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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
author workflow4metabolomics
date Mon, 16 May 2022 09:25:01 +0000
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a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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1 #' Calcul des grandeurs "diagnostiques"
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2 #'
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3 #' Script adapte de http://www.ime.unicamp.br/~cnaber/residdiag_nlme_v22.R pour fonctionner
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4 #' avec un modele lmer (et non lme), des sujets avec des identifiants non numeriques,
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5 #' et des observations non ordonnees sujet par sujet (dernier point a verifier.)
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6 #'
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7 #' @detail Les graphiques, les calculs associés et les notations utilisees dans le script suivent
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8 #' l'article de Singer et al (2016) Graphical Tools for detedcting departures from linear
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9 #' mixed model assumptions and some remedial measures, International Statistical Review
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10 #' (doi:10.1111/insr.12178)
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11 #'
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12 #' @param mfl A linear mixed model fitted via lmer or a data frame containing data
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13 #' @return A list
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14 #' @author Natacha Lenuzza
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15 #' @examples
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16 #' print("hello !")
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17 #'
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18 #' @export lmer.computeDiag
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22 lmer.computeDiag <- function(mfl) {
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24 ## Check arguments ---------------------------------------------------------
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26 if (length(mfl@flist) > 1)
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27 stop("Several 'grouping level' for random effect not implemented yet.")
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30 ## extracting information from mfl models -------------------------------------------------------------
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31 # data
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32 df <- mfl@frame
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33 responseC <- names(df)[1]
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34 unitC <- names(mfl@flist)[1]
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35 # observations
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36 yVn <- df[, responseC]
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37 nobsN <- length(yVn)
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38 # units
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39 idunitVc <- levels(mfl@flist[[1]])
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40 nunitN <- length(unique(idunitVc))
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41 #X
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42 xMN <- mfl@pp$X
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43 pN <- ncol(xMN)
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44 #Z
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45 zMN <- t(as.matrix(mfl@pp$Zt))
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46 # Estimated covariance matrix of random effects (Gam)
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47 aux <- VarCorr(mfl)[[1]] ## assuming only one level of grouping
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48 aux2 <- attr(aux, "stddev")
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49 gMN <- attr(aux, "correlation") * (aux2 %*% t(aux2))
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50 gammaMN <- as.matrix(kronecker(diag(nunitN), gMN))
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51 q <- dim(gMN)[1]
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52 # Estimated covariance matrix of conditonal error (homoskedastic conditional independance model)
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53 sigsqN <- attr(VarCorr(mfl), "sc")^2
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54 rMN <- sigsqN * diag(nobsN)
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55 # Estimated covariance matrix of Y
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56 vMN <- (zMN %*% gammaMN %*% t(zMN)) + rMN
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57 invvMN <- MASS::ginv(vMN)
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58 # H and Q matrix
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59 hMN <- MASS::ginv(t(xMN) %*% invvMN %*% xMN)
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60 qMN <- invvMN - invvMN %*% xMN %*% (hMN) %*% t(xMN) %*% invvMN
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61 # eblue and eblup
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62 eblueVn <- mfl@beta
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63 eblupVn <- gammaMN %*% t(zMN) %*% invvMN %*% (yVn - xMN %*% eblueVn) ## equivalent de ranef(mfl)
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64 rownames(eblupVn) <- colnames(zMN)
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65 ## Calculs of matrices and vectors used in graph diagnosics ---------------------------------------------
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66 ## Marginal and individual predictions, residuals and variances
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67 marpredVn <- xMN %*% eblueVn
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68 marresVn <- yVn - marpredVn
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69 marvarMN <- vMN - xMN %*% hMN %*% t(xMN)
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70 condpredVn <- marpredVn + zMN %*% eblupVn
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71 condresVn <- yVn - condpredVn
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72 condvarMN <- rMN %*% qMN %*% rMN
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73 ## Analysis of marginal and conditional residuals
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74 stmarresVn <- stcondresVn <- rep(0, nobsN)
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75 lesverVn <- rep(0, nunitN)
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76 names(lesverVn) <- idunitVc
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77 for (i in 1:nunitN) {
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78 idxiVn <- which(df[, unitC] == idunitVc[i]) ## position des observations du sujet i
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79 miN <- length(idxiVn)
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80 ## standardization of marginal residual
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81 stmarresVn[idxiVn] <- as.vector(solve(sqrtmF(marvarMN[idxiVn, idxiVn])) %*% marresVn[idxiVn])
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82 ##Standardized Lessafre and Verbeke's measure
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83 auxMN <- diag(1, ncol = miN, nrow = miN) - stmarresVn[idxiVn] %*% t(stmarresVn[idxiVn])
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84 lesverVn[i] <- sum(diag(auxMN %*% t(auxMN)))
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85 ## standardization of conditional residual
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86 stcondresVn[idxiVn] <- as.vector(solve(sqrtmF(condvarMN[idxiVn, idxiVn])) %*% condresVn[idxiVn])
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87 }
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88 lesverVn <- lesverVn / sum(lesverVn)
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89 ## Least confounded conditional residuals
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90 ## EBLUP analysis (Mahalanobis' distance)
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91 varbMN <- gammaMN %*% t(zMN) %*% qMN %*% zMN %*% gammaMN
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92 mdistVn <- rep(0, nunitN)
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93 qm <- q - 1
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94 for (j in 1:nunitN) {
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95 gbi <- varbMN[(q * j - qm):(q * j), (q * j - qm):(q * j)]
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96 eblupi <- eblupVn[(q * j - qm):(q * j)]
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97 mdistVn[j] <- t(eblupi) %*% ginv(gbi) %*% eblupi
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98 }
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99 names(mdistVn) <- levels(mfl@flist[[1]])
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100 ## output ----------------------------------------------
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101 return(list(
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102 data = df,
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103 q = q,
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104 eblue = eblueVn,
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105 eblup = eblupVn,
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106 marginal.prediction = marpredVn,
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107 conditional.prediction = condpredVn,
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108 std.marginal.residuals = stmarresVn,
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109 std.conditional.residuals = stcondresVn,
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110 mahalanobis.distance = mdistVn,
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111 std.mahalanobis.distance = mdistVn / sum(mdistVn),
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112 std.lesaffreverbeke.measure = lesverVn
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113 ))
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114 }
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115
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116
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117 #' Wrapper function for diagnostic plots of 'lmer' linear mixed models
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118 #'
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119 #' (W4M mixmod)
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120 #'
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121 #' @param mfl A linear mixed model fitted via lmer or a data frame containing data
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122 #' @param title aa
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123 #' @param outlier.limit aa
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124 #' @param pvalCutof aa
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125 #' @param resC aa
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126 #' @param uniC aa
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127 #' @param fixC aa
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128 #' @param lest.confounded Not used yet.
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129 #' @return NULL
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130 #' @author Natacha Lenuzza
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131 #' @examples
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132 #' print("hello !")
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133 #'
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134 #' @export diagmflF
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135
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136
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137 diagmflF <- function(mfl,
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138 title = "",
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139 outlier.limit = 3,
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140 pvalCutof = 0.05,
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141 resC = "vd",
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142 uniC = "subject",
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143 timC = "time",
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144 fixC = "fixfact",
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145 least.confounded = FALSE) {
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146 ## diagnostics
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147 diagLs <- lmer.computeDiag(mfl)
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148 ## plots
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149 blank <- rectGrob(gp = gpar(col = "white"))
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150 rectspacer <- rectGrob(height = unit(0.1, "npc"), gp = gpar(col = "grey"))
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151 grid.arrange(blank,
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152 plot_linearity(diagLs, hlimitN = outlier.limit, plotL = FALSE,
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153 label_factor = c(uniC, fixC, timC)),
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154 blank,
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155 plot_conditionalResiduals(diagLs, hlimitN = outlier.limit, plotL = FALSE,
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156 label_factor = c(uniC, fixC, timC)),
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157 blank,
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158 plot_condresQQplot(diagLs, plotL = FALSE),
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159 blank,
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160 plot_lesaffreVeerbeke(diagLs, plotL = FALSE),
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161 blank,
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162 plot_randomEffect(mfl, plotL = FALSE)[[1]],
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163 blank,
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164 plot_mahalanobisKhi2(diagLs, plotL = FALSE),
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165 blank,
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166 plot_mahalanobis(diagLs, plotL = FALSE),
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167 blank,
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168 blank,
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169 blank,
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170 top = textGrob(title, gp = gpar(fontsize = 40, font = 4)),
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171 layout_matrix = matrix(c(rep(1, 7),
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172 2, 3, rep(4, 3), 20, 21,
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173 rep(5, 7),
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174 6:12,
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175 rep(13, 7),
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176 14:18, rep(19, 2)),
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177 ncol = 7, nrow = 6, byrow = TRUE),
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178 heights = c(0.1 / 3, 0.3, 0.1 / 3, 0.3, 0.1 / 3, 0.3),
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179 widths = c(0.22, 0.04, 0.22, 0.04, 0.22, 0.04, 0.22))
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180 }
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181
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182 #######################################################################################################
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183 ## Raw data time courses
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184 #######################################################################################################
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185
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186 #' Visualization of raw time course
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187 #'
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188 #' Une
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189 #'
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190 #' @param mfl A linear mixed model fitted via lmer or a data frame containing data
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191 #' @param responseC Name of the 'response' variable
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192 #' @param timeC Name of the 'time' variable
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193 #' @param subjectC Name of the 'subject' variable
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194 #' @param fixfactC Name of the 'fixed factor' variable (e.g.treatment)
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195 #' @param offset_subject Boolean indicating if an offset value (subject's mean) should substracted to each data point. Default is FALSE
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196 #' @param plotL Boolean
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197 #' @param colorType One of NA, FIXFACT or SUBJECT
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198 #' @param shapeType One of NA, FIXFACT or SUBJECT
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199 #' @param lineType One of NA, FIXFACT or SUBJECT
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200 #' @return A plot
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201 #' @author Natacha Lenuzza
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202 #' @examples
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203 #' print("hello !")
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204 #'
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205 #' @export plot_timeCourse
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206
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207
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208
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209 plot_timeCourse <- function(mfl,
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210 responseC,
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211 timeC,
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212 subjectC,
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213 fixfactC = NULL,
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214 offset_subject = FALSE,
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215 plotL = TRUE,
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216 colorType = NA, ## subject, fixfact, none or NA
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217 shapeType = NA, ## subject, fixfact, none or NA
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218 lineType = NA ## subject, fixfact, none or NA
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219 ) {
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220 ## Data -----
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221 if (class(mfl) %in% c("merModLmerTest", "lmerMod", "lmerModLmerTest")) {
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222 DF <- mfl@frame
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223 } else if (class(mfl) == "data.frame") {
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224 DF <- mfl
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225 } else {
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226 stop("'mfl' argument must be a linear mixed effect model or a data frame.")
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227 }
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228 ## Format data -----
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229 if (is.null(fixfactC)) {
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230 DF <- DF[, c(responseC, timeC, subjectC)]
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231 colnames(DF) <- c("DV", "TIME", "SUBJECT")
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232 meanDF <- aggregate(DF$DV,
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233 by = list(SUBJECT = DF$SUBJECT,
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234 TIME = DF$TIME),
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235 FUN = mean,
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236 na.rm = TRUE)
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237 colnames(meanDF) <- c("SUBJECT", "TIME", "DV")
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238 meanDF$GROUP <- meanDF$SUBJECT
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239 } else{
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240 DF <- DF[, c(responseC, fixfactC, timeC, subjectC)]
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241 colnames(DF) <- c("DV", "FIXFACT", "TIME", "SUBJECT")
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242 meanDF <- aggregate(DF$DV,
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243 by = list(SUBJECT = DF$SUBJECT,
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244 TIME = DF$TIME,
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245 FIXFACT = DF$FIXFACT),
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246 FUN = mean,
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247 na.rm = TRUE)
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248 colnames(meanDF) <- c("SUBJECT", "TIME", "FIXFACT", "DV")
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249 meanDF$GROUP <- paste(meanDF$SUBJECT, meanDF$FIXFACT, sep = "_")
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250 }
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251 ## Offset -----
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252 if (offset_subject) {
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253 offsetMN <- aggregate(DF$DV, by = list(DF$SUBJECT), mean, na.rm = TRUE)
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254 offsetVn <- offsetMN[, 2]
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255 names(offsetVn) <- offsetMN[, 1]
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256 rm(offsetMN)
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257 DF$DV <- DF$DV - offsetVn[DF$SUBJECT]
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258 meanDF$DV <- meanDF$DV - offsetVn[as.character(meanDF$SUBJECT)]
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259 }
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260 ## Graphical parameters -----
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261 xlabC <- timeC
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262 ylabC <- responseC
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263 titC <- "Individual time-courses"
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264 if (offset_subject) {
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265 ylabC <- paste(ylabC, "minus 'within-subject' empirical mean")
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266 titC <- paste(titC, "('within-subject' empirical mean offset)")
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267 }
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268 ## color
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269 if (is.na(colorType)) { ## automaticatical attribution
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270 if (is.null(fixfactC)) {
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271 colorType <- "SUBJECT"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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272 } else {
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273 colorType <- "FIXFACT"
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274 }
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275 colTxt <- paste(", colour=", colorType)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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276 } else if (colorType == "none") {
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277 colTxt <- ""
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278 } else {
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279 colTxt <- paste(", colour=", colorType)
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280 }
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281 ## lineType
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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282 if (is.na(lineType)) { ## automaticatical attribution
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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283 if (is.null(fixfactC)) {
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284 linTxt <- ""
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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285 } else {
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286 linTxt <- paste(", linetype=",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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287 ifelse(colorType == "SUBJECT", "FIXFACT", "SUBJECT"))
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288 }
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289 } else if (lineType == "none") {
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290 linTxt <- ""
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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291 } else {
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292 linTxt <- paste(", linetype=", lineType)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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293 }
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294 ## shapeType
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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295 if (is.na(shapeType)) { ## automaticatical attribution
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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296 if (is.null(fixfactC)) {
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297 shaTxt <- ""
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298 } else {
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299 shaTxt <- paste(", shape=",
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workflow4metabolomics
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300 ifelse(colorType == "SUBJECT", "FIXFACT", "SUBJECT"))
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301 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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302 } else if (shapeType == "none") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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303 shaTxt <- ""
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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304 } else {
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305 shaTxt <- paste(", shape=", shapeType)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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306 }
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workflow4metabolomics
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307 ## aes mapping
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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308 txtMap <- paste("aes(x = TIME, y = DV",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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309 colTxt, shaTxt, ")", sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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310 txtLineMap <- paste("aes(x = TIME, y = DV, group = GROUP ",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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311 colTxt, linTxt, ")", sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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312 ## plot and output
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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313 p <- ggplot(data = DF, mapping = eval(parse(text = txtMap))) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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314 ggtitle(titC) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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315 xlab(xlabC) + ylab(ylabC) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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316 theme(legend.position = "left",
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317 plot.title = element_text(size = rel(1.2), face = "bold")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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318 geom_point() +
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workflow4metabolomics
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319 geom_line(eval(parse(text = txtLineMap)), data = meanDF) +
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workflow4metabolomics
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320 theme_bw() +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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321 NULL
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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322 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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323 invisible(p)
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workflow4metabolomics
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324 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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325
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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326 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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327 ## Post-hoc estimate
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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328 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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329 #' Visualization of fixed effects (post-hoc estimates)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
330 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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331 #' Description
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
332 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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333 #' @param mfl A linear mixed model fitted via lmer or a data frame containing data
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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334 #' @param pvalCutof User pvalue cut of
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
335 #' @param plotL Boolean
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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336 #' @param titC Title of the plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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337 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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338 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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339 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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340 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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341 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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342 #' @export plot_posthoc
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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343 plot_posthoc <- function(mfl, pvalCutof = 0.05, plotL = TRUE, titC = "Post-hoc estimates") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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344 ddlsm1 <- as.data.frame(difflsmeans(mfl, test.effs = NULL))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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345 colnames(ddlsm1)[ncol(ddlsm1)] <- "pvalue"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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346 ddlsm1$Significance <- rep("NS", nrow(ddlsm1))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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347 ## modif JF pour tenir compte du seuil de pvalues defini par le user
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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348 ddlsm1$Significance[which(ddlsm1$pvalue < pvalCutof)] <- paste("p-value < ", pvalCutof, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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349 ddlsm1$Significance[which(ddlsm1$pvalue < pvalCutof / 5)] <- paste("p-value < ", pvalCutof / 5, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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350 ddlsm1$Significance[which(ddlsm1$pvalue < pvalCutof / 10)] <- paste("p-value < ", pvalCutof / 10, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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351 ddlsm1$levels <- rownames(ddlsm1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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352 ddlsm1$term <- sapply(rownames(ddlsm1), function(namC) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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353 strsplit(namC, split = " ", fixed = TRUE)[[1]][1]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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354 })
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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355 colValue <- c("grey", "yellow", "orange", "red")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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356 names(colValue) <- c("NS",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
357 paste("p-value < ", pvalCutof, sep = ""),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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diff changeset
358 paste("p-value < ", pvalCutof / 5, sep = ""),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
359 paste("p-value < ", pvalCutof / 10, sep = ""))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
360 p <- ggplot(ddlsm1, aes(x = levels, y = Estimate)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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361 facet_grid(facets = ~term, ddlsm1, scales = "free", space = "free") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
362 geom_bar(aes(fill = Significance), stat = "identity") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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363 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
364 scale_fill_manual(values = colValue) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
365 geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.25) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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366 ggtitle(titC) + xlab("") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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367 NULL
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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368 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
369 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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370 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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parents:
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371
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
372 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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373 ## Visualisation des effets aléatoires
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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374 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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375 #' Visualization of random effects
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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376 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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377 #' Equivalent of dotplot(ranef)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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378 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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379 #' @param mfl A linear mixed model fitted via lmer or a data frame containing data
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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380 #' @param plotL Logical
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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381 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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382 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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383 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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parents:
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384 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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385 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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386 #' @export plot_randomEffect
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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387
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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388
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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389 plot_randomEffect <- function(mfl, plotL = TRUE) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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390 ## Estimation et format des effets aléatoires
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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391 randomEffect <- ranef(mfl, condVar = TRUE)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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392 DF <- data.frame(randomEffect = rep(names(randomEffect),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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393 times = sapply(seq_len(length(randomEffect)),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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394 function(lsi) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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395 return(length(unlist(randomEffect[[lsi]])))})))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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396 DF$condVar <- DF$estimate <- DF$x2 <- DF$x1 <- rep(NA, nrow(DF))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
397 for (rafC in names(randomEffect)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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398 eff <- randomEffect[[rafC]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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399 DF$x1[which(DF$randomEffect == rafC)] <- rep(colnames(eff), each = nrow(eff))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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400 DF$x2[which(DF$randomEffect == rafC)] <- rep(rownames(eff), ncol(eff))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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401 DF$estimate[which(DF$randomEffect == rafC)] <- unlist(eff)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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402 condvar <- attr(randomEffect[[rafC]], "postVar")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
403 se <- NULL
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
404 for (coli in seq_len(ncol(eff))) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
405 se <- c(se,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
406 sapply(seq_len(nrow(eff)),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
407 function(i) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
408 return(condvar[coli, coli, i])}))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
409 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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diff changeset
410 DF$condVar[which(DF$randomEffect == rafC)] <- se
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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411 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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412 DF$se <- sqrt(DF$condVar)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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413 DF$lower <- DF$estimate - 1.96 * DF$se
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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414 DF$upper <- DF$estimate + 1.96 * DF$se
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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415 ## Plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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416 plotLs <- vector("list", length(randomEffect))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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417 names(plotLs) <- names(randomEffect)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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418 for (pi in seq_len(length(plotLs))) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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419 subDF <- DF[DF$randomEffect == names(plotLs)[pi], ]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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420 subDF <- subDF[order(subDF$x1, subDF$estimate, decreasing = FALSE), ]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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421 p <- ggplot(data = subDF,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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422 mapping = aes(x = estimate, y = reorder(x2, estimate))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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423 ) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
424 geom_point(size = 3) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
425 geom_segment(aes(xend = lower, yend = x2)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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426 geom_segment(aes(xend = upper, yend = x2)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
427 facet_wrap(~x1, ncol = length(unique(subDF$x1))) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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428 ylab("") + xlab("") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
429 ggtitle(paste("Random effect - ", names(plotLs)[pi], sep = "")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
430 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
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431 geom_vline(xintercept = 0, linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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432 theme_bw()
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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433 plotLs[[pi]] <- p
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
434 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
435 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
436 invisible(plotLs)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
437 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
438
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
439 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
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440 ## Linearité des effets et outlying observations
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
441 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
442 #' Linarity of the fixed effect with regard to the continuous time
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
443 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
444 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
445 #' @param hlimitN Limit value for outliers (e.g.2 or 3)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
446 #' @param plotL Boolean
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
447 #' @param label_factor Column of observation names used to label outlying values
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
448 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
449 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
450 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
451 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
452 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
453 #' @export plot_linearity
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
454 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
455
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
456 plot_linearity <- function(diagLs, hlimitN, plotL = TRUE, label_factor = NULL) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
457 df <- cbind.data.frame(diagLs$data,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
458 marginal.prediction = diagLs$marginal.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
459 standardized.marginal.residuals = diagLs$std.marginal.residuals)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
460 # outlier annotation
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
461 df$outliers <- rep("", nrow(df))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
462 outidx <- which(abs(df$standardized.marginal.residuals) > hlimitN)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
463 df[outidx, "outliers"] <- (seq_len(nrow(df)))[outidx]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
464 if (length(label_factor) >= 1) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
465 df[outidx, "outliers"] <- paste(df[outidx, "outliers"],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
466 df[outidx, label_factor[1]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
467 sep = "_")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
468 if (length(label_factor) > 1) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
469 for (li in 2:length(label_factor)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
470 df[outidx, "outliers"] <- paste(df[outidx, "outliers"],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
471 df[outidx, label_factor[li]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
472 sep = ".")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
473 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
474 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
475 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
476 p <- ggplot(data = df,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
477 aes(x = marginal.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
478 y = standardized.marginal.residuals)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
479 geom_point(size = 2) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
480 geom_hline(yintercept = 0, col = "grey") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
481 geom_smooth(aes(x = marginal.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
482 y = standardized.marginal.residuals), data = df, se = FALSE, col = "blue", method = "loess") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
483 ggtitle("Linearity of effects/outlying obervations") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
484 xlab("Marginal predictions") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
485 ylab("Standardized marginal residuals") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
486 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
487 geom_hline(yintercept = c(-1, 1) * hlimitN, linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
488 geom_text(aes(label = outliers), hjust = 0, vjust = 0)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
489 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
490 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
491 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
492
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
493
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
494 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
495 ## EBLUP
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
496 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
497
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
498
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
499 #' Mahalanobis distance
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
500 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
501 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
502 #' @param plotL Boolean
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
503 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
504 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
505 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
506 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
507 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
508 #' @export plot_mahalanobis
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
509 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
510
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
511
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
512 plot_mahalanobis <- function(diagLs, plotL = TRUE) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
513 unitDf <- data.frame(unit = names(diagLs$std.mahalanobis.distance),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
514 mal = diagLs$std.mahalanobis.distance)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
515 ## Outlying subjects
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
516 p <-
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
517 ggplot(aes(y = mal, x = unit), data = unitDf) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
518 geom_point(size = 3) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
519 ylab("Standardized Mahalanobis distance") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
520 geom_vline(xintercept = 0, linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
521 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
522 geom_hline(yintercept = 2 * mean(unitDf$mal), linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
523 geom_text(aes(label = unit),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
524 data = unitDf[unitDf$mal > 2 * mean(unitDf$mal), ],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
525 hjust = 1, vjust = 0) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
526 ggtitle("Outlying unit") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
527 xlab("unit")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
528 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
529 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
530 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
531
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
532
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
533
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
534
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
535
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
536
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
537 #' Mahalanobis distance (Chi2)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
538 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
539 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
540 #' @param plotL aa
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
541 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
542 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
543 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
544 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
545 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
546 #' @export plot_mahalanobisKhi2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
547 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
548
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
549
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
550 plot_mahalanobisKhi2 <- function(diagLs, plotL = TRUE) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
551 unitDf <- data.frame(unit = names(diagLs$std.mahalanobis.distance),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
552 mal = diagLs$mahalanobis.distance)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
553 p <- qqplotF(x = unitDf$mal,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
554 distribution = "chisq",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
555 df = diagLs$q,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
556 line.estimate = NULL,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
557 conf = 0.95) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
558 xlab("Chi-squared quantiles") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
559 ylab("Mahalanobis distance") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
560 ggtitle("Normality of random effect") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
561 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
562 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
563 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
564 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
565
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
566
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
567
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
568
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
569
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
570
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
571
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
572 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
573 ## Residus conditionels
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
574 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
575
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
576 ## Presence of outlying observations and homoscedacity of residuals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
577
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
578 #' Homoskedacity of conditionalresiduals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
579 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
580 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
581 #' @param hlimitN Limit value for outliers (e.g.2 or 3)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
582 #' @param plotL Boolean
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
583 #' @param label_factor Column of observation names used to label outlying values
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
584 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
585 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
586 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
587 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
588 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
589 #' @export plot_conditionalResiduals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
590 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
591
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
592
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
593 plot_conditionalResiduals <- function(diagLs, hlimitN, plotL = TRUE, label_factor = NULL) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
594 df <- cbind.data.frame(diagLs$data,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
595 conditional.prediction = diagLs$conditional.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
596 standardized.conditional.residuals = diagLs$std.conditional.residuals)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
597 # outlier annotation
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
598 df$outliers <- rep("", nrow(df))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
599 outidx <- which(abs(df$standardized.conditional.residuals) > hlimitN)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
600 df[outidx, "outliers"] <- (seq_len(nrow(df)))[outidx]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
601 if (length(label_factor) >= 1) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
602 df[outidx, "outliers"] <- paste(df[outidx, "outliers"],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
603 df[outidx, label_factor[1]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
604 sep = "_")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
605 if (length(label_factor) > 1) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
606 for (li in 2:length(label_factor)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
607 df[outidx, "outliers"] <- paste(df[outidx, "outliers"],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
608 df[outidx, label_factor[li]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
609 sep = ".")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
610 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
611 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
612 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
613 p <- ggplot(data = df,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
614 aes(x = conditional.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
615 y = standardized.conditional.residuals)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
616 geom_point(size = 2) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
617 geom_hline(yintercept = 0, col = "grey") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
618 geom_smooth(aes(x = conditional.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
619 y = standardized.conditional.residuals),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
620 data = df, se = FALSE, col = "blue", method = "loess") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
621 ggtitle("Homoscedasticity of conditional residuals/outlying observations") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
622 xlab("Individual predictions") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
623 ylab("Standardized conditional residuals") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
624 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold")) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
625 geom_hline(yintercept = c(-1, 1) * hlimitN, linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
626 geom_text(aes(label = outliers), hjust = 0, vjust = 0)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
627 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
628 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
629 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
630
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
631
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
632
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
633
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
634 #' Normality of conditionalresiduals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
635 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
636 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
637 #' @param plotL aa
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
638 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
639 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
640 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
641 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
642 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
643 #' @export plot_condresQQplot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
644 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
645
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
646
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
647 plot_condresQQplot <- function(diagLs, plotL = TRUE) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
648 df <- cbind.data.frame(diagLs$data,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
649 conditional.prediction = diagLs$conditional.prediction,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
650 standardized.conditional.residuals = diagLs$std.conditional.residuals)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
651 p <- qqplotF(x = df$standardized.conditional.residuals,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
652 distribution = "norm",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
653 line.estimate = NULL,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
654 conf = 0.95) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
655 xlab("Standard normal quantiles") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
656 ylab("Standardized conditional residual quantiles") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
657 ggtitle("Normality of conditional error") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
658 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
659 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
660 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
661 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
662
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
663
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
664
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
665
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
666
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
667 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
668 ## Within-units covariance structure
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
669 #######################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
670
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
671
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
672 #' Lesaffre-Veerbeke measure
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
673 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
674 #' @param diagLs diagnostic list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
675 #' @param plotL aa
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
676 #' @return A plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
677 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
678 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
679 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
680 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
681 #' @export plot_lesaffreVeerbeke
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
682 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
683
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
684
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
685 plot_lesaffreVeerbeke <- function(diagLs, plotL = TRUE) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
686 unitDf <- data.frame(unit = names(diagLs$std.lesaffreverbeke.measure),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
687 lvm = diagLs$std.lesaffreverbeke.measure)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
688 p <- ggplot(data = unitDf,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
689 aes(x = unit,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
690 y = lvm)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
691 geom_point(size = 2) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
692 theme(legend.position = "none") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
693 xlab("units") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
694 ylab("Standardized Lesaffre-Verbeke measure") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
695 geom_hline(yintercept = 2 * mean(unitDf$lvm), linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
696 geom_text(aes(label = unit),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
697 data = unitDf[unitDf$lvm > 2 * mean(unitDf$lvm), ],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
698 hjust = 0, vjust = 0) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
699 ggtitle("Within-units covariance matrice") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
700 theme(legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
701 if (plotL) plot(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
702 invisible(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
703 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
704
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
705 ##-------------------------------------------------------------------------------------------------##
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
706 ## Helpers
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
707 ##-------------------------------------------------------------------------------------------------##
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
708
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
709
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
710 ## square root of a matrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
711 ## From Rocha, Singer and Nobre
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
712
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
713 #' square root of a matrix (Rocha)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
714 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
715 #' Description
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
716 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
717 #' @param mat Matrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
718 #' @return A list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
719 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
720 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
721 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
722 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
723 #' @export sqrt.matrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
724
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
725 sqrt.matrix <- function(mat) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
726 mat <- as.matrix(mat) # new line of code
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
727 singular_dec <- svd(mat, LINPACK = F)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
728 U <- singular_dec$u
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
729 V <- singular_dec$v
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
730 D <- diag(singular_dec$d)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
731 sqrtmatrix <- U %*% sqrt(D) %*% t(V)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
732 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
733
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
734
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
735 ## square root of a matrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
736 ## http://www.cs.toronto.edu/~jepson/csc420/notes/introSVD.pdf (page 6)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
737 ## (for matMN a n x n matrix that symetric and non-negative definite)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
738
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
739 #' square root of a matrix (Rocha)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
740 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
741 #' @param mat Matrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
742 #' @return A list
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
743 #' @author Natacha Lenuzza
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
744 #' @examples
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
745 #' print("hello !")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
746 #'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
747 #' @export sqrtmF
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
748
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
749 sqrtmF <- function(matMN) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
750 matMN <- as.matrix(matMN)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
751 ## check that matMN is symetric: if (!all(t(matMN == matMN))) stop("matMN must be symetric.")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
752 svd_dec <- svd(matMN)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
753 invisible(svd_dec$u %*% sqrt(diag(svd_dec$d)) %*% t(svd_dec$v))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
754 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
755
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
756
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
757 ## qqplotF
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
758 ## adapted from https://gist.github.com/rentrop/d39a8406ad8af2a1066c
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
759
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
760 qqplotF <- function(x,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
761 distribution = "norm", ...,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
762 line.estimate = NULL,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
763 conf = 0.95,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
764 labels = names(x)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
765 q.function <- eval(parse(text = paste0("q", distribution)))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
766 d.function <- eval(parse(text = paste0("d", distribution)))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
767 x <- na.omit(x)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
768 ord <- order(x)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
769 n <- length(x)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
770 P <- ppoints(length(x))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
771 daf <- data.frame(ord.x = x[ord], z = q.function(P, ...))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
772 if (is.null(line.estimate)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
773 Q.x <- quantile(daf$ord.x, c(0.25, 0.75))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
774 Q.z <- q.function(c(0.25, 0.75), ...)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
775 b <- diff(Q.x) / diff(Q.z)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
776 coef <- c(Q.x[1] - b * Q.z[1], b)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
777 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
778 coef <- coef(line.estimate(ord.x ~ z))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
779 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
780 zz <- qnorm(1 - (1 - conf) / 2)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
781 SE <- (coef[2] / d.function(daf$z, ...)) * sqrt(P * (1 - P) / n)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
782 fit.value <- coef[1] + coef[2] * daf$z
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
783 daf$upper <- fit.value + zz * SE
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
784 daf$lower <- fit.value - zz * SE
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
785 if (!is.null(labels)) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
786 daf$label <- ifelse(daf$ord.x > daf$upper | daf$ord.x < daf$lower, labels[ord], "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
787 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
788 p <- ggplot(daf, aes(x = z, y = ord.x)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
789 geom_point() +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
790 geom_abline(intercept = coef[1], slope = coef[2], col = "red") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
791 geom_line(aes(x = z, y = lower), daf, col = "red", linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
792 geom_line(aes(x = z, y = upper), daf, col = "red", linetype = "dashed") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
793 xlab("") + ylab("")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
794 if (!is.null(labels)) p <- p + geom_text(aes(label = label))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
795 return(p)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
796 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
797
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
798
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
799 ## histogramm
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
800 histF <- function(x, sd_x = NULL, breaks = "scott") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
801 if (is.null(sd_x))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
802 sd_x <- sd(x)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
803 ## Bandwith estimation (default is Scott)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
804 if (!breaks %in% c("sqrt", "sturges", "rice", "scott", "fd"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
805 breaks <- "scott"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
806 if (breaks %in% c("sqrt", "sturges", "rice")) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
807 k <- switch(breaks,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
808 sqrt = sqrt(length(x)),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
809 sturges = floor(log2(x)) + 1,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
810 rice = floor(2 * length(x) ^ (1 / 3))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
811 )
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
812 bw <- diff(range(x)) / k
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
813 }else{
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
814 bw <- switch(breaks,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
815 scott = 3.5 * sd_x / length(x) ^ (1 / 3),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
816 fd = diff(range(x)) / (2 * IQR(x) / length(x) ^ (1 / 3))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
817 )
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
818 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
819
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
820
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
821 daf <- data.frame(x = x)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
822 ## graph
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
823 return(ggplot(data = daf, aes(x)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
824 geom_histogram(aes(y = ..density..),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
825 col = "black", fill = "grey", binwidth = bw) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
826 geom_density(size = 1.2,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
827 col = "blue",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
828 linetype = "blank",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
829 fill = rgb(0, 0, 1, 0.1)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
830 stat_function(fun = dnorm,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
831 args = list(mean = 0, sd = sd_x),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
832 col = "blue", size = 1.2) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
833 theme(legend.position = "none") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
834 xlab(""))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
835 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
836
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
837
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
838 plot.res.Lmixed <- function(mfl, df, title = "", pvalCutof = 0.05) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
839
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
840 ## define subscript of the different columns depending if we have only time (ncol(df)=3) or not
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
841 if (ncol(df) > 3) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
842 varidx <- 4
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
843 ffidx <- 1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
844 timidx <- 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
845 individx <- 3
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
846 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
847 varidx <- 3
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
848 ffidx <- 1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
849 timidx <- 1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
850 individx <- 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
851 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
852 nameVar <- colnames(df)[varidx]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
853 fflab <- colnames(df)[ffidx]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
854 ## Individual time-course
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
855 rawPlot <-
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
856 ggplot(data = df, aes(x = df[[timidx]], y = df[[varidx]], colour = df[[ffidx]], group = df[[individx]])) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
857 geom_point() +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
858 geom_line() + ggtitle("Individual time-courses (raw data)") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
859 ylab(nameVar) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
860 xlab(label = colnames(df)[2]) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
861 theme(legend.title = element_blank(), legend.position = "none", plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
862 ## Boxplot of fixed factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
863 bPlot <-
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
864 ggplot(data = df, aes(y = df[[varidx]], x = df[[ffidx]], color = df[[ffidx]])) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
865 geom_boxplot(outlier.colour = "red", outlier.shape = 8, outlier.size = 4) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
866 ggtitle(paste("Boxplot by ", fflab, sep = "")) + xlab("") + ylab("") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
867 theme(legend.title = element_blank(), plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
868 ## Post-hoc estimates
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
869 ddlsm1 <- mfl
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
870 ddlsm1$name <- rownames(ddlsm1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
871 ddlsm1$Significance <- rep("NS", nrow(ddlsm1))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
872 ## modif JF pour tenir compte du seuil de pvalues defini par le user
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
873 options("scipen" = 100, "digits" = 5)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
874 pvalCutof <- as.numeric(pvalCutof)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
875 bs <- 0.05; bm <- 0.01; bi <- 0.005
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
876 if (pvalCutof > bm) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
877 bs <- pvalCutof
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
878 } else
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
879 if (pvalCutof < bm & pvalCutof > bi) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
880 bm <- pvalCutof; bs <- pvalCutof
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
881 } else
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
882 if (pvalCutof < bi) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
883 bi <- pvalCutof; bm <- pvalCutof; bs <- pvalCutof
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
884 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
885 lbs <- paste("p-value < ", bs, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
886 lbm <- paste("p-value < ", bm, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
887 lbi <- paste("p-value < ", bi, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
888 cols <- paste("p-value < ", bs, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
889 colm <- paste("p-value < ", bm, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
890 coli <- paste("p-value < ", bi, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
891 valcol <- c("grey", "yellow", "orange", "red")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
892 names(valcol) <- c("NS", lbs, lbm, lbi)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
893 ddlsm1$Significance[which(ddlsm1$p.value <= bs)] <- lbs
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
894 ddlsm1$Significance[which(ddlsm1$p.value < bs & ddlsm1$p.value >= bm)] <- lbm
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
895 ddlsm1$Significance[which(ddlsm1$p.value < bi)] <- lbi
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
896 ddlsm1$levels <- rownames(ddlsm1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
897 ddlsm1$term <- sapply(rownames(ddlsm1), function(namC) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
898 strsplit(namC, split = " ", fixed = TRUE)[[1]][1]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
899 })
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
900
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
901 phPlot <-
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
902 ggplot(ddlsm1, aes(x = levels, y = Estimate)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
903 facet_grid(facets = ~term, ddlsm1, scales = "free", space = "free") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
904 geom_bar(aes(fill = Significance), stat = "identity") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
905 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
906 scale_fill_manual(
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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907 values = valcol) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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908 geom_errorbar(aes(ymin = Lower.CI, ymax = Upper.CI), width = 0.25) +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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909 ggtitle("Post-hoc estimates ") + xlab("") +
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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910 theme(plot.title = element_text(size = rel(1.2), face = "bold"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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911
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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912 ## Final plotting
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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913 grid.arrange(arrangeGrob(rawPlot, bPlot, ncol = 2),
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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914 phPlot, nrow = 2,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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915 top = textGrob(title, gp = gpar(fontsize = 32, font = 4))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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916 )
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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917
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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918 }