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comparison EstimEndem.R @ 0:f7a55ccf2a3e draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
author ecology
date Tue, 20 May 2025 09:52:29 +0000
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children f3a977826375
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-1:000000000000 0:f7a55ccf2a3e
1 #!/bin/Rscript
2 # phyloregions
3
4 args = commandArgs(trailingOnly=TRUE)
5 #args = c("input/matrix_file", "input/tree_file.txt", "input/grid_aq_3_PF.shp")
6
7 # library
8 library(phyloregion)
9 library(ape)
10 library(Matrix)
11 library(SparseArray)
12 library(sf)
13 library(sp)
14 library(raster)
15 library(dplyr)
16
17
18 save_sf <- function(){
19 #st_write(phyloreg_sf[,-(3:5)], paste0(tempdir(), "/", "output.shp"), delete_layer = TRUE)
20 write_sf(phyloreg_sf, "output.shp")
21 }
22
23
24 if (length(args)<5){stop('Usage : sparseMatrix.csv tree.txt grid.shp nb_clust clust_method')
25 }else{
26 # read enter files
27 comm_tree <- read.tree(args[1])
28
29 comm_matrix <- readSparseCSV(args[2], sep = "\t")
30 comm_matrix <- as(comm_matrix,"dgCMatrix")
31
32 grid <- read_sf(args[3])
33
34 nb_clust <- as.integer(args[4])
35
36 clust_method <- toString(args[5])
37
38 # calculate phylogenetic Beta diversity - a phylogenetic distance matrix between grid cells
39 phylo_beta <- phylobeta(comm_matrix, comm_tree, index.family = "sorensen")
40
41 #select the less distorting clustering method, best fitting between phylogenetic distances in phylobeta matrix
42 # and raw distances from branch lengths of the tree
43 select_linkage(phylo_beta[[1]])
44
45 #select optimal number of clusters with selected method
46 optim <- optimal_phyloregion(phylo_beta[[3]], k = 30)
47 print(paste("the best number of cluster is :", optim$optimal$k))
48 #plot(optim$df$k, optim$df$ev, pch = 20) # k - nbr of clusters VS explained variance given k
49 # k has to be selected by a user
50
51 # pass the grid cell to spatial format
52 grid_sp <- as_Spatial(grid)
53 #proj4string(grid_sp)
54
55 # calculate phyloregions clusters
56 y <- phyloregion(phylo_beta[[3]], pol = grid_sp, k = nb_clust, method = clust_method)
57 #summary(y)
58 #phylo_nmds <- y$NMDS
59
60 # take an shp spatial file for phyloregions and put it to sf format
61 phyloreg_sf <- y$pol
62 # print(st_crs(phyloreg_sf))
63 #plot(phyloreg_sf)
64 phyloreg_sf <- st_as_sf(phyloreg_sf, crs = st_crs(grid))
65 # print(st_crs(phyloreg_sf))
66
67 names(phyloreg_sf)[3:8] <- c("R_val", "G_val", "B_val", "r_code", "g_code", "b_code")
68
69
70 save_sf()
71 }
72
73
74 # sf_recup <- read_sf("output.shp")
75