Mercurial > repos > ecology > ecoregion_cluster_estimate

annotate nb_clust_G.R @ 1:c9109f90d229 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit c41939f1cdc03331ec021d47495576a6b0c5fd14
author ecology
date Wed, 16 Oct 2024 11:44:42 +0000
parents 92ca83b60089
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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3 #load packages
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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4 library(cluster)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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5 library(dplyr)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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6 library(tidyverse)
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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8 #load arguments
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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9 args = commandArgs(trailingOnly=TRUE)
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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")
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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13 }else{
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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14 enviro <- args[1]
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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15 taxa_list <- args[2]
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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16 preds <- args[3]
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17 max_k <- as.numeric(args[4])
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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18 metric <- args[5]
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19 sample <- as.numeric(args[6])
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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20 }
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22 #load data
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24 env.data <- read.table(enviro, sep="\t", header = TRUE, dec = ".", na.strings = "-9999")
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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26 ##List of modelled taxa used for clustering
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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")
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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30 ################Grouping of taxa if multiple prediction files entered ################
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32 data_split = str_split(preds,",")
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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33 data.bio = NULL
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35 for (i in 1:length(data_split[[1]])) {
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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36 data.bio1 <- read.table(data_split[[1]][i], dec=".", sep="\t", header=T, na.strings = "NA")
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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37 data.bio <- rbind(data.bio,data.bio1)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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38 remove(data.bio1)
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39 }
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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41 names(data.bio) <- c("lat", "long", "pred", "taxon")
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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43 #keep selected taxa
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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44 data.bio <- data.bio[which(data.bio$taxon %in% tv$a),]
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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46 write.table(data.bio,file="data_bio.tsv",sep="\t",quote=F,row.names=F)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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48 #format data
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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50 test3 <- matrix(data.bio$pred , nrow = nrow(env.data), ncol = nrow(data.bio)/nrow(env.data))
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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51 test3 <- data.frame(test3)
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52 names(test3) <- unique(data.bio$taxon)
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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))
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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()