Mercurial > repos > ecology > ecoregion_eco_map
view cluster_ceamarc.R @ 1:b38b954b92b9 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92
author | ecology |
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date | Wed, 24 Jan 2024 15:53:20 +0000 |
parents | 3d750279158b |
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##13/04/2023 ##Seguineau Pauline ### Clustering with Clara algorithm #load library library(cluster) library(dplyr) library(tidyverse) #load arguments args = commandArgs(trailingOnly=TRUE) if (length(args)==0) { stop("This tool needs at least one argument") }else{ data <- args[1] enviro <- args[2] data.bio <- args[3] k <- as.numeric(args[4]) metric <- args[5] sample <- as.numeric(args[6]) } #load data env.data <- read.table(enviro, header=TRUE, sep="\t",dec = ".", na.strings = "-9999") data.bio <- read.table(data.bio, header=TRUE, sep="\t") test3 <- read.table(data, header = TRUE, sep="\t") ###################################################################################################### #Make clustering k <- k #number of clusters test5 <- clara(test3, k, metric = metric, samples = sample, sampsize = min(nrow(test3), (nrow(data.bio)/nrow(test3))+2*k)) ####################################################################################################### #save results png("sih.png") plot(silhouette(test5)) dev.off() clus <- cbind(data.bio[1:nrow(test3), 1:2],test5$clustering) names(clus) <- c("lat", "long", "cluster") clus <- cbind(clus,test3,env.data[,3:19]) write.table(clus[1:3], file = "points_clus.tsv", quote = FALSE, sep="\t", row.names = FALSE) write.table(clus, file = "clus.tsv", quote = FALSE, sep="\t", row.names = FALSE)