Mercurial > repos > ecology > ecology_stat_presence_abs

annotate graph_stat_presence_abs.r @ 0:e5552099d0e3 draft

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
author ecology
date Tue, 27 Jul 2021 16:57:02 +0000
parents
children 9a2e0195bb43
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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1 #Rscript
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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2
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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3 ################################
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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4 ## Median and dispersion ##
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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5 ################################
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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7 #####Packages : Cowplot
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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8 # ggplot2
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9
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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10 #####Load arguments
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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12 args <- commandArgs(trailingOnly = TRUE)
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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14 if (length(args) == 0) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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15 stop("This tool needs at least one argument")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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16 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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17 table <- args[1]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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18 hr <- args[2]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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19 var <- as.numeric(args[3])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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20 spe <- as.numeric(args[4])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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21 loc <- as.numeric(args[5])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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22 time <- as.numeric(args[6])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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23 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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25 if (hr == "false") {
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26 hr <- FALSE
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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27 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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28 hr <- TRUE
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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29 }
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31 #####Import data
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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32 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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33 data <- na.omit(data)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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34 colvar <- colnames(data)[var]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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35 colspe <- colnames(data)[spe]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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36 colloc <- colnames(data)[loc]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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37 coltime <- colnames(data)[time]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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39 data <- data[grep("^$", data[, spe], invert = TRUE), ]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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40 time <- as.integer(substring(data[, time], first = 1, last = 4))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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42 #####Your analysis
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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44 ####Median and data dispersion####
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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45
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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46 #Median
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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47 graph_median <- function(data, var) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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48 graph_median <- ggplot2::ggplot(data, ggplot2::aes_string(y = var)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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49 ggplot2::geom_boxplot(color = "darkblue") +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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50 ggplot2::theme(legend.position = "none") + ggplot2::ggtitle("Median")
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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52 return(graph_median)
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54 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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55
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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56 #Dispersion
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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57 dispersion <- function(data, var, var2) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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58 graph_dispersion <- ggplot2::ggplot(data) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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59 ggplot2::geom_point(ggplot2::aes_string(x = var2, y = var, color = var2)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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60 ggplot2::scale_fill_brewer(palette = "Set3") +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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61 ggplot2::theme(legend.position = "none", axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), plot.title = ggplot2::element_text(color = "black", size = 12, face = "bold")) + ggplot2::ggtitle("Dispersion")
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62
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63 return(graph_dispersion)
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64
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65 }
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67 #The 2 graph
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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68 med_disp <- function(med, disp) {
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69 graph <- cowplot::plot_grid(med, disp, ncol = 1, nrow = 2, vjust = -5, scales = "free")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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71 ggplot2::ggsave("Med_Disp.png", graph, width = 12, height = 20, units = "cm")
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72 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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73
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75 #### Zero problem in data ####
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77 #Put data in form
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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78 make_table_analyse <- function(data, var, spe, var2, var3) {
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79 tab <- reshape(data
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80 , v.names = var
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81 , idvar = c(var2, var3)
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82 , timevar = spe
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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83 , direction = "wide")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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84 tab[is.na(tab)] <- 0 ###### remplace les na par des 0 / replace NAs by 0
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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85
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86 colnames(tab) <- sub(var, "", colnames(tab))### remplace le premier pattern "abond." par le second "" / replace the column names "abond." by ""
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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87 return(tab)
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88 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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89 data_num <- make_table_analyse(data, colvar, colspe, colloc, coltime)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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90 nb_spe <- length(unique(data[, spe]))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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91 nb_col <- ncol(data_num) - nb_spe + 1
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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92 data_num <- data_num[, nb_col:ncol(data_num)]
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93
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94 #Presence of zeros in the data
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95 mat_corr <- function(data) {
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96 cor(data)
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97 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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98 p_mat <- function(data) {
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99 ggcorrplot::cor_pmat(data)
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100 } # compute a matrix of correlation p-values
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101
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102 graph_corr <- function(data_num) {
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103 graph <- ggcorrplot::ggcorrplot(mat_corr(data_num), method = "circle", p.mat = p_mat(data_num), #barring the no significant coefficient
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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104 ggtheme = ggplot2::theme_gray, colors = c("#00AFBB", "#E7B800", "#FC4E07"))
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105
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106 ggplot2::ggsave("0_pb.png", graph)
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107 }
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108
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109 ##Med and disp
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110 med <- graph_median(data, var = colvar)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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111 disp <- dispersion(data, var = colvar, var2 = colspe)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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112 med_disp(med = med, disp = disp)
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113
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114 ##O problem
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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115 graph_corr(data_num)