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annotate nb_clust_G.R @ 2:0958e3a0a34c 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 10:11:54 +0000
parents d35254cb9092
children
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d35254cb9092 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
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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3 #load packages
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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4 library(cluster)
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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5 library(dplyr)
d35254cb9092 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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d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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8 #load arguments
d35254cb9092 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")
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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13 }else{
d35254cb9092 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]
d35254cb9092 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]
d35254cb9092 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]
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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17 max_k <- as.numeric(args[4])
d35254cb9092 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]
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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19 sample <- as.numeric(args[6])
d35254cb9092 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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d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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22 #load data
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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24 env.data <- read.table(enviro, sep="\t", header = TRUE, dec = ".", na.strings = "-9999")
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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d35254cb9092 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
d35254cb9092 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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d35254cb9092 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,",")
d35254cb9092 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]])) {
d35254cb9092 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")
d35254cb9092 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)
d35254cb9092 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 }
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d35254cb9092 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")
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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d35254cb9092 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
d35254cb9092 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),]
d35254cb9092 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)
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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48 #format data
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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d35254cb9092 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$pred , nrow = nrow(env.data), ncol = nrow(data.bio)/nrow(env.data))
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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51 test3 <- data.frame(test3)
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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52 names(test3) <- unique(data.bio$taxon)
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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))
d35254cb9092 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
d35254cb9092 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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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()