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annotate crea_carte_G.R @ 0:92ca83b60089 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
author ecology
date Wed, 11 Sep 2024 09:18:48 +0000
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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 #Author : Seguineau Pauline
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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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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4 #Create a map from cluster
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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6 library(sf)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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7 library(tmap)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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8 library(dplyr)
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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10 args = commandArgs(trailingOnly=TRUE)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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11 if (length(args)==0)
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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12 {
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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13 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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14 }else{
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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15 data <- args[1]
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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16 }
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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18 clus <- read.table(data, sep="\t" ,header=TRUE, 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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92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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20 #tmap method
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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22 sf_data <- st_as_sf(clus, coords = c("long", "lat"), crs =4326)
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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24 grouped_data <- sf_data %>%
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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25 group_by(cluster) %>%
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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26 summarize()
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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28 map <- tm_shape(grouped_data) +
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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29 tm_dots(col = "cluster", palette = "Accent", n=256, size = 0.1, title = "ecoregions")+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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30 tm_scale_bar(position = c("right","top"))+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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31 tm_compass(position = c("right","top"))+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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32 tm_layout(frame = FALSE,legend.position = c("left","bottom"))+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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33 tm_xlab("Longitude")+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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34 tm_ylab("Latitude")+
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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35 tm_grid(alpha = 0.2)
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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37 #Save the map
92ca83b60089 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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38 tmap_save(map, "ecoregions.png")