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