annotate DrawFunctions.R @ 7:122df1bf0a8c draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
author workflow4metabolomics
date Fri, 11 Jul 2025 08:33:38 +0000
parents 5e64657b4fe5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 library(ggplot2) # nice plots
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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2 library(gridExtra) # nice plots
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3 library(reshape2) # data manipulation
2
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4
7
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5 Draw <- function(Signal_data, type.draw = c("signal", "pca"), output = c(
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6 "default",
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7 "window", "png", "pdf"
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8 ), dirpath = ".", filename = "%003d", height = 480,
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9 width = 640, pdf.onefile = TRUE, ...) {
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10 # Data initialisation and checks ----------------------------------------------
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11 type.draw <- match.arg(type.draw)
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12 output <- match.arg(output)
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13 fullpath <- paste(file.path(dirpath, filename), output, sep = ".")
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14 createFile <- TRUE
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15 createWindow <- FALSE
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17 # Drawing --------------------------------------------------------------------
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18 # output
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19 switch(output,
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20 default = {
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21 createFile <- FALSE
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22 },
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23 window = {
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24 createWindow <- TRUE
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25 createFile <- FALSE
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26 },
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27 png = {
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28 grDevices::png(fullpath, width, height)
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29 },
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30 pdf = {
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31 grDevices::pdf(fullpath,
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32 width = width / 72, height = height / 72,
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33 onefile = pdf.onefile
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34 )
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35 },
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36 {
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37 stop("Unknown output type.")
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38 }
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39 )
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40
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41 # Drawing type (signal/spectrum or PCA)
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42 funs <- list(signal = DrawSignal, pca = DrawPCA)
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43 if (type.draw %in% names(funs)) {
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44 fun <- funs[[type.draw]]
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45 } else {
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46 stop(paste("Unknown type:", type.draw))
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47 }
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48
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49 # Plot finalisation ----------------------------------------------
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50 if (is.vector(Signal_data)) {
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51 Signal_data <- vec2mat(Signal_data)
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52 }
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53 fun(Signal_data, createWindow = createWindow, ...)
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54 if (createFile) {
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55 grDevices::dev.off()
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56 }
2
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57 }
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58
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59
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60
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61 ##### DrawSignal
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62
7
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63 DrawSignal <- function(Signal_data, subtype = c(
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64 "stacked", "together",
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65 "separate", "diffmean", "diffmedian", "diffwith"
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66 ),
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67 ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
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68 xlab = "rowname", RowNames = NULL, row = 1, num.stacked = 4,
2
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69 main = NULL, createWindow) {
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70 # nticks
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71
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72 # Data initialisation and checks ----------------------------------------------
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73
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74 subtype <- match.arg(subtype)
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75 vec <- is.vector(Signal_data)
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76 if (vec) {
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77 Signal_data <- vec2mat(Signal_data)
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78 }
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79
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80 n <- nrow(Signal_data)
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81 m <- ncol(Signal_data)
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82
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83 if (n < num.stacked) {
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84 num.stacked <- n
2
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85 }
7
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86
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87 scale <- colnames(Signal_data)
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88
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89 num.plot <- sum(ReImModArg)
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90
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91 Var <- rowname <- value <- NULL # only for R CMD check
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92
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93 # Drawing array
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94 if (num.plot <= 0) {
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95 stop("Nothing selected in ReImModArg.")
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96 } else if (num.plot <= 2) {
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97 if (vertical) {
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98 nrow <- num.plot
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99 ncol <- 1
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100 } else {
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101 nrow <- 1
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102 ncol <- num.plot
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103 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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104 } else {
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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105 nrow <- 2
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106 ncol <- 2
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107 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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108
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109 # RowNames
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110 if (is.null(RowNames)) {
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111 RowNames <- rownames(Signal_data)
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112 if (is.null(RowNames)) {
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113 RowNames <- 1:n
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114 }
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115 } else {
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116 if (!is.vector(RowNames)) {
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117 stop("RowNames is not a vector")
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118 }
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119 if (length(RowNames) != n) {
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120 stop(paste("RowNames has length", length(RowNames), "and there are", n, "FIDs."))
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121 }
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122 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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123
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124 if (n == 1) {
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125 RowNames <- deparse(substitute(Signal_data))
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126 }
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127
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128 elements <- list()
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129 if (ReImModArg[1]) {
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130 elements[["Re"]] <- Re(Signal_data)
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131 rownames(elements[["Re"]]) <- RowNames
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132 }
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133 if (ReImModArg[2]) {
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134 elements[["Im"]] <- Im(Signal_data)
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135 rownames(elements[["Im"]]) <- RowNames
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136 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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137 if (ReImModArg[3]) {
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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138 elements[["Mod"]] <- Mod(Signal_data)
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139 rownames(elements[["Mod"]]) <- RowNames
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140 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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141 if (ReImModArg[4]) {
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142 elements[["Arg"]] <- Arg(Signal_data)
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143 rownames(elements[["Arg"]]) <- RowNames
2
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lecorguille
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144 }
7
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145
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146
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147
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148
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149 # Drawing --------------------------------------------------------------------
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150
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151 y <- x <- NULL # only for R CMD check
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152
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153
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154 # SEPARATE or STACKED ===============
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155 if (subtype == "separate" | subtype == "stacked") {
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156 i <- 1
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157 while (i <= n) {
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158 if (createWindow) {
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159 grDevices::dev.new(noRStudioGD = TRUE)
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160 }
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161 if (subtype == "separate") {
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162 # The other uses gridExtra to do that
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163 graphics::par(mfrow = c(nrow, ncol))
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164 }
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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165 plots <- list()
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166 if (subtype == "separate") {
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167 last <- i
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168 } else {
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169 last <- min(i + num.stacked - 1, n)
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170 }
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171 for (name in names(elements)) {
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172 if (subtype == "separate") {
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173 if (n == 1) {
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174 df <- data.frame(x = as.numeric(scale), y = elements[[name]])
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175 } else {
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176 df <- data.frame(x = as.numeric(scale), y = elements[[name]][i, ])
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177 }
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178
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179 plots[[name]] <- ggplot2::ggplot(data = df, ggplot2::aes(x = x, y = y)) +
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180 ggplot2::geom_line(size = 1) +
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181 ggplot2::theme(legend.position = "none") +
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182 ggplot2::labs(x = xlab, y = name) +
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183 ggplot2::ggtitle(RowNames[i]) +
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184 ggplot2::theme_bw()
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185
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186 if ((df[1, "x"] - df[(dim(df)[1]), "x"]) > 0) {
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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187 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
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188 }
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189 } else {
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190 if (n == 1) {
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191 melted <- data.frame(
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192 rowname = rep(name, m),
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193 Var = as.numeric(scale), value = elements[[name]][i, ]
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194 )
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195 } else if (last == i) {
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196 melted <- data.frame(
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197 rowname = rep(rownames(elements[[name]])[i], m),
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198 Var = as.numeric(scale), value = elements[[name]][i, ]
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199 )
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200 } else {
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201 melted <- reshape2::melt(elements[[name]][i:last, ], varnames = c("rowname", "Var"))
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202 }
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203
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204
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205 plots[[name]] <- ggplot2::ggplot(data = melted, ggplot2::aes(x = Var, y = value)) +
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206 ggplot2::geom_line(size = 0.3) +
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207 ggplot2::facet_grid(rowname ~ ., scales = "free_y") +
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208 ggplot2::theme(legend.position = "none") +
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209 ggplot2::labs(x = xlab, y = name) +
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210 ggplot2::ggtitle(label = main) +
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211 ggplot2::theme_bw()
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212
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213 if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) > 0) {
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214 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
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215 }
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216 }
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217 }
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218
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219 if (subtype == "stacked") {
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220 do.call(gridExtra::grid.arrange, c(plots, list(nrow = nrow, ncol = ncol)))
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221 }
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222
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223 i <- last + 1
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224 }
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225 } else if (subtype %in% c("together", "diffmean", "diffmedian", "diffwith")) {
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226 # TOGHETER or DIFFMEAN or DIFFMEDIAN or DIFFWITH ===============
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227
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228 rainbow_colors <- grDevices::rainbow(n)
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229
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230 if (createWindow) {
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231 grDevices::dev.new(noRStudioGD = TRUE)
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232 }
2
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233 graphics::par(mfrow = c(nrow, ncol))
7
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234
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235 plots <- list()
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236
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237 # Loop for Re, Im, Mod and Arg
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238 for (name in names(elements)) {
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239 # Get this part of the signal
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240 element <- elements[[name]]
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241
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242 # Express the signal according to a reference if asked by `subtype'
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243 if (subtype == "diffmean") {
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244 element <- sweep(element, MARGIN = 2, colMeans(element), `-`)
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245 } else if (subtype == "diffmedian") {
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246 element <- sweep(element, MARGIN = 2, matrixStats::colMedians(element), `-`)
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247 } else if (subtype == "diffwith") {
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248 element <- sweep(element, MARGIN = 2, element[row, ], `-`)
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249 if (row == 1 & n > 1) {
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250 # Since we use plot on the first row and lines on the following, the y
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251 # scale is calculated at the first row so if the first row is all 0, it
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252 # causes problems
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253 tmp <- element[1, ]
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254 element[1, ] <- element[2, ]
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255 element[2, ] <- tmp
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256 }
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257 }
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258 melted <- reshape2::melt(elements[[name]][i:last, ], varnames = c("rowname", "Var"))
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259
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260 plots[[name]] <- ggplot2::ggplot(melted, ggplot2::aes(
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261 x = Var,
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262 y = value, group = rowname, colour = rowname
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263 )) +
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264 ggplot2::geom_line() +
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265 ggplot2::labs(x = xlab, y = name) +
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266 ggplot2::scale_colour_discrete(name = NULL) +
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267 ggplot2::ggtitle(main)
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268
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269 if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) >
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270 0) {
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271 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
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272 }
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273
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274 do.call(gridExtra::grid.arrange, c(plots, list(
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275 nrow = nrow,
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276 ncol = ncol
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277 )))
2
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278 }
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279 }
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280 }