Mercurial > repos > ecology > ecology_presence_abs_abund

annotate graph_lcbd.r @ 1:4ed07d2d442b draft default tip

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:16:26 +0000
parents
children
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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1 #Rscript
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3 #########################
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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4 ## Beta diversity ##
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5 #########################
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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7 #####Packages : ggplot2
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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8 # vegan
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9 # adespatial
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10 # dplyr
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11 # tibble
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12 # tdyr
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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14 #####Load arguments
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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16 args <- commandArgs(trailingOnly = TRUE)
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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18 if (length(args) < 2) {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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19 stop("This tool needs at least 2 arguments")
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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20 }else{
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21 table <- args[1]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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22 hr <- args[2]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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23 abund <- as.numeric(args[3])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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24 loc <- as.numeric(args[4])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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25 spe <- as.numeric(args[5])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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26 date <- as.numeric(args[6])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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27 map <- as.logical(args[7])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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28 sepa <- as.logical(args[8])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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29 not <- as.logical(args[9])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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30 lat <- as.numeric(args[10])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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31 long <- as.numeric(args[11])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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32 var <- as.numeric(args[12])
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33 source(args[13])
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34 }
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35
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36 if (hr == "false") {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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37 hr <- FALSE
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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38 }else{
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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39 hr <- TRUE
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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40 }
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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41
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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42 #####Import data
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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43 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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44 colabund <- colnames(data)[abund]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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45 colloc <- colnames(data)[loc]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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46 if (map) {
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47 collat <- colnames(data)[lat]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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48 collong <- colnames(data)[long]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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49 }
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50 colspe <- colnames(data)[spe]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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51 coldate <- colnames(data)[date]
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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52 data[, coldate] <- as.factor(data[, coldate])
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54 data <- data[grep("^$", data[, spe], invert = TRUE), ]
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55
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56 if (sepa) {
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57 colvar <- colnames(data)[var]
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58 }
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59
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60 # Data for species
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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61 data_num <- make_table_analyse(data, colabund, colspe, colloc, coldate)
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62 nb_spe <- length(unique(data[, spe]))
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63 nb_col <- ncol(data_num) - nb_spe + 1
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64
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65 #Data with coordinates and environmental
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66 if (map) {
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67 data_xy <- data_num[, c(collat, collong)]
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68 colnames(data_xy) <- c("latitude", "longitude")
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69 # Data for environment
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70 data_env <- data_num[, c(colloc, collat, collong)]
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71 colnames(data_env) <- c("site", "latitude", "longitude")
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72 }
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73
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74 # Data with only species and their abundance
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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75 data_spe <- data_num[, nb_col:ncol(data_num)]
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76 rownames(data_spe) <- paste0(data_num[, colloc], " - ", data_num[, coldate])
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77
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78 #####Your analysis
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79
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80 # Computation beta.div {adespatial}
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81 # Beta.div on Hellinger-transformed species data
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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82 data_beta <- adespatial::beta.div(data_spe, method = "hellinger", nperm = 9999)
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83
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84 save(data_beta, file = "beta_diversity.Rdata")
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85 cat("##############################################################################",
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86 "\n########################### Beta Diversity Summary ###########################",
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87 "\n##############################################################################",
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88 "\n\n### All data ###",
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89 "\nBeta diversity: ", data_beta$beta[[2]],
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90 "\nSum of Squares: ", data_beta$beta[[1]],
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91 "\n\n### Vector of Local Contributions to Beta Diversity (LCBD) for the sites each date ###",
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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92 "\n", capture.output(data_beta$LCBD),
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93 "\n\n### Vector of P-values associated with the LCBD indices ###",
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94 "\n", capture.output(data_beta$p.LCBD),
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95 "\n\n### Vector of Corrected P-values for the LCBD indices, Holm correction ###",
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96 "\n", capture.output(data_beta$p.adj),
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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97 "\n\n### Vector of Species contributions to beta diversity (SCBD) ###",
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98 "\n", capture.output(data_beta$SCBD), file = "LCBD.txt", fill = 1, append = TRUE)
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99
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100 # Which species have a SCBD larger than the mean SCBD?
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101 scbd <- capture.output(data_beta$SCBD[data_beta$SCBD >= mean(data_beta$SCBD)])
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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102 write(scbd, "SCBD.txt")
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103
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104 ##1st fonction
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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105 beta_div_ext <- function(data_beta, data_xy, data_env) {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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106 data_beta_ext <- data.frame(data_xy, data_env, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05)
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107
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108 graph_beta_ext <- ggplot2::ggplot(data = data_beta_ext, ggplot2::aes(x = latitude, y = longitude, size = LCBD, col = signif)) +
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109 ggplot2::geom_point() +
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110 ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05") +
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111 ggplot2::xlab("Longitude") + ggplot2::ylab("Latitude")
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112
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113 ggplot2::ggsave("Beta_diversity_through_space.png", graph_beta_ext)
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114 }
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115
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116 ## Boyé et al. 2017 JSR Fig R
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117 ####################################################
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118
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119 ####LCBD####
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120 lcbd_site <- adespatial::beta.div(data_spe, "hellinger", nperm = 999)
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121
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122 compute_lcbd <- function(data_beta, data_spe, data_num) {
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123
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124 #############
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125 mat_lcbd_site <- data.frame(data_spe, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05, site = data_num[, colloc], date = data_num[, coldate])
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126
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127 ## Map spatio-temp
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128 ##################
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129 p1 <- ggplot2::qplot(date, site, size = LCBD, col = signif, data = mat_lcbd_site)
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130 p1 <- p1 + ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05")
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131 p1 <- p1 + ggplot2::theme_bw() + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90)) + ggplot2::xlab("Date") + ggplot2::ylab("Site")
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132
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133 ggplot2::ggsave("LCBD_sites_time.png", p1)
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134
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135
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136 ## Par années
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137 #############
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138 mean_time <- tapply(mat_lcbd_site$LCBD, mat_lcbd_site$date, mean)
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139 sd_time <- tapply(mat_lcbd_site$LCBD, mat_lcbd_site$date, sd)
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140 date <- unique(mat_lcbd_site$date)
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141
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142 data <- data.frame(date, mean_time, sd_time)
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143
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144 time <- ggplot2::ggplot() + ggplot2::geom_pointrange(ggplot2::aes(x = date, y = mean_time, ymin = mean_time - sd_time, ymax = mean_time + sd_time), data = data)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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145 time <- time + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90), axis.line.y = ggplot2::element_line(size = 0.5)) + ggplot2::ylab("mean LCBD")
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146
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147 ggplot2::ggsave("Mean_LCBD_through_time.png", time)
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148 }
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149
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150 ## Choose another graph
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151 #######################
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152 compute_lcbd2 <- function(data_beta, data_spe, data_num) {
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153
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154 #############
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155 mat_lcbd_site <- data.frame(data_spe, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05, site = data_num[, colloc], date = data_num[, coldate], variable = data_num[, colvar])
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156
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157 p1 <- ggplot2::qplot(date, variable, size = LCBD, col = signif, data = mat_lcbd_site)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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158 p1 <- p1 + ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05")
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159 p1 <- p1 + ggplot2::theme_bw() + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90)) + ggplot2::xlab("Date") + ggplot2::ylab(colvar)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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160
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161 ggplot2::ggsave(paste0("LCBD_per_", colvar, "_through_time.png"), p1)
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162 }
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163
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164 ####SCBD###
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165 # Function to compute SCBD
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166 library(dplyr)
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167 make_scbd_uvc <- function(data_spe, z, data_beta) {
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168 # Computation using beta.div {adespatial} on
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169 # Hellinger-transformed species data
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170
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171 # Which species have a SCBD larger than the mean SCBD?
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172 spe_scbd <- data_beta$SCBD[data_beta$SCBD >= mean(data_beta$SCBD)] %>%
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173 as.data.frame() %>%
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174 tibble::rownames_to_column(var = "Taxon") %>%
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175 dplyr::mutate("Methode" = z)
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176
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177 return(spe_scbd)
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178 }
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179
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180 # Function to make a radar plot
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181
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182 coord_radar <- function(theta = "x", start = 0, direction = 1) {
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183 theta <- match.arg(theta, c("x", "y"))
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184 r <- if (theta == "x") "y" else "x"
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185 ggplot2::ggproto("CordRadar", ggplot2::coord_polar(theta = theta, start = start,
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186 direction = sign(direction)),
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187 is_linear = function(coord) TRUE)
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188 }
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189
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190 # Make the radar plot
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191 radar_plot <- function(scbd_uvc_tc) {
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192 uvc_rd_plot_data <- scbd_uvc_tc %>%
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193 rename(scbd_score = ".")
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194
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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195 rad_uvc <- ggplot2::ggplot(uvc_rd_plot_data, ggplot2::aes(x = Taxon, y = scbd_score, group = Methode)) +
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
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196 ggplot2::geom_line() +
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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197 ggplot2::geom_point(size = 3) +
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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198 coord_radar() +
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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199 ggplot2::theme_bw() +
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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200 ggplot2::theme(axis.text.x = ggplot2::element_text(size = 10),
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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201 legend.position = "bottom")
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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202
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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203 ggplot2::ggsave("SCBD_Species_Radar_plot.png", rad_uvc)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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204 }
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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205
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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206 ## LCBD
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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207
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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208 if (map) {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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209 #Beta diversity
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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210 beta_div_ext(data_beta, data_xy, data_env)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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211 }
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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212
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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213 #Lcbd per places and time
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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214 compute_lcbd(data_beta, data_spe, data_num)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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215
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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216 #Lcbd of your choice
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
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217 if (sepa) {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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218 compute_lcbd2(data_beta, data_spe, data_num)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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219 }
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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220
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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221 ##SCBD
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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222
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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223 scbd_uvc_tc <- make_scbd_uvc(data_spe, z = "TC", data_beta)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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224
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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225 radar_plot(scbd_uvc_tc)