diff cluster_ceamarc.R @ 0:e3cd588fd14a draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 2a2ae892fa2dbc1eff9c6a59c3ad8f3c27c1c78d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster_ceamarc.R	Wed Oct 18 09:58:17 2023 +0000
@@ -0,0 +1,52 @@
+##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=" ",dec = ".", na.strings = "-9999.00")
+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.txt",quote = FALSE, row.names = FALSE)
+write.table(clus, file = "clus.txt",quote = FALSE, row.names = FALSE)
+
+
+
+
+