparison chromeister/bin/make-cluster.R @ 0:ee6b15b409e5 draft
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| author | bitlab |
|---|---|
| date | Thu, 13 Dec 2018 06:27:57 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:ee6b15b409e5 |
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| 1 #!/usr/bin/env Rscript | |
| 2 library(ape) | |
| 3 | |
| 4 args = commandArgs(trailingOnly=TRUE) | |
| 5 | |
| 6 if(length(args) < 1){ | |
| 7 stop("USE: Rscript --vanilla make-cluster.R <csv>") | |
| 8 } | |
| 9 | |
| 10 | |
| 11 path = args[1] | |
| 12 | |
| 13 inputcsv <- read.csv(path, sep ="-", header=FALSE) | |
| 14 | |
| 15 # Make indexing table | |
| 16 | |
| 17 indexing_table <- table(inputcsv[,1]) | |
| 18 n_species <- length(indexing_table) | |
| 19 | |
| 20 for(i in 1:n_species){ | |
| 21 indexing_table[i] <- i | |
| 22 } | |
| 23 | |
| 24 | |
| 25 distmat <- matrix(NA, nrow=n_species, ncol=n_species) | |
| 26 rownames(distmat) <- rownames(indexing_table) | |
| 27 colnames(distmat) <- rownames(indexing_table) | |
| 28 | |
| 29 for(i in 1:n_species){ | |
| 30 distmat[i,i] <- 0 | |
| 31 } | |
| 32 | |
| 33 | |
| 34 for(i in 1:length(inputcsv[,1])){ | |
| 35 redirX <- (as.character(inputcsv[i,1])) | |
| 36 redirY <- (as.character(inputcsv[i,2])) | |
| 37 | |
| 38 distmat[indexing_table[redirX],indexing_table[redirY]] <- as.numeric(inputcsv[i,3]) | |
| 39 distmat[indexing_table[redirY],indexing_table[redirX]] <- as.numeric(inputcsv[i,3]) | |
| 40 } | |
| 41 | |
| 42 cluster <- hclust(dist(distmat), method = "average") | |
| 43 | |
| 44 # Rooted hierarchical cluster | |
| 45 #plot(cluster, main = "Clustering based on automatic scoring", xlab = "Organisms") | |
| 46 | |
| 47 # Unrooted | |
| 48 plot(as.phylo(cluster), type = "unrooted", cex = 0.6, main = "Unrooted clustering based on automatic") | |
| 49 | |
| 50 # Fan cluster | |
| 51 #plot(as.phylo(cluster), type = "fan") | |
| 52 | |
| 53 | |
| 54 |