Mercurial > repos > ecology > ecoregion_geonearestneighbor
annotate crea_carte_G.R @ 0:5cde56683579 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
author | ecology |
---|---|
date | Thu, 21 Mar 2024 14:05:01 +0000 |
parents | |
children |
rev | line source |
---|---|
0
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
1 #Author : Seguineau Pauline |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
2 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
3 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
4 #Create a map from cluster |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
5 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
6 library(sf) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
7 library(tmap) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
8 library(dplyr) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
9 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
10 args = commandArgs(trailingOnly=TRUE) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
11 if (length(args)==0) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
12 { |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
13 stop("This tool needs at least one argument") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
14 }else{ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
15 data <- args[1] |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
16 } |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
17 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
18 clus <- read.table(data, sep="\t" ,header=TRUE, na.strings = "na") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
19 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
20 #tmap method |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
21 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
22 sf_data <- st_as_sf(clus, coords = c("long", "lat"), crs =4326) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
23 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
24 grouped_data <- sf_data %>% |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
25 group_by(cluster) %>% |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
26 summarize() |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
27 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
28 map <- tm_shape(grouped_data) + |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
29 tm_dots(col = "cluster", palette = "Accent", n=256, size = 0.1, title = "ecoregions")+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
30 tm_scale_bar(position = c("right","top"))+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
31 tm_compass(position = c("right","top"))+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
32 tm_layout(frame = FALSE,legend.position = c("left","bottom"))+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
33 tm_xlab("Longitude")+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
34 tm_ylab("Latitude")+ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
35 tm_grid(alpha = 0.2) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
36 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
37 #Save the map |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
parents:
diff
changeset
|
38 tmap_save(map, "ecoregions.png") |