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annotate nb_clust_G.R @ 0:52d4151e00d8 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
author ecology
date Wed, 28 May 2025 10:12:06 +0000
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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1 # Script to determine the optimal number of clusters thanks to the optimization of the SIH index and to produce the files needed in the next step of clustering
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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3 #load packages
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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4 library(cluster)
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5 library(dplyr)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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6 library(tidyverse)
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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8 #load arguments
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9 args = commandArgs(trailingOnly=TRUE)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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10 if (length(args)==0)
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11 {
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12 stop("This tool needs at least one argument")
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13 }else{
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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14 enviro <- args[1]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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15 taxa_list <- args[2]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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16 preds <- args[3]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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17 max_k <- as.numeric(args[4])
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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18 metric <- args[5]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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19 sample <- as.numeric(args[6])
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20 }
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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22 #load data
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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24 env.data <- read.table(enviro, sep="\t", header = TRUE, dec = ".", na.strings = "-9999")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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26 ##List of modelled taxa used for clustering
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27 tv <- read.table(taxa_list, dec=".", sep=" ", header=F, na.strings = "NA")
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28 names(tv) <- c("a")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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30 ################Grouping of taxa if multiple prediction files entered ################
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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32 data_split = str_split(preds,",")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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33 data.bio = NULL
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35 for (i in 1:length(data_split[[1]])) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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36 data.bio1 <- read.table(data_split[[1]][i], dec=".", sep="\t", header=T, na.strings = "NA")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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37 data.bio <- rbind(data.bio,data.bio1)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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38 remove(data.bio1)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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39 }
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41 names(data.bio) <- c("lat", "long", "pred", "taxon")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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43 #keep selected taxa
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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44 data.bio <- data.bio[which(data.bio$taxon %in% tv$a),]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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46 write.table(data.bio,file="data_bio.tsv",sep="\t",quote=F,row.names=F)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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48 #format data
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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50 test3 <- matrix(data.bio$pred , nrow = nrow(env.data), ncol = nrow(data.bio)/nrow(env.data))
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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51 test3 <- data.frame(test3)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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52 names(test3) <- unique(data.bio$taxon)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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54 write.table(test3, file="data_to_clus.tsv", sep="\t",quote=F,row.names=F)
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56 #Max number of clusters to test
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57 max_k <- max_k
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59 # Initialization of vectors to store SIH indices
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60 sih_values <- rep(0, max_k)
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62 # Calculation of the SIH index for each number of clusters
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63 for (k in 2:max_k) {
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64 # Clara execution
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65 clara_res <- clara(test3, k, metric =metric, samples = sample, sampsize = min(nrow(test3), (nrow(data.bio)/nrow(test3))+2*k))
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66 # Calculation of the SIH index
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67 sih_values[k] <- clara_res$silinfo$avg.width
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68 }
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70 # Plot SIH Index Chart by Number of Clusters
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71 png("Indices_SIH.png")
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72 plot(2:max_k, sih_values[2:max_k], type = "b", xlab = "Number of clusters", ylab = "SIH index")
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73 dev.off()