Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_calc.R @ 12:ddaf84e15d06 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
author eschen42
date Thu, 08 Nov 2018 23:06:09 -0500
parents ddcc33ff3205
children 2ae2d26e3270
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1 # center with 'colMeans()' - ref: http://gastonsanchez.com/visually-enforced/how-to/2014/01/15/Center-data-in-R/
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2 center_colmeans <- function(x) {
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3 xcenter = colMeans(x)
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4 x - rep(xcenter, rep.int(nrow(x), ncol(x)))
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5 }
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6
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7 #### OPLS-DA
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8 algoC <- "nipals"
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9
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10 do_detail_plot <- function(
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11 x_dataMatrix
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12 , x_predictor
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13 , x_is_match
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14 , x_algorithm
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15 , x_prefix
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16 , x_show_labels
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17 , x_progress = print
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18 , x_env
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19 , x_crossval_i
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20 ) {
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21 off <- function(x) if (x_show_labels == "0") 0 else x
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22 if ( x_is_match
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23 && ncol(x_dataMatrix) > 0
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24 && length(unique(x_predictor))> 1
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25 && x_crossval_i < nrow(x_dataMatrix)
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26 ) {
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27 my_oplsda <- opls(
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28 x = x_dataMatrix
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29 , y = x_predictor
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30 , algoC = x_algorithm
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31 , predI = 1
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32 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0
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33 , printL = FALSE
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34 , plotL = FALSE
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35 , crossvalI = x_crossval_i
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36 , scaleC = "pareto" # data centered and pareto scaled here only. This line fixes issue #2.
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37 )
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38 # strip out variables having negligible variance
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39 x_dataMatrix <- x_dataMatrix[,names(my_oplsda@vipVn), drop = FALSE]
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40 my_oplsda_suppLs_y_levels <- levels(as.factor(my_oplsda@suppLs$y))
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41
0
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42 fctr_lvl_1 <- my_oplsda_suppLs_y_levels[1]
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43 fctr_lvl_2 <- my_oplsda_suppLs_y_levels[2]
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44 do_s_plot <- function(
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45 x_env
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46 , predictor_projection_x = TRUE
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47 , cplot_x = FALSE
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48 , cor_vs_cov_x = NULL
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49 )
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50 {
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51 if (cplot_x) {
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52 cplot_y_correlation <- (x_env$cplot_y == "correlation")
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53 }
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54 if (is.null(cor_vs_cov_x)) {
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55 my_cor_vs_cov <- cor_vs_cov(
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56 matrix_x = x_dataMatrix
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57 , ropls_x = my_oplsda
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58 , predictor_projection_x = predictor_projection_x
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59 , x_progress
6
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60 )
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61 } else {
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62 my_cor_vs_cov <- cor_vs_cov_x
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63 }
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64 # str(my_cor_vs_cov)
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65 if (is.null(my_cor_vs_cov) || sum(!is.na(my_cor_vs_cov$tsv1$covariance)) < 2) {
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66 if (is.null(cor_vs_cov_x)) {
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67 x_progress("No cor_vs_cov data produced")
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68 }
6
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69 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")
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70 text(x=1, y=1, labels="too few covariance data")
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71 return(my_cor_vs_cov)
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72 }
5
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73 with(
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74 my_cor_vs_cov
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75 , {
6
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76 min_x <- min(covariance, na.rm = TRUE)
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77 max_x <- max(covariance, na.rm = TRUE)
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78 lim_x <- max(sapply(X=c(min_x, max_x), FUN=abs))
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79 covariance <- covariance / lim_x
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80 lim_x <- 1.2
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81 # "It is generally accepted that a variable should be selected if vj>1, [27–29],
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82 # but a proper threshold between 0.83 and 1.21 can yield more relevant variables according to [28]."
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83 # (Mehmood 2012 doi:10.1186/1748-7188-6-27)
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84 plus_cor <- correlation
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85 plus_cov <- covariance
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86 cex <- 0.65
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87 which_projection <- if (projection == 1) "t1" else "o1"
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88 which_loading <- if (projection == 1) "parallel" else "orthogonal"
6
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89 if (projection == 1) { # predictor-projection
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90 vipcp <- pmax(0, pmin(1,(vip4p-0.83)/(1.21-0.83)))
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91 if (!cplot_x) { # S-plot predictor-projection
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92 my_xlab <- "relative covariance(feature,t1)"
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93 my_x <- plus_cov
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94 my_ylab <- "correlation(feature,t1)"
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95 my_y <- plus_cor
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96 } else { # C-plot predictor-projection
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97 my_xlab <- "variable importance in predictor-projection"
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98 my_x <- vip4p
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99 if (cplot_y_correlation) {
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100 my_ylab <- "correlation(feature,t1)"
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101 my_y <- plus_cor
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102 } else {
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103 my_ylab <- "relative covariance(feature,t1)"
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104 my_y <- plus_cov
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105 }
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106 }
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107 if (cplot_x) {
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108 lim_x <- max(my_x, na.rm = TRUE) * 1.1
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109 my_xlim <- c( 0, lim_x + off(0.2) )
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110 } else {
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111 my_xlim <- c( -lim_x - off(0.2), lim_x + off(0.2) )
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112 }
5
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113 my_ylim <- c( -1.0 - off(0.2), 1.0 + off(0.2) )
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114 my_load_distal <- loadp
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115 my_load_proximal <- loado
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116 red <- as.numeric(correlation > 0) * vipcp
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117 blue <- as.numeric(correlation < 0) * vipcp
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118 alpha <- 0.1 + 0.4 * vipcp
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119 red[is.na(red)] <- 0
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120 blue[is.na(blue)] <- 0
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121 alpha[is.na(alpha)] <- 0
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122 my_col <- rgb(blue = blue, red = red, green = 0, alpha = alpha)
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123 main_label <- sprintf("%s for level %s versus %s"
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124 , x_prefix, fctr_lvl_1, fctr_lvl_2)
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125 } else { # orthogonal projection
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126 vipco <- pmax(0, pmin(1,(vip4o-0.83)/(1.21-0.83)))
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127 if (!cplot_x) {
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128 my_xlab <- "relative covariance(feature,to1)"
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129 my_x <- -plus_cov
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130 } else {
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131 my_xlab <- "variable importance in orthogonal projection"
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132 my_x <- vip4o
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133 }
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134 if (!cplot_x) { # S-plot orthogonal projection
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135 my_xlim <- c( -lim_x - off(0.2), lim_x + off(0.2) )
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136 my_ylab <- "correlation(feature,to1)"
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137 my_y <- plus_cor
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138 } else { # C-plot orthogonal projection
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139 lim_x <- max(my_x, na.rm = TRUE) * 1.1
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140 my_xlim <- c( 0, lim_x + off(0.2) )
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141 if (cplot_y_correlation) {
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142 my_ylab <- "correlation(feature,to1)"
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143 my_y <- plus_cor
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144 } else {
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145 my_ylab <- "relative covariance(feature,to1)"
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146 my_y <- plus_cov
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147 }
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148 }
5
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149 my_ylim <- c( -1.0 - off(0.2), 1.0 + off(0.2) )
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150 my_load_distal <- loado
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151 my_load_proximal <- loadp
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152 alpha <- 0.1 + 0.4 * vipco
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153 alpha[is.na(alpha)] <- 0
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154 my_col <- rgb(blue = 0, red = 0, green = 0, alpha = alpha)
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155 main_label <- sprintf(
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156 "Features influencing orthogonal projection for %s versus %s"
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157 , fctr_lvl_1, fctr_lvl_2)
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158 }
5
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159 main_cex <- min(1.0, 46.0/nchar(main_label))
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160 my_feature_label_slant <- -30 # slant feature labels 30 degrees downward
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161 my_pch <- sapply(X = cor_p_value, function(x) if (x < 0.01) 16 else if (x < 0.05) 17 else 18)
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162 plot(
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163 y = my_y
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164 , x = my_x
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165 , type = "p"
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166 , xlim = my_xlim
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167 , ylim = my_ylim
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168 , xlab = my_xlab
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169 , ylab = my_ylab
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170 , main = main_label
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171 , cex.main = main_cex
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172 , cex = cex
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173 , pch = my_pch
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174 , col = my_col
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175 )
5
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176 low_x <- -0.7 * lim_x
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177 high_x <- 0.7 * lim_x
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178 if (projection == 1 && !cplot_x) {
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179 text(x = low_x, y = -0.05, labels = fctr_lvl_1, col = "blue")
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180 text(x = high_x, y = 0.05, labels = fctr_lvl_2, col = "red")
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181 }
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182 if ( x_show_labels != "0" ) {
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183 names(my_load_distal) <- tsv1$featureID
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184 names(my_load_proximal) <- tsv1$featureID
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185 if ( x_show_labels == "ALL" ) {
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186 n_labels <- length(my_load_distal)
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187 } else {
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188 n_labels <- as.numeric(x_show_labels)
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189 }
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190 n_labels <- min( n_labels, (1 + length(my_load_distal)) / 2 )
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191 labels_to_show <- c(
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192 names(head(sort(my_load_distal),n = n_labels))
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193 , names(tail(sort(my_load_distal),n = n_labels))
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194 )
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195 labels <- unname(
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196 sapply(
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197 X = tsv1$featureID
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198 , FUN = function(x) if( x %in% labels_to_show ) x else ""
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199 )
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200 )
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201 x_text_offset <- 0.024
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202 y_text_off <- 0.017
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203 if (!cplot_x) { # S-plot
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204 y_text_offset <- if (projection == 1) -y_text_off else y_text_off
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205 } else { # C-plot
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206 y_text_offset <-
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207 sapply(
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208 X = (my_y > 0)
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209 , FUN = function(x) { if (x) y_text_off else -y_text_off }
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210 )
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211 }
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212 label_features <- function(x_arg, y_arg, labels_arg, slant_arg) {
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213 if (length(labels_arg) > 0) {
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214 unique_slant <- unique(slant_arg)
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215 if (length(unique_slant) == 1) {
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216 text(
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217 y = y_arg
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218 , x = x_arg + x_text_offset
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219 , cex = 0.4
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220 , labels = labels_arg
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221 , col = rgb(blue = 0, red = 0, green = 0, alpha = 0.5) # grey semi-transparent labels
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222 , srt = slant_arg
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223 , adj = 0 # left-justified
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224 )
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225 } else {
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226 for (slant in unique_slant) {
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227 text(
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228 y = y_arg[slant_arg == slant]
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229 , x = x_arg[slant_arg == slant] + x_text_offset
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230 , cex = 0.4
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231 , labels = labels_arg[slant_arg == slant]
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232 , col = rgb(blue = 0, red = 0, green = 0, alpha = 0.5) # grey semi-transparent labels
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233 , srt = slant
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234 , adj = 0 # left-justified
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235 )
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236 }
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237 }
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238 }
5
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239 }
6
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240 if (!cplot_x) {
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241 my_slant <- (if (projection == 1) 1 else -1) * my_feature_label_slant
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242 } else {
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243 my_slant <- sapply(
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244 X = (my_y > 0)
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245 , FUN = function(x) if (x) 2 else -2
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246 ) * my_feature_label_slant
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247 }
5
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248 if (length(my_x) > 1) {
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249 label_features(
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250 x_arg = my_x [my_x > 0]
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251 , y_arg = my_y [my_x > 0] - y_text_offset
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252 , labels_arg = labels[my_x > 0]
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253 , slant_arg = (if (!cplot_x) -my_slant else (my_slant))
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254 )
6
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255 if (!cplot_x) {
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256 label_features(
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257 x_arg = my_x [my_x < 0]
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258 , y_arg = my_y [my_x < 0] + y_text_offset
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259 , labels_arg = labels[my_x < 0]
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260 , slant_arg = my_slant
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261 )
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262 }
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263 } else {
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264 if (!cplot_x) {
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265 my_slant <- (if (my_x > 1) -1 else 1) * my_slant
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266 my_y_arg = my_y + (if (my_x > 1) -1 else 1) * y_text_offset
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267 } else {
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268 my_slant <- (if (my_y > 1) -1 else 1) * my_slant
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269 my_y_arg = my_y + (if (my_y > 1) -1 else 1) * y_text_offset
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270 }
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271 label_features(
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272 x_arg = my_x
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273 , y_arg = my_y_arg
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274 , labels_arg = labels
5
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275 , slant_arg = my_slant
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276 )
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277 }
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278 }
0
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279 }
5
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280 )
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281 return (my_cor_vs_cov)
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282 }
6
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283 my_cor_vs_cov <- do_s_plot(
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284 x_env = x_env
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285 , predictor_projection_x = TRUE
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286 , cplot_x = FALSE
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287 )
0
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288 typeVc <- c("correlation", # 1
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289 "outlier", # 2
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290 "overview", # 3
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291 "permutation", # 4
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292 "predict-train", # 5
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293 "predict-test", # 6
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294 "summary", # 7 = c(2,3,4,9)
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295 "x-loading", # 8
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296 "x-score", # 9
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297 "x-variance", # 10
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298 "xy-score", # 11
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299 "xy-weight" # 12
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300 ) # [c(3,8,9)] # [c(4,3,8,9)]
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301 if ( length(my_oplsda@orthoVipVn) > 0 ) {
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302 my_typevc <- typeVc[c(9,3,8)]
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303 } else {
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304 my_typevc <- c("(dummy)","overview","(dummy)")
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305 }
6
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306 my_ortho_cor_vs_cov_exists <- FALSE
0
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307 for (my_type in my_typevc) {
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308 if (my_type %in% typeVc) {
4
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309 tryCatch({
5
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310 if ( my_type != "x-loading" ) {
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311 plot(
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312 x = my_oplsda
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313 , typeVc = my_type
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314 , parCexN = 0.4
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315 , parDevNewL = FALSE
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316 , parLayL = TRUE
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317 , parEllipsesL = TRUE
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318 )
6
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319 if (my_type == "overview") {
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320 sub_label <- sprintf("%s versus %s", fctr_lvl_1, fctr_lvl_2)
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321 title(sub = sub_label)
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322 }
5
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323 } else {
6
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324 my_ortho_cor_vs_cov <- do_s_plot(
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325 x_env = x_env
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diff changeset
326 , predictor_projection_x = FALSE
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diff changeset
327 , cplot_x = FALSE
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diff changeset
328 )
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329 my_ortho_cor_vs_cov_exists <- TRUE
5
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330 }
4
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331 }, error = function(e) {
6
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332 x_progress(
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diff changeset
333 sprintf(
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diff changeset
334 "factor level %s or %s may have only one sample - %s"
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335 , fctr_lvl_1
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diff changeset
336 , fctr_lvl_2
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diff changeset
337 , e$message
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338 )
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339 )
4
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340 })
0
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341 } else {
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342 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")
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343 text(x=1, y=1, labels="no orthogonal projection is possible")
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344 }
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345 }
6
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346 cplot_p <- x_env$cplot_p
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347 cplot_o <- x_env$cplot_o
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348 if (cplot_p || cplot_o) {
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349 if (cplot_p) {
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diff changeset
350 do_s_plot(
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351 x_env = x_env
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352 , predictor_projection_x = TRUE
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diff changeset
353 , cplot_x = TRUE
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354 , cor_vs_cov_x = my_cor_vs_cov
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355 )
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356 did_plots <- 1
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357 } else {
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358 did_plots <- 0
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diff changeset
359 }
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diff changeset
360 if (cplot_o) {
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diff changeset
361 if (my_ortho_cor_vs_cov_exists) {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
362 do_s_plot(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
363 x_env = x_env
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diff changeset
364 , predictor_projection_x = FALSE
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
365 , cplot_x = TRUE
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
366 , cor_vs_cov_x = my_ortho_cor_vs_cov
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
367 )
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
368 } else {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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369 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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370 text(x=1, y=1, labels="no orthogonal projection is possible")
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
371 }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
372 did_plots <- 1 + did_plots
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
373 }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
374 if (did_plots == 1) {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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375 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n", fg = "white")
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
376 }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
377 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
378 return (my_cor_vs_cov)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
379 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
380 return (NULL)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
381 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
382 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
383
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
384 # S-PLOT and OPLS reference: Wiklund_2008 doi:10.1021/ac0713510
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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385 corcov_calc <- function(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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386 calc_env
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
387 , failure_action = stop
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
388 , progress_action = function(x) { }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
389 , corcov_tsv_action = function(t) { }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
390 , salience_tsv_action = function(t) { }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
391 , extra_plots = c()
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
392 ) {
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
393 if ( ! is.environment(calc_env) ) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
394 failure_action("corcov_calc: fatal error - 'calc_env' is not an environment")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
395 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
396 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
397 if ( ! is.function(corcov_tsv_action) ) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
398 failure_action("corcov_calc: fatal error - 'corcov_tsv_action' is not a function")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
399 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
400 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
401 if ( ! is.function(salience_tsv_action) ) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
402 failure_action("salience_calc: fatal error - 'salience_tsv_action' is not a function")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
403 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
404 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
405
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
406 # extract parameters from the environment
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
407 vrbl_metadata <- calc_env$vrbl_metadata
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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408 vrbl_metadata_names <- vrbl_metadata[,1]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
409 smpl_metadata <- calc_env$smpl_metadata
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
410 data_matrix <- calc_env$data_matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
411 pairSigFeatOnly <- calc_env$pairSigFeatOnly
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
412 facC <- calc_env$facC
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
413 tesC <- calc_env$tesC
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
414 # extract the levels from the environment
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
415 originalLevCSV <- levCSV <- calc_env$levCSV
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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416 # matchingC is one of { "none", "wildcard", "regex" }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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417 matchingC <- calc_env$matchingC
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
418 labelFeatures <- calc_env$labelFeatures
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
419
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
420 # arg/env checking
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
421 if (!(facC %in% names(smpl_metadata))) {
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
422 failure_action(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
423 sprintf("bad parameter! Factor name '%s' not found in sampleMetadata"
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
424 , facC))
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
425 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
426 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
427
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
428 mz <- vrbl_metadata$mz
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
429 names(mz) <- vrbl_metadata$variableMetadata
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
430 mz_lookup <- function(feature) unname(mz[feature])
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
431
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
432 rt <- vrbl_metadata$rt
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
433 names(rt) <- vrbl_metadata$variableMetadata
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
434 rt_lookup <- function(feature) unname(rt[feature])
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
435
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
436 # calculate salience_df as data.frame(feature, max_level, max_median, max_rcv, mean_median, salience, salient_rcv)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
437 salience_df <- calc_env$salience_df <- w4msalience(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
438 data_matrix = data_matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
439 , sample_class = smpl_metadata[,facC]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
440 , failure_action = failure_action
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
441 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
442 salience_tsv_action({
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
443 my_df <- data.frame(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
444 featureID = salience_df$feature
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
445 , salientLevel = salience_df$max_level
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
446 , salientRCV = salience_df$salient_rcv
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
447 , salience = salience_df$salience
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
448 , mz = mz_lookup(salience_df$feature)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
449 , rt = rt_lookup(salience_df$feature)
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
450 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
451 my_df[order(-my_df$salience),]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
452 })
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
453
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
454 # transform wildcards to regexen
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
455 if (matchingC == "wildcard") {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
456 # strsplit(x = "hello,wild,world", split = ",")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
457 levCSV <- gsub("[.]", "[.]", levCSV)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
458 levCSV <- strsplit(x = levCSV, split = ",")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
459 levCSV <- sapply(levCSV, utils::glob2rx, trim.tail = FALSE)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
460 levCSV <- paste(levCSV, collapse = ",")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
461 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
462 # function to determine whether level is a member of levCSV
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
463 isLevelSelected <- function(lvl) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
464 matchFun <- if (matchingC != "none") grepl else `==`
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
465 return(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
466 Reduce(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
467 f = "||"
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
468 , x = sapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
469 X = strsplit(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
470 x = levCSV
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
471 , split = ","
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
472 , fixed = TRUE
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
473 )[[1]]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
474 , FUN = matchFun
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
475 , lvl
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
476 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
477 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
478 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
479 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
480
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
481 # transpose matrix because ropls matrix is the transpose of XCMS matrix
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
482 tdm <- t(data_matrix)
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
483 # Wiklund_2008 centers and pareto-scales data before OPLS-DA S-plot
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
484 # However, data should be neither centered nor pareto scaled here because ropls::opls does that; this fixes issue #2.
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
485
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
486 # pattern to match column names like k10_kruskal_k4.k3_sig
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
487 col_pattern <- sprintf('^%s_%s_(.*)[.](.*)_sig$', facC, tesC)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
488 # column name like k10_kruskal_sig
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
489 intersample_sig_col <- sprintf('%s_%s_sig', facC, tesC)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
490 # get the facC column from sampleMetadata, dropping to one dimension
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
491 smpl_metadata_facC <- smpl_metadata[,facC]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
492
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
493 # allocate a slot in the environment for the contrast_list, each element of which will be a data.frame with this structure:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
494 # - feature ID
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
495 # - value1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
496 # - value2
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
497 # - Wiklund_2008 correlation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
498 # - Wiklund_2008 covariance
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
499 # - Wiklund_2008 VIP
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
500 calc_env$contrast_list <- list()
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
501
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
502
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
503 did_plot <- FALSE
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
504 if (tesC != "none") {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
505 # for each column name, extract the parts of the name matched by 'col_pattern', if any
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
506 the_colnames <- colnames(vrbl_metadata)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
507 if ( ! Reduce( f = "||", x = grepl(tesC, the_colnames) ) ) {
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
508 failure_action(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
509 sprintf(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
510 "bad parameter! variableMetadata must contain results of W4M Univariate test '%s'."
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
511 , tesC))
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
512 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
513 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
514 col_matches <- lapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
515 X = the_colnames,
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
516 FUN = function(x) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
517 regmatches( x, regexec(col_pattern, x) )[[1]]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
518 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
519 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
520 ## first contrast each selected level with all other levels combined into one "super-level" ##
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
521 # process columns matching the pattern
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
522 level_union <- c()
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
523 for (i in 1:length(col_matches)) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
524 col_match <- col_matches[[i]]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
525 if (length(col_match) > 0) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
526 # it's an actual match; extract the pieces, e.g., k10_kruskal_k4.k3_sig
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
527 vrbl_metadata_col <- col_match[1] # ^^^^^^^^^^^^^^^^^^^^^ # Column name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
528 fctr_lvl_1 <- col_match[2] # ^^ # Factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
529 fctr_lvl_2 <- col_match[3] # ^^ # Factor-level 2
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
530 # only process this column if both factors are members of lvlCSV
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
531 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
532 if (is_match) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
533 level_union <- c(level_union, col_match[2], col_match[3])
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
534 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
535 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
536 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
537 level_union <- unique(sort(level_union))
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
538 overall_significant <- 1 == (
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
539 if (intersample_sig_col %in% colnames(vrbl_metadata)) {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
540 vrbl_metadata[,intersample_sig_col]
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
541 } else {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
542 1
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
543 }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
544 )
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
545 if ( length(level_union) > 2 ) {
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
546 chosen_samples <- smpl_metadata_facC %in% level_union
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
547 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
548 col_selector <- vrbl_metadata_names[ overall_significant ]
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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diff changeset
549 my_matrix <- tdm[ chosen_samples, col_selector, drop = FALSE ]
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
550 plot_action <- function(fctr_lvl_1, fctr_lvl_2) {
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
551 progress_action(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
552 sprintf("calculating/plotting contrast of %s vs. %s"
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
553 , fctr_lvl_1, fctr_lvl_2)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
554 )
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
555 predictor <- sapply(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
556 X = chosen_facC
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
557 , FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
558 )
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
559 my_cor_cov <- do_detail_plot(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
560 x_dataMatrix = my_matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
561 , x_predictor = predictor
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
562 , x_is_match = TRUE
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
563 , x_algorithm = algoC
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
564 , x_prefix = if (pairSigFeatOnly) {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
565 "Significantly contrasting features"
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
566 } else {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
567 "Significant features"
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
568 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
569 , x_show_labels = labelFeatures
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
570 , x_progress = progress_action
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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parents: 3
diff changeset
571 , x_crossval_i = min(7, length(chosen_samples))
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
572 , x_env = calc_env
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
573 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
574 if ( is.null(my_cor_cov) ) {
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
575 progress_action("NOTHING TO PLOT")
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
576 } else {
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
577 my_tsv <- my_cor_cov$tsv1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
578 my_tsv$mz <- mz_lookup(my_tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
579 my_tsv$rt <- rt_lookup(my_tsv$featureID)
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
580 my_tsv["level1Level2Sig"] <- vrbl_metadata[
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
581 match(my_tsv$featureID, vrbl_metadata_names)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
582 , vrbl_metadata_col
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
583 ]
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
584 tsv <<- my_tsv
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
585 corcov_tsv_action(tsv)
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
586 did_plot <<- TRUE
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
587 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
588 }
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
589 if ( length(level_union) != 2 ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
590 fctr_lvl_2 <- "other"
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
591 for ( fctr_lvl_1 in level_union[1:length(level_union)] ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
592 plot_action(fctr_lvl_1, fctr_lvl_2)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
593 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
594 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
595 plot_action(fctr_lvl_1 = level_union[1], fctr_lvl_2 = level_union[2])
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
596 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
597 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
598
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
599 if ( length(level_union) > 1 ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
600 ## next, contrast each selected level with each of the other levels individually ##
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
601 # process columns matching the pattern
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
602 for (i in 1:length(col_matches)) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
603 # for each potential match of the pattern
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
604 col_match <- col_matches[[i]]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
605 if (length(col_match) > 0) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
606 # it's an actual match; extract the pieces, e.g., k10_kruskal_k4.k3_sig
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
607 vrbl_metadata_col <- col_match[1] # ^^^^^^^^^^^^^^^^^^^^^ # Column name
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
608 fctr_lvl_1 <- col_match[2] # ^^ # Factor-level 1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
609 fctr_lvl_2 <- col_match[3] # ^^ # Factor-level 2
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
610 # only process this column if both factors are members of lvlCSV
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
611 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
11
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diff changeset
612 if (is_match) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
613 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
614 sprintf("calculating/plotting contrast of %s vs. %s."
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
615 , fctr_lvl_1, fctr_lvl_2
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
616 )
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
617 )
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
618 # choose only samples with one of the two factors for this column
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
619 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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620 predictor <- smpl_metadata_facC[chosen_samples]
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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621 # extract only the significantly-varying features and the chosen samples
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622 fully_significant <- 1 == vrbl_metadata[,vrbl_metadata_col] *
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623 ( if (intersample_sig_col %in% colnames(vrbl_metadata)) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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624 vrbl_metadata[,intersample_sig_col]
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625 } else {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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626 1
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627 }
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628 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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629 col_selector <- vrbl_metadata_names[
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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630 if ( pairSigFeatOnly ) fully_significant else overall_significant
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631 ]
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632 my_matrix <- tdm[ chosen_samples, col_selector, drop = FALSE ]
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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633 my_cor_cov <- do_detail_plot(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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634 x_dataMatrix = my_matrix
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635 , x_predictor = predictor
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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636 , x_is_match = is_match
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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637 , x_algorithm = algoC
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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638 , x_prefix = if (pairSigFeatOnly) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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639 "Significantly contrasting features"
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640 } else {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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641 "Significant features"
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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642 }
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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643 , x_show_labels = labelFeatures
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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644 , x_progress = progress_action
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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645 , x_crossval_i = min(7, length(chosen_samples))
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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646 , x_env = calc_env
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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647 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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648 if ( is.null(my_cor_cov) ) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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649 progress_action("NOTHING TO PLOT.")
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650 } else {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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651 tsv <- my_cor_cov$tsv1
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652 tsv$mz <- mz_lookup(tsv$featureID)
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653 tsv$rt <- rt_lookup(tsv$featureID)
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654 tsv["level1Level2Sig"] <- vrbl_metadata[
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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655 match(tsv$featureID, vrbl_metadata_names)
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656 , vrbl_metadata_col
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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657 ]
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658 corcov_tsv_action(tsv)
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659 did_plot <- TRUE
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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660 }
1
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661 } else {
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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662 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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663 sprintf("skipping contrast of %s vs. %s."
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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664 , fctr_lvl_1, fctr_lvl_2
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
665 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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666 )
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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667 }
0
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668 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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669 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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670 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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671 } else { # tesC == "none"
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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672 # find all the levels for factor facC in sampleMetadata
0
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673 level_union <- unique(sort(smpl_metadata_facC))
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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674 # identify the selected levels for factor facC from sampleMetadata
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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675 level_include <- sapply(X = level_union, FUN = isLevelSelected)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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676 # discard the non-selected levels for factor facC
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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677 level_union <- level_union[level_include]
0
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diff changeset
678 if ( length(level_union) > 1 ) {
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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679 if ( length(level_union) > 2 ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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680 ## pass 1 - contrast each selected level with all other levels combined into one "super-level" ##
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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681 completed <- c()
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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682 lapply(
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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683 X = level_union
6
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684 , FUN = function(x) {
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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685 fctr_lvl_1 <- x[1]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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686 fctr_lvl_2 <- {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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687 if ( fctr_lvl_1 %in% completed )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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688 return("DUMMY")
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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689 # strF(completed)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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690 completed <<- c(completed, fctr_lvl_1)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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691 setdiff(level_union, fctr_lvl_1)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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692 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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693 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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694 fctr_lvl_2 <- "other"
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695 if (length(unique(chosen_samples)) < 1) {
11
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696 progress_action(
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697 sprintf("Skipping contrast of %s vs. %s; there are no chosen samples."
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698 , fctr_lvl_1, fctr_lvl_2)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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699 )
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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700 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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701 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
6
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702 predictor <- sapply(
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703 X = chosen_facC
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diff changeset
704 , FUN = function(fac) {
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
705 if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
706 }
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
707 )
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
708 my_matrix <- tdm[ chosen_samples, , drop = FALSE ]
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
709 # only process this column if both factors are members of lvlCSV
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
710 is_match <- isLevelSelected(fctr_lvl_1)
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
711 if (is_match) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
712 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
713 sprintf("Calculating/plotting contrast of %s vs. %s"
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
714 , fctr_lvl_1, fctr_lvl_2)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
715 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
716 my_cor_cov <- do_detail_plot(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
717 x_dataMatrix = my_matrix
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
718 , x_predictor = predictor
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
719 , x_is_match = is_match
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
720 , x_algorithm = algoC
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
721 , x_prefix = "Features"
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
722 , x_show_labels = labelFeatures
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
723 , x_progress = progress_action
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
724 , x_crossval_i = min(7, length(chosen_samples))
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
725 , x_env = calc_env
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
726 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
727 if ( is.null(my_cor_cov) ) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
728 progress_action("NOTHING TO PLOT...")
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
729 } else {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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diff changeset
730 tsv <- my_cor_cov$tsv1
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
731 tsv$mz <- mz_lookup(tsv$featureID)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
732 tsv$rt <- rt_lookup(tsv$featureID)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
733 corcov_tsv_action(tsv)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
734 did_plot <<- TRUE
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
735 }
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
736 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
737 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
738 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
739 "dummy" # need to return a value; otherwise combn fails with an error
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
740 }
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
741 )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
742 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
743 ## pass 2 - contrast each selected level with each of the other levels individually ##
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
744 completed <- c()
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
745 utils::combn(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
746 x = level_union
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
747 , m = 2
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
748 , FUN = function(x) {
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
749 fctr_lvl_1 <- x[1]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
750 fctr_lvl_2 <- x[2]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
751 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
752 if (length(unique(chosen_samples)) < 1) {
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
753 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
754 sprintf("Skipping contrast of %s vs. %s. - There are no chosen samples."
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
755 , fctr_lvl_1, fctr_lvl_2
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
756 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
757 )
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
758 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
759 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
760 predictor <- chosen_facC
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
761 my_matrix <- tdm[ chosen_samples, , drop = FALSE ]
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
762 # only process this column if both factors are members of lvlCSV
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
763 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
764 if (is_match) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
765 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
766 sprintf("Calculating/plotting contrast of %s vs. %s."
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
767 , fctr_lvl_1, fctr_lvl_2)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
768 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
769 my_cor_cov <- do_detail_plot(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
770 x_dataMatrix = my_matrix
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
771 , x_predictor = predictor
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
772 , x_is_match = is_match
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
773 , x_algorithm = algoC
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
774 , x_prefix = "Features"
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
775 , x_show_labels = labelFeatures
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
776 , x_progress = progress_action
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
777 , x_crossval_i = min(7, length(chosen_samples))
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
778 , x_env = calc_env
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
779 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
780 if ( is.null(my_cor_cov) ) {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
781 progress_action("NOTHING TO PLOT.....")
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
782 } else {
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
783 tsv <- my_cor_cov$tsv1
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
784 tsv$mz <- mz_lookup(tsv$featureID)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
785 tsv$rt <- rt_lookup(tsv$featureID)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
786 corcov_tsv_action(tsv)
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
787 did_plot <<- TRUE
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
788 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
789 } else {
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
790 progress_action(
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
791 sprintf("Skipping contrast of %s vs. %s."
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
792 , fctr_lvl_1, fctr_lvl_2
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
793 )
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
eschen42
parents: 7
diff changeset
794 )
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
795 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
796 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
797 "dummy" # need to return a value; otherwise combn fails with an error
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
798 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
799 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
800 } else {
11
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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parents: 7
diff changeset
801 progress_action("NOTHING TO PLOT......")
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
802 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
803 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
804 if (!did_plot) {
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
805 failure_action(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
806 sprintf(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
807 "bad parameter! sampleMetadata must have at least two levels of factor '%s' matching '%s'"
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
808 , facC, originalLevCSV))
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
809 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
810 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
811 return ( TRUE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
812 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
813
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
814 # Calculate data for correlation-versus-covariance plot
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
815 # Adapted from:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
816 # Wiklund_2008 doi:10.1021/ac0713510
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
817 # Galindo_Prieto_2014 doi:10.1002/cem.2627
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
818 # https://github.com/HegemanLab/extra_tools/blob/master/generic_PCA.R
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
819 cor_vs_cov <- function(
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
820 matrix_x
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
821 , ropls_x
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
822 , predictor_projection_x = TRUE
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
823 , x_progress = print
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
824 ) {
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
825 tryCatch({
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
826 return(
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
827 cor_vs_cov_try( matrix_x, ropls_x, predictor_projection_x, x_progress)
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
828 )
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
829 }, error = function(e) {
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
830 x_progress(
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
831 sprintf(
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
832 "cor_vs_cov fatal error - %s"
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
833 , as.character(e) # e$message
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
834 )
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
835 )
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
836 return ( NULL )
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
837 })
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
838 }
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
eschen42
parents: 6
diff changeset
839
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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parents: 6
diff changeset
840 cor_vs_cov_try <- function(
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
841 matrix_x # rows are samples; columns, features
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
842 , ropls_x # an instance of ropls::opls
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
843 , predictor_projection_x = TRUE # TRUE for predictor projection; FALSE for orthogonal projection
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
eschen42
parents: 11
diff changeset
844 , x_progress = print # function to produce progress and error messages
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
845 ) {
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
846 x_class <- class(ropls_x)
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
847 if ( !( as.character(x_class) == "opls" ) ) {
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
848 stop(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
849 paste(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
850 "cor_vs_cov: Expected ropls_x to be of class ropls::opls but instead it was of class "
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
851 , as.character(x_class)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
852 )
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
eschen42
parents: 5
diff changeset
853 )
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
854 }
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
855 if ( !ropls_x@suppLs$algoC == "nipals" ) {
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
856 # suppLs$algoC - Character: algorithm used - "svd" for singular value decomposition; "nipals" for NIPALS
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
857 stop(
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
858 paste(
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
859 "cor_vs_cov: Expected ropls::opls instance to have been computed by the NIPALS algorithm rather than "
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
eschen42
parents: 11
diff changeset
860 , ropls_x@suppLs$algoC
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
eschen42
parents: 11
diff changeset
861 )
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
eschen42
parents: 11
diff changeset
862 )
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
eschen42
parents: 11
diff changeset
863 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
864 result <- list()
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
865 result$projection <- projection <- if (predictor_projection_x) 1 else 2
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
866
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
867 # I used equations (1) and (2) from Wiklund 2008, doi:10.1021/ac0713510
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
868 # (and not from the supplement despite the statement that, for the NIPALS algorithm,
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
869 # the equations from the supplement should be used) because of the definition of the
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
870 # Pearson/Galton coefficient of correlation is defined as
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
871 # $$
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
872 # \rho_{X,Y}= \frac{\operatorname{cov}(X,Y)}{\sigma_X \sigma_Y}
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
873 # $$
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
874 # as described (among other places) on Wikipedia at
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
875 # https://en.wikipedia.org/wiki/Pearson_correlation_coefficient#For_a_population
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
876 # The equations in the supplement said to use, for the predictive component t1,
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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877 # \rho_{t1,X_i}= \frac{\operatorname{cov}(t1,X_i)}{(\operatorname{mag}(t1))(\operatorname{mag}(X_i))}
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878 # but the results that I got were dramatically different from published results for S-PLOTs;
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879 # perhaps my data are not centered exactly the same way that theirs were.
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880 # The correlations calculated here are in agreement with those calculated with the code from
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881 # page 22 of https://cran.r-project.org/web/packages/muma/muma.pdf
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882 # I did transform covariance to "relative covariance" (relative to the maximum value)
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883 # to keep the figures consistent with one another.
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884
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885 # count the features (one column for each sample)
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886 Nfeatures <- ncol(matrix_x)
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887 # count the samples (one row for each sample)
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888 Nobservations <- nrow(matrix_x)
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889 # a one-dimensional magnitude function (i.e., take the vector norm)
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890 vector_norm <- function(one_dimensional) sqrt(sum(one_dimensional * one_dimensional))
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891 # calculate the standard deviation for each feature
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892 sd_xi <- sapply(X = 1:Nfeatures, FUN = function(x) sd(matrix_x[,x]))
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893 # choose whether to plot the predictive score vector or orthogonal score vector
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894 if (predictor_projection_x)
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895 score_matrix <- ropls_x@scoreMN
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896 else
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897 score_matrix <- ropls_x@orthoScoreMN
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898 # transpose the score (or orthoscore) vector for use as a premultiplier in covariance calculation
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899 score_matrix_transposed <- t(score_matrix)
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900 # compute the norm of the vector (i.e., the magnitude)
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901 score_matrix_magnitude <- vector_norm(score_matrix)
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902 # compute the standard deviation of the vector
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903 score_matrix_sd <- sd(score_matrix)
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904 # compute the relative covariance of each feature with the score vector
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905 result$covariance <-
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906 score_matrix_transposed %*% matrix_x / ( score_matrix_magnitude * score_matrix_magnitude )
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907 # compute the correlation of each feature with the score vector
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908 result$correlation <-
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909 score_matrix_transposed %*% matrix_x / ( (Nobservations - 1) * ( score_matrix_sd * sd_xi ) )
0
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910
12
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911 # convert covariance and correlation from one-dimensional matrices to arrays of values,
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912 # which are accessed by feature name below
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913 p1 <- result$covariance <- result$covariance [ 1, , drop = TRUE ]
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914 # x_progress("strF(p1)")
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915 # x_progress(strF(p1))
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916
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917 pcorr1 <- result$correlation <- result$correlation[ 1, , drop = TRUE ]
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918 # x_progress("pearson strF(pcorr1)")
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919 # x_progress(strF(pcorr1))
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920 # x_progress(typeof(pcorr1))
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921 # x_progress(str(pcorr1))
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922
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923 # # this is how to use Spearman correlation instead of pearson
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924 # result$spearcor <- sapply(
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925 # X = 1:Nfeatures
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926 # , FUN = function(i) {
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927 # stats::cor(
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928 # x = as.vector(score_matrix)
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929 # , y = as.vector(matrix_x[,i])
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930 # # , method = "spearman"
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931 # , method = "pearson"
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932 # )
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933 # }
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934 # )
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935 # names(result$spearcor) <- names(p1)
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936 # pcorr1 <- result$spearcor
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937 # x_progress("spearman strF(pcorr1)")
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938 # x_progress(strF(pcorr1))
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939 # x_progress(typeof(pcorr1))
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940 # x_progress(str(pcorr1))
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941 # pcorr1 <- result$correlation <- result$spearcor
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942
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943 # correl.ci(r, n, a = 0.05, rho = 0)
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944 correl_pci <- lapply(
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945 X = 1:Nfeatures
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946 , FUN = function(i) correl.ci(r = pcorr1[i], n = Nobservations)
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947 )
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948 result$p_value_raw <- sapply(
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949 X = 1:Nfeatures
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950 , FUN = function(i) correl_pci[[i]]$p.value
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951 )
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952 result$p_value_raw[is.na(result$p_value_raw)] <- 0.0
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953 result$ci_lower <- sapply(
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954 X = 1:Nfeatures
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955 , FUN = function(i) correl_pci[[i]]$CI['lower']
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956 )
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957 result$ci_upper <- sapply(
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958 X = 1:Nfeatures
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959 , FUN = function(i) correl_pci[[i]]$CI['upper']
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960 )
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diff changeset
961
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diff changeset
962
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diff changeset
963 # extract "variant 4 of Variable Influence on Projection for OPLS" (see Galindo_Prieto_2014, DOI 10.1002/cem.2627)
0
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964 # Length = number of features; labels = feature identifiers. (The same is true for $correlation and $covariance.)
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965 result$vip4p <- as.numeric(ropls_x@vipVn)
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966 result$vip4o <- as.numeric(ropls_x@orthoVipVn)
12
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967 if (length(result$vip4o) == 0) result$vip4o <- NA
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968 # extract the loadings
1
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969 result$loadp <- as.numeric(ropls_x@loadingMN)
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970 result$loado <- as.numeric(ropls_x@orthoLoadingMN)
0
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diff changeset
971 # get the level names
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972 level_names <- sort(levels(as.factor(ropls_x@suppLs$y)))
1
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973 fctr_lvl_1 <- level_names[1]
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974 fctr_lvl_2 <- level_names[2]
0
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975 feature_count <- length(ropls_x@vipVn)
1
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976 result$level1 <- rep.int(x = fctr_lvl_1, times = feature_count)
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977 result$level2 <- rep.int(x = fctr_lvl_2, times = feature_count)
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978 greaterLevel <- sapply(
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979 X = result$correlation
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980 , FUN = function(my_corr)
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981 tryCatch({
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982 if ( is.nan( my_corr ) ) {
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983 NA
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984 } else {
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985 if ( my_corr < 0 ) fctr_lvl_1 else fctr_lvl_2
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986 }
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987 }, error = function(e) {
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988 x_progress(
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989 sprintf(
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990 "cor_vs_cov -> sapply: error - substituting NA - %s"
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991 , as.character(e)
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992 )
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993 )
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994 NA
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995 })
6
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996 )
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997
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998 # begin fixes for https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/issues/1
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999 featureID <- names(ropls_x@vipVn)
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1000 greaterLevel <- greaterLevel[featureID]
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1001 result$correlation <- result$correlation[featureID]
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1002 result$covariance <- result$covariance[featureID]
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1003 # end fixes for https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/issues/1
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1004
12
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1005 # build a data frame to hold the content for the tab-separated values file
6
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1006 tsv1 <- data.frame(
12
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1007 featureID = featureID
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1008 , factorLevel1 = result$level1
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1009 , factorLevel2 = result$level2
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1010 , greaterLevel = greaterLevel
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1011 , projection = result$projection
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1012 , correlation = result$correlation
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1013 , covariance = result$covariance
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1014 , vip4p = result$vip4p
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1015 , vip4o = result$vip4o
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1016 , loadp = result$loadp
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1017 , loado = result$loado
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1018 , cor_p_val_raw = result$p_value_raw
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1019 , cor_p_value = p.adjust(p = result$p_value_raw, method = "BY")
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1020 , cor_ci_lower = result$ci_lower
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1021 , cor_ci_upper = result$ci_upper
0
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1022 )
12
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1023 rownames(tsv1) <- tsv1$featureID
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1024
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1025 # build the superresult, i.e., the result returned by this function
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1026 superresult <- list()
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1027 superresult$projection <- result$projection
0
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1028 superresult$covariance <- result$covariance
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1029 superresult$correlation <- result$correlation
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1030 superresult$vip4p <- result$vip4p
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1031 superresult$vip4o <- result$vip4o
1
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1032 superresult$loadp <- result$loadp
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1033 superresult$loado <- result$loado
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1034 superresult$cor_p_value <- tsv1$cor_p_value
0
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1035 superresult$details <- result
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1036
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1037 # remove any rows having NA for covariance or correlation
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1038 tsv1 <- tsv1[!is.na(tsv1$correlation),]
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1039 tsv1 <- tsv1[!is.na(tsv1$covariance),]
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1040 superresult$tsv1 <- tsv1
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1041
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1042 # # I did not include these but left them commentd out in case future
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1043 # # consumers of this routine want to use it in currently unanticipated ways
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1044 # result$superresult <- superresult
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1045 # result$oplsda <- ropls_x
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1046 # result$predictor <- ropls_x@suppLs$y
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1047
0
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1048 return (superresult)
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1049 }
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1050
12
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1051 # Code for correl.ci was adapted from correl function from:
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1052 # @book{
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1053 # Tsagris_2018,
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1054 # author = {Tsagris, Michail},
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1055 # year = {2018},
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1056 # link = {https://www.researchgate.net/publication/324363311_Multivariate_data_analysis_in_R},
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1057 # title = {Multivariate data analysis in R}
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1058 # }
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1059 # which follows
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1060 # https://en.wikipedia.org/wiki/Fisher_transformation#Definition
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1061
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1062 correl.ci <- function(r, n, a = 0.05, rho = 0) {
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1063 ## r is the calculated correlation coefficient for n pairs
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1064 ## a is the significance level
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1065 ## rho is the hypothesised correlation
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1066 zh0 <- atanh(rho) # 0.5*log((1+rho)/(1-rho)), i.e., Fisher's z-transformation for Ho
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1067 zh1 <- atanh(r) # 0.5*log((1+r)/(1-r)), i.e., Fisher's z-transformation for H1
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1068 se <- (1 - r^2)/sqrt(n - 3) ## standard error for Fisher's z-transformation of Ho
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1069 test <- (zh1 - zh0)/se ### test statistic
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1070 pvalue <- 2*(1 - pnorm(abs(test))) ## p-value
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1071 zL <- zh1 - qnorm(1 - a/2)*se
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1072 zH <- zh1 + qnorm(1 - a/2)*se
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1073 fishL <- tanh(zL) # (exp(2*zL)-1)/(exp(2*zL)+1), i.e., lower confidence limit
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1074 fishH <- tanh(zH) # (exp(2*zH)-1)/(exp(2*zH)+1), i.e., upper confidence limit
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1075 CI <- c(fishL, fishH)
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1076 names(CI) <- c('lower', 'upper')
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1077 list(correlation = r, p.value = pvalue, CI = CI)
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1078 }
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1079
5
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1080 # vim: sw=2 ts=2 et :