Mercurial > repos > ecology > ecoregion_taxa_seeker
comparison cluster_ceamarc.R @ 1:9dc992f80c25 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92
| author | ecology |
|---|---|
| date | Wed, 24 Jan 2024 15:52:43 +0000 |
| parents | e3cd588fd14a |
| children | 2152f424e7a2 |
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| 0:e3cd588fd14a | 1:9dc992f80c25 |
|---|---|
| 20 metric <- args[5] | 20 metric <- args[5] |
| 21 sample <- as.numeric(args[6]) | 21 sample <- as.numeric(args[6]) |
| 22 } | 22 } |
| 23 | 23 |
| 24 #load data | 24 #load data |
| 25 env.data <- read.table(enviro, header=TRUE, sep=" ",dec = ".", na.strings = "-9999.00") | 25 env.data <- read.table(enviro, header=TRUE, sep="\t",dec = ".", na.strings = "-9999") |
| 26 data.bio <- read.table(data.bio, header=TRUE, sep="\t") | 26 data.bio <- read.table(data.bio, header=TRUE, sep="\t") |
| 27 test3 <- read.table(data, header = TRUE, sep="\t") | 27 test3 <- read.table(data, header = TRUE, sep="\t") |
| 28 | 28 |
| 29 ###################################################################################################### | 29 ###################################################################################################### |
| 30 #Make clustering | 30 #Make clustering |
| 41 | 41 |
| 42 clus <- cbind(data.bio[1:nrow(test3), 1:2],test5$clustering) | 42 clus <- cbind(data.bio[1:nrow(test3), 1:2],test5$clustering) |
| 43 names(clus) <- c("lat", "long", "cluster") | 43 names(clus) <- c("lat", "long", "cluster") |
| 44 clus <- cbind(clus,test3,env.data[,3:19]) | 44 clus <- cbind(clus,test3,env.data[,3:19]) |
| 45 | 45 |
| 46 write.table(clus[1:3], file = "points_clus.txt",quote = FALSE, row.names = FALSE) | 46 write.table(clus[1:3], file = "points_clus.tsv", quote = FALSE, sep="\t", row.names = FALSE) |
| 47 write.table(clus, file = "clus.txt",quote = FALSE, row.names = FALSE) | 47 write.table(clus, file = "clus.tsv", quote = FALSE, sep="\t", row.names = FALSE) |
| 48 | 48 |
| 49 | 49 |
| 50 | 50 |
| 51 | 51 |
| 52 | 52 |