Mercurial > repos > ecology > phylogenetic_occupancy_matcher

annotate PhylOccuMatcher.R @ 0:e260f1a598da draft default tip

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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 09:53:38 +0000
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e260f1a598da planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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1 #!/bin/Rscript
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2 # Matice Phylo/Commu
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4 args = commandArgs(trailingOnly=TRUE)
e260f1a598da planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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5 #args = c( "pycnogonida_tree_2024", "pycnogonida_occ_2024.csv")
e260f1a598da planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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7 library(phyloregion)
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8 library(ape)
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9 library(Matrix)
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10 library(SparseArray)
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12 #install.packages("remotes")
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13 #remotes::install_github("Bioconductor/SparseArray")
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15 save_as_tabular_fun <- function(){
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16 #writeMM(obj = comm_matrix, file = "output.mtx")
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17 writeSparseCSV(comm_matrix, out_grid, sep="\t", transpose=FALSE, write.zeros=FALSE)
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18 }
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21 save_as_tree_fun <- function(){
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22 write.tree(comm_tree, file = out_tree)
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23 }
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26 if (length(args)<4){stop('Usage : input_tree_file input_grid_file output_tree_file output_grid_file')
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27 }else{
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28 tree <- read.tree(args[1])
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29 grid <- read.csv2(args[2], dec = ".", sep = "\t", header = T, na.strings = "")
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30 out_tree <- args[3]
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31 out_grid <- args[4]
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33 sparse_grid <- long2sparse(grid, grid = "grids", species = "newscientificname")
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35 com.data <- match_phylo_comm(tree, sparse_grid, delete_empty_rows = F)
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37 comm_matrix <- com.data$comm
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38 #test
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39 #sum_matrix <- summary(comm_matrix)
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41 comm_tree <- com.data$phy
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43 save_as_tabular_fun()
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44 save_as_tree_fun()
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45 }
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47 #comm_matrix_recup <- readSparseCSV("output")
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48 #comm_matrix_recup <- as(comm_matrix_recup,"dgCMatrix")