Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_calc.R @ 5:50f60f94c034 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
author eschen42
date Fri, 30 Mar 2018 14:59:19 -0400
parents 8bba31f628da
children 7bd523ca1f9a
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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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7 #### OPLS-DA
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8 algoC <- "nipals"
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9
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10 do_detail_plot <- function(x_dataMatrix, x_predictor, x_is_match, x_algorithm, x_prefix, x_show_labels, x_progress = print, x_env, x_crossval_i) {
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11 off <- function(x) if (x_show_labels == "0") 0 else x
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12 if ( x_is_match && ncol(x_dataMatrix) > 0 && length(unique(x_predictor))> 1 && x_crossval_i < nrow(x_dataMatrix) ) {
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13 my_oplsda <- opls(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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14 x = x_dataMatrix
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15 , y = x_predictor
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16 , algoC = x_algorithm
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17 , predI = 1
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18 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0
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19 , printL = FALSE
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20 , plotL = FALSE
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21 , crossvalI = x_crossval_i
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22 )
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23 my_oplsda_suppLs_y_levels <- levels(as.factor(my_oplsda@suppLs$y))
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24 fctr_lvl_1 <- my_oplsda_suppLs_y_levels[1]
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25 fctr_lvl_2 <- my_oplsda_suppLs_y_levels[2]
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26 do_s_plot <- function(parallel_x) {
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27 my_cor_vs_cov <- cor_vs_cov(
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28 matrix_x = x_dataMatrix
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29 , ropls_x = my_oplsda
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30 , parallel_x = parallel_x
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31 )
5
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32 with(
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33 my_cor_vs_cov
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34 , {
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35 min_x <- min(covariance)
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36 max_x <- max(covariance)
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37 lim_x <- max(sapply(X=c(min_x, max_x), FUN=abs))
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38 covariance <- covariance / lim_x
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39 lim_x <- 1.2
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40 # "It is generally accepted that a variable should be selected if vj>1, [27–29],
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41 # but a proper threshold between 0.83 and 1.21 can yield more relevant variables according to [28]."
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42 # (Mehmood 2012 doi:10.1186/1748-7188-6-27)
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43 plus_cor <- correlation
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44 plus_cov <- covariance
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45 cex <- 0.75
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46 which_projection <- if (projection == 1) "t1" else "o1"
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47 which_loading <- if (projection == 1) "parallel" else "orthogonal"
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48 if (projection == 1) {
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49 my_xlab <- "relative covariance(feature,t1)"
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50 my_x <- plus_cov
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51 my_ylab <- "correlation(feature,t1) [~ parallel loading]"
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52 my_y <- plus_cor
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53 my_xlim <- c( -lim_x - off(0.2), lim_x + off(0.2) )
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54 my_ylim <- c( -1.0 - off(0.2), 1.0 + off(0.2) )
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55 my_load_distal <- loadp
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56 my_load_proximal <- loado
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57 vipcp <- pmax(0, pmin(1,(vip4p-0.83)/(1.21-0.83)))
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58 red <- as.numeric(correlation > 0) * vipcp
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59 blue <- as.numeric(correlation < 0) * vipcp
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60 alpha <- 0.1 + 0.4 * vipcp
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61 my_col = rgb(blue = blue, red = red, green = 0, alpha = alpha)
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62 main_label <- sprintf("%s for level %s versus %s", x_prefix, fctr_lvl_1, fctr_lvl_2)
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63 } else {
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64 my_xlab <- "relative covariance(feature,to1)"
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65 my_x <- -plus_cov
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66 my_xlim <- c( -lim_x - off(0.2), lim_x + off(0.2) )
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67 my_ylab <- "correlation(feature,to1) [~ orthogonal loading]"
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68 my_y <- plus_cor
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69 my_ylim <- c( -1.0 - off(0.2), 1.0 + off(0.2) )
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70 my_load_distal <- loado
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71 my_load_proximal <- loadp
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72 vipco <- pmax(0, pmin(1,(vip4o-0.83)/(1.21-0.83)))
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73 alpha <- 0.1 + 0.4 * vipco
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74 my_col = rgb(blue = 0, red = 0, green = 0, alpha = alpha)
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75 main_label <- sprintf("Features influencing orthogonal projection for level %s versus %s", fctr_lvl_1, fctr_lvl_2)
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76 }
5
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77 main_cex <- min(1.0, 46.0/nchar(main_label))
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78 my_feature_label_slant <- -30 # slant feature labels 30 degrees downward
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79 plot(
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80 y = my_y
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81 , x = my_x
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82 , type = "p"
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83 , xlim = my_xlim
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84 , ylim = my_ylim
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85 , xlab = my_xlab
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86 , ylab = my_ylab
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87 , main = main_label
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88 , cex.main = main_cex
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89 , cex = cex
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90 , pch = 16
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91 , col = my_col
1
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92 )
5
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93 low_x <- -0.7 * lim_x
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94 high_x <- 0.7 * lim_x
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95 if (projection == 1) {
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96 text(x = low_x, y = -0.05, labels = fctr_lvl_1, col = "blue")
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97 text(x = high_x, y = 0.05, labels = fctr_lvl_2, col = "red")
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98 }
5
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99 if ( x_show_labels != "0" ) {
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100 names(my_load_distal) <- tsv1$featureID
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101 names(my_load_proximal) <- tsv1$featureID
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102 if ( x_show_labels == "ALL" ) {
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103 n_labels <- length(my_load_distal)
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104 } else {
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105 n_labels <- as.numeric(x_show_labels)
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106 }
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107 n_labels <- min( n_labels, (1 + length(my_load_distal)) / 2 )
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108 labels_to_show <- c(
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109 names(head(sort(my_load_distal),n = n_labels))
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110 , names(tail(sort(my_load_distal),n = n_labels))
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111 )
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112 labels <- unname(sapply( X = tsv1$featureID, FUN = function(x) if( x %in% labels_to_show ) x else "" ))
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113 x_text_offset <- 0.024
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114 y_text_offset <- (if (projection == 1) 1 else -1) * -0.017
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115 label_features <- function(x_arg, y_arg, labels_arg, slant_arg) {
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116 print("str(x_arg)")
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117 print(str(x_arg))
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118 print("str(y_arg)")
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119 print(str(y_arg))
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120 print("str(labels_arg)")
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121 print(str(labels_arg))
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122 text(
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123 y = y_arg
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124 , x = x_arg + x_text_offset
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125 , cex = 0.4
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126 , labels = labels_arg
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127 , col = rgb(blue = 0, red = 0, green = 0, alpha = 0.5) # grey semi-transparent labels
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128 , srt = slant_arg
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129 , adj = 0 # left-justified
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130 )
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131 }
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132 my_slant <- (if (projection == 1) 1 else -1) * my_feature_label_slant
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133 if (length(my_x) > 1) {
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134 label_features(
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135 x_arg = my_x [my_x > 0]
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136 , y_arg = my_y [my_x > 0] - y_text_offset
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137 , labels_arg = labels[my_x > 0]
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138 , slant_arg = -my_slant
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139 )
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140 label_features(
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141 x_arg = my_x [my_x < 0]
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142 , y_arg = my_y [my_x < 0] + y_text_offset
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143 , labels_arg = labels[my_x < 0]
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144 , slant_arg = my_slant
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145 )
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146 } else {
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147 label_features(
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148 x_arg = my_x
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149 , y_arg = my_y + (if (my_x > 1) -1 else 1) * y_text_offset
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150 , labels_arg = labels
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151 , slant_arg = (if (my_x > 1) -1 else 1) * my_slant
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152 )
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153 }
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154 }
0
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155 }
5
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156 )
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157 return (my_cor_vs_cov)
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158 }
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159 my_cor_vs_cov <- do_s_plot( parallel_x = TRUE )
0
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160 typeVc <- c("correlation", # 1
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161 "outlier", # 2
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162 "overview", # 3
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163 "permutation", # 4
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164 "predict-train", # 5
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165 "predict-test", # 6
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166 "summary", # 7 = c(2,3,4,9)
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167 "x-loading", # 8
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168 "x-score", # 9
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169 "x-variance", # 10
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170 "xy-score", # 11
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171 "xy-weight" # 12
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172 ) # [c(3,8,9)] # [c(4,3,8,9)]
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173 if ( length(my_oplsda@orthoVipVn) > 0 ) {
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174 my_typevc <- typeVc[c(9,3,8)]
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175 } else {
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176 my_typevc <- c("(dummy)","overview","(dummy)")
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177 }
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178 for (my_type in my_typevc) {
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179 if (my_type %in% typeVc) {
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180 tryCatch({
5
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181 if ( my_type != "x-loading" ) {
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182 plot(
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183 x = my_oplsda
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184 , typeVc = my_type
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185 , parCexN = 0.4
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186 , parDevNewL = FALSE
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187 , parLayL = TRUE
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188 , parEllipsesL = TRUE
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189 )
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190 } else {
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191 do_s_plot( parallel_x = FALSE )
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192 }
4
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193 }, error = function(e) {
5
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194 x_progress( sprintf( "factor level %s or %s may have only one sample - %s", fctr_lvl_1, fctr_lvl_2, e$message ) )
4
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195 })
0
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196 } else {
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197 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")
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198 text(x=1, y=1, labels="no orthogonal projection is possible")
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199 }
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200 }
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201 return (my_cor_vs_cov)
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202 } else {
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203 return (NULL)
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204 }
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205 }
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206
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207 # S-PLOT and OPLS reference: Wiklund_2008 doi:10.1021/ac0713510
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208 corcov_calc <- function(calc_env, failure_action = stop, progress_action = function(x){}, corcov_tsv_action = function(t){}, salience_tsv_action = function(t){}) {
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209 if ( ! is.environment(calc_env) ) {
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210 failure_action("corcov_calc: fatal error - 'calc_env' is not an environment")
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211 return ( FALSE )
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212 }
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213 if ( ! is.function(corcov_tsv_action) ) {
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214 failure_action("corcov_calc: fatal error - 'corcov_tsv_action' is not a function")
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215 return ( FALSE )
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216 }
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217 if ( ! is.function(salience_tsv_action) ) {
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218 failure_action("salience_calc: fatal error - 'salience_tsv_action' is not a function")
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219 return ( FALSE )
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220 }
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221
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222 # extract parameters from the environment
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223 vrbl_metadata <- calc_env$vrbl_metadata
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224 vrbl_metadata_names <- vrbl_metadata[,1]
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225 smpl_metadata <- calc_env$smpl_metadata
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226 data_matrix <- calc_env$data_matrix
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227 pairSigFeatOnly <- calc_env$pairSigFeatOnly
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228 facC <- calc_env$facC
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229 tesC <- calc_env$tesC
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230 # extract the levels from the environment
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231 originalLevCSV <- levCSV <- calc_env$levCSV
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232 # matchingC is one of { "none", "wildcard", "regex" }
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233 matchingC <- calc_env$matchingC
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234 labelFeatures <- calc_env$labelFeatures
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235
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236 # arg/env checking
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237 if (!(facC %in% names(smpl_metadata))) {
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238 failure_action(sprintf("bad parameter! Factor name '%s' not found in sampleMetadata", facC))
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239 return ( FALSE )
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240 }
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241
1
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242 mz <- vrbl_metadata$mz
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243 names(mz) <- vrbl_metadata$variableMetadata
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244 mz_lookup <- function(feature) unname(mz[feature])
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245
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246 rt <- vrbl_metadata$rt
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247 names(rt) <- vrbl_metadata$variableMetadata
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248 rt_lookup <- function(feature) unname(rt[feature])
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249
0
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250 # calculate salience_df as data.frame(feature, max_level, max_median, max_rcv, mean_median, salience, salient_rcv)
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251 salience_df <- calc_env$salience_df <- w4msalience(
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252 data_matrix = data_matrix
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253 , sample_class = smpl_metadata[,facC]
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254 , failure_action = failure_action
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255 )
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256 salience_tsv_action({
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257 my_df <- data.frame(
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258 featureID = salience_df$feature
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259 , salientLevel = salience_df$max_level
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260 , salientRCV = salience_df$salient_rcv
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261 , salience = salience_df$salience
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262 , mz = mz_lookup(salience_df$feature)
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263 , rt = rt_lookup(salience_df$feature)
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264 )
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265 my_df[order(-my_df$salience),]
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266 })
1
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267
0
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268 # transform wildcards to regexen
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269 if (matchingC == "wildcard") {
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270 # strsplit(x = "hello,wild,world", split = ",")
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271 levCSV <- gsub("[.]", "[.]", levCSV)
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272 levCSV <- strsplit(x = levCSV, split = ",")
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273 levCSV <- sapply(levCSV, utils::glob2rx, trim.tail = FALSE)
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274 levCSV <- paste(levCSV, collapse = ",")
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275 }
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276 # function to determine whether level is a member of levCSV
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277 isLevelSelected <- function(lvl) {
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278 matchFun <- if (matchingC != "none") grepl else `==`
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279 return(
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280 Reduce(
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281 f = "||"
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282 , x = sapply(
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283 X = strsplit(
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284 x = levCSV
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285 , split = ","
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286 , fixed = TRUE
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287 )[[1]]
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288 , FUN = matchFun
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289 , lvl
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290 )
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291 )
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292 )
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293 }
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294
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295 # transpose matrix because ropls matrix is the transpose of XCMS matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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296 # Wiklund_2008 centers and pareto-scales data before OPLS-DA S-plot
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297 # center
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298 cdm <- center_colmeans(t(data_matrix))
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299 # pareto-scale
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300 my_scale <- sqrt(apply(cdm, 2, sd, na.rm=TRUE))
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301 scdm <- sweep(cdm, 2, my_scale, "/")
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302
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303 # pattern to match column names like k10_kruskal_k4.k3_sig
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304 col_pattern <- sprintf('^%s_%s_(.*)[.](.*)_sig$', facC, tesC)
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305 # column name like k10_kruskal_sig
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306 intersample_sig_col <- sprintf('%s_%s_sig', facC, tesC)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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307 # get the facC column from sampleMetadata, dropping to one dimension
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308 smpl_metadata_facC <- smpl_metadata[,facC]
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309
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310 # allocate a slot in the environment for the contrast_list, each element of which will be a data.frame with this structure:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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311 # - feature ID
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312 # - value1
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313 # - value2
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314 # - Wiklund_2008 correlation
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315 # - Wiklund_2008 covariance
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316 # - Wiklund_2008 VIP
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317 calc_env$contrast_list <- list()
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318
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319
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320 did_plot <- FALSE
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321 if (tesC != "none") {
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322 # for each column name, extract the parts of the name matched by 'col_pattern', if any
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323 the_colnames <- colnames(vrbl_metadata)
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324 if ( ! Reduce( f = "||", x = grepl(tesC, the_colnames) ) ) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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325 failure_action(sprintf("bad parameter! variableMetadata must contain results of W4M Univariate test '%s'.", tesC))
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326 return ( FALSE )
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327 }
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328 col_matches <- lapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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329 X = the_colnames,
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330 FUN = function(x) {
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331 regmatches( x, regexec(col_pattern, x) )[[1]]
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332 }
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333 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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334 ## 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
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335 # process columns matching the pattern
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336 level_union <- c()
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337 for (i in 1:length(col_matches)) {
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338 col_match <- col_matches[[i]]
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339 if (length(col_match) > 0) {
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340 # 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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341 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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342 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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343 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
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344 # 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
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345 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
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346 if (is_match) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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347 level_union <- c(level_union, col_match[2], col_match[3])
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348 }
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349 }
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350 }
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351 level_union <- unique(sort(level_union))
1
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352 overall_significant <- 1 == ( if (intersample_sig_col %in% colnames(vrbl_metadata)) vrbl_metadata[,intersample_sig_col] else TRUE )
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353 if ( length(level_union) > 2 ) {
0
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354 chosen_samples <- smpl_metadata_facC %in% level_union
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355 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
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356 col_selector <- vrbl_metadata_names[ overall_significant ]
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357 my_matrix <- scdm[ chosen_samples, col_selector, drop = FALSE ]
1
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358 plot_action <- function(fctr_lvl_1, fctr_lvl_2) {
0
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359 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
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360 predictor <- sapply( X = chosen_facC, FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2 )
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361 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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362 x_dataMatrix = my_matrix
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363 , x_predictor = predictor
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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364 , x_is_match = is_match
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365 , x_algorithm = algoC
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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366 , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features"
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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367 , x_show_labels = labelFeatures
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368 , x_progress = progress_action
4
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369 , x_crossval_i = min(7, length(chosen_samples))
0
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370 , x_env = calc_env
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371 )
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372 if ( is.null(my_cor_cov) ) {
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373 progress_action("NOTHING TO PLOT.")
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374 } else {
1
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375 my_tsv <- my_cor_cov$tsv1
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376 my_tsv$mz <- mz_lookup(my_tsv$featureID)
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377 my_tsv$rt <- rt_lookup(my_tsv$featureID)
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378 my_tsv["level1Level2Sig"] <- vrbl_metadata[ match(my_tsv$featureID, vrbl_metadata_names), vrbl_metadata_col ]
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379 tsv <<- my_tsv
0
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380 corcov_tsv_action(tsv)
1
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381 did_plot <<- TRUE
0
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382 }
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383 }
1
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384 if ( length(level_union) != 2 ) {
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385 fctr_lvl_2 <- "other"
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386 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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387 plot_action(fctr_lvl_1, fctr_lvl_2)
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388 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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389 } else {
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390 plot_action(fctr_lvl_1 = level_union[1], fctr_lvl_2 = level_union[2])
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391 }
0
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392 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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393
1
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394 if ( length(level_union) > 1 ) {
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395 ## 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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396 # process columns matching the pattern
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397 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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398 # for each potential match of the pattern
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399 col_match <- col_matches[[i]]
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400 if (length(col_match) > 0) {
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401 # 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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402 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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403 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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404 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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405 # 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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406 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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407 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", 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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408 # choose only samples with one of the two factors for this column
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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409 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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410 predictor <- smpl_metadata_facC[chosen_samples]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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411 # extract only the significantly-varying features and the chosen samples
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412 fully_significant <- 1 == vrbl_metadata[,vrbl_metadata_col] * ( if (intersample_sig_col %in% colnames(vrbl_metadata)) vrbl_metadata[,intersample_sig_col] else TRUE )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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413 col_selector <- vrbl_metadata_names[ if ( pairSigFeatOnly ) fully_significant else overall_significant ]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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414 my_matrix <- scdm[ chosen_samples, col_selector, drop = FALSE ]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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415 my_cor_cov <- do_detail_plot(
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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416 x_dataMatrix = my_matrix
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417 , x_predictor = predictor
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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418 , x_is_match = is_match
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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419 , x_algorithm = algoC
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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420 , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features"
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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421 , x_show_labels = labelFeatures
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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422 , x_progress = progress_action
4
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423 , x_crossval_i = min(7, length(chosen_samples))
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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424 , x_env = calc_env
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425 )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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426 if ( is.null(my_cor_cov) ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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427 progress_action("NOTHING TO PLOT.")
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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428 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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429 tsv <- my_cor_cov$tsv1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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430 tsv$mz <- mz_lookup(tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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431 tsv$rt <- rt_lookup(tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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432 tsv["level1Level2Sig"] <- vrbl_metadata[ match(tsv$featureID, vrbl_metadata_names), vrbl_metadata_col ]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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433 corcov_tsv_action(tsv)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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434 did_plot <- TRUE
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
435 }
0
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436 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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437 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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438 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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439 } else { # tesC == "none"
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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440 level_union <- unique(sort(smpl_metadata_facC))
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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441 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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442 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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443 ## 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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444 completed <- c()
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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445 lapply(
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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446 X = level_union
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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447 , FUN = function(x) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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448 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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449 fctr_lvl_2 <- {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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450 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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451 return("DUMMY")
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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452 # strF(completed)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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453 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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454 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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455 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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456 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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457 fctr_lvl_2 <- "other"
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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458 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", 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
459 if (length(unique(chosen_samples)) < 1) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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460 progress_action("NOTHING TO PLOT...")
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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461 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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462 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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463 predictor <- sapply( X = chosen_facC, FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2 )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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464 my_matrix <- scdm[ chosen_samples, , drop = FALSE ]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
465 # 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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466 is_match <- isLevelSelected(fctr_lvl_1)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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467 my_cor_cov <- do_detail_plot(
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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468 x_dataMatrix = my_matrix
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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469 , x_predictor = predictor
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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470 , x_is_match = is_match
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
471 , x_algorithm = algoC
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
472 , x_prefix = "Features"
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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473 , x_show_labels = labelFeatures
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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474 , x_progress = progress_action
4
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475 , x_crossval_i = min(7, length(chosen_samples))
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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476 , x_env = calc_env
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
477 )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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478 if ( is.null(my_cor_cov) ) {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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479 progress_action("NOTHING TO PLOT")
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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480 } else {
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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481 tsv <- my_cor_cov$tsv1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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482 tsv$mz <- mz_lookup(tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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483 tsv$rt <- rt_lookup(tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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484 corcov_tsv_action(tsv)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
485 did_plot <<- TRUE
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
486 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
487 }
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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488 "dummy" # need to return a value; otherwise combn fails with an error
0
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489 }
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
490 )
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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491 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
492 ## 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
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493 completed <- c()
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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494 utils::combn(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
495 x = level_union
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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496 , m = 2
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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497 , FUN = function(x) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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498 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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499 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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500 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
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501 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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502 if (length(unique(chosen_samples)) < 1) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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503 progress_action("NOTHING TO PLOT...")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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504 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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505 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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506 predictor <- chosen_facC
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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507 my_matrix <- scdm[ chosen_samples, , drop = FALSE ]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
508 # 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
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509 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
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510 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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511 x_dataMatrix = my_matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
512 , x_predictor = predictor
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
513 , x_is_match = is_match
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
514 , x_algorithm = algoC
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_prefix = "Features"
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
516 , x_show_labels = labelFeatures
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
517 , 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
518 , 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
eschen42
parents:
diff changeset
519 , x_env = calc_env
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
520 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
521 if ( is.null(my_cor_cov) ) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
522 progress_action("NOTHING TO PLOT")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
523 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
524 tsv <- my_cor_cov$tsv1
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
525 tsv$mz <- mz_lookup(tsv$featureID)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
526 tsv$rt <- rt_lookup(tsv$featureID)
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
527 corcov_tsv_action(tsv)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
528 did_plot <<- TRUE
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
529 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
530 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
531 "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
eschen42
parents:
diff changeset
532 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
533 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
534 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
535 progress_action("NOTHING TO PLOT....")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
536 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
537 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
538 if (!did_plot) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
539 failure_action(sprintf("bad parameter! sampleMetadata must have at least two levels of factor '%s' matching '%s'", facC, originalLevCSV))
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
540 return ( FALSE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
541 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
542 return ( TRUE )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
543 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
544
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
545 # 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
546 # Adapted from:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
547 # 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
548 # 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
549 # https://github.com/HegemanLab/extra_tools/blob/master/generic_PCA.R
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
550 cor_vs_cov <- function(matrix_x, ropls_x, parallel_x = TRUE) {
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
551 x_class <- class(ropls_x)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
552 if ( !( as.character(x_class) == "opls" ) ) { # || !( attr(class(x_class),"package") == "ropls" ) )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
553 stop( "cor_vs_cov: Expected ropls_x to be of class ropls::opls but instead it was of class ", as.character(x_class) )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
554 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
555 result <- list()
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
diff changeset
556 result$projection <- projection <- if (parallel_x) 1 else 2
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
557 # suppLs$algoC - Character: algorithm used - "svd" for singular value decomposition; "nipals" for NIPALS
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
558 if ( ropls_x@suppLs$algoC == "nipals") {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
559 # Equations (1) and (2) from *Supplement to* 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
560 mag <- function(one_dimensional) sqrt(sum(one_dimensional * one_dimensional))
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
561 mag_xi <- sapply(X = 1:ncol(matrix_x), FUN = function(x) mag(matrix_x[,x]))
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
562 if (parallel_x)
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
563 score_matrix <- ropls_x@scoreMN
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
564 else
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
565 score_matrix <- ropls_x@orthoScoreMN
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
566 score_matrix_transposed <- t(score_matrix)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
567 score_matrix_magnitude <- mag(score_matrix)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
568 result$covariance <- score_matrix_transposed %*% matrix_x / ( score_matrix_magnitude * score_matrix_magnitude )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
569 result$correlation <- score_matrix_transposed %*% matrix_x / ( score_matrix_magnitude * mag_xi )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
570 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
571 # WARNING - untested code - I don't have test data to exercise this branch
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
572 # Equations (1) and (2) from Wiklund 2008, doi:10.1021/ac0713510
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
573 # scoreMN - Numerical matrix of x scores (T; dimensions: nrow(x) x predI) X = TP' + E; Y = TC' + F
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
574 if (parallel_x)
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
575 score_matrix <- ropls_x@scoreMN
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
576 else
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
eschen42
parents: 4
diff changeset
577 score_matrix <- ropls_x@orthoScoreMN
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
578 score_matrix_transposed <- t(score_matrix)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
579 cov_divisor <- nrow(matrix_x) - 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
580 result$covariance <- sapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
581 X = 1:ncol(matrix_x)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
582 , FUN = function(x) score_matrix_transposed %*% matrix_x[,x] / cov_divisor
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
583 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
584 score_sd <- sapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
585 X = 1:ncol(score_matrix)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
586 , FUN = function(x) sd(score_matrix[,x])
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
587 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
588 # xSdVn - Numerical vector: variable standard deviations of the 'x' matrix
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
589 xSdVn <- ropls_x@xSdVn
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
590 result$correlation <- sapply(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
591 X = 1:ncol(matrix_x)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
592 , FUN = function(x) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
593 ( score_matrix_transposed / score_sd ) %*% ( matrix_x[,x] / (xSdVn[x] * cov_divisor) )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
594 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
595 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
596 }
5
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597 result$correlation <- result$correlation[ 1, , drop = TRUE ]
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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598 result$covariance <- result$covariance [ 1, , drop = TRUE ]
0
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599
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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600 # Variant 4 of Variable Influence on Projection for OPLS from Galindo_Prieto_2014
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601 # Length = number of features; labels = feature identifiers. (The same is true for $correlation and $covariance.)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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602 result$vip4p <- as.numeric(ropls_x@vipVn)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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603 result$vip4o <- as.numeric(ropls_x@orthoVipVn)
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604 result$loadp <- as.numeric(ropls_x@loadingMN)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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605 result$loado <- as.numeric(ropls_x@orthoLoadingMN)
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23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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606 # get the level names
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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607 level_names <- sort(levels(as.factor(ropls_x@suppLs$y)))
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0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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608 fctr_lvl_1 <- level_names[1]
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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609 fctr_lvl_2 <- level_names[2]
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23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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610 feature_count <- length(ropls_x@vipVn)
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611 result$level1 <- rep.int(x = fctr_lvl_1, times = feature_count)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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612 result$level2 <- rep.int(x = fctr_lvl_2, times = feature_count)
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23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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613 superresult <- list()
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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614 if (length(result$vip4o) == 0) result$vip4o <- NA
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615 greaterLevel <- sapply( X = result$correlation, FUN = function(my_corr) if ( my_corr < 0 ) fctr_lvl_1 else fctr_lvl_2 )
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23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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616 superresult$tsv1 <- data.frame(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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617 featureID = names(ropls_x@vipVn)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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618 , factorLevel1 = result$level1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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619 , factorLevel2 = result$level2
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620 , greaterLevel = greaterLevel
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621 , projection = result$projection
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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622 , correlation = result$correlation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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623 , covariance = result$covariance
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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624 , vip4p = result$vip4p
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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625 , vip4o = result$vip4o
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626 , loadp = result$loadp
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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627 , loado = result$loado
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23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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628 , row.names = NULL
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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629 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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630 rownames(superresult$tsv1) <- superresult$tsv1$featureID
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631 superresult$projection <- result$projection
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632 superresult$covariance <- result$covariance
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633 superresult$correlation <- result$correlation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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634 superresult$vip4p <- result$vip4p
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635 superresult$vip4o <- result$vip4o
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636 superresult$loadp <- result$loadp
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637 superresult$loado <- result$loado
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638 superresult$details <- result
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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639 result$superresult <- superresult
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640 # Include thise in case future consumers of this routine want to use it in currently unanticipated ways
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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641 result$oplsda <- ropls_x
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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642 result$predictor <- ropls_x@suppLs$y # in case future consumers of this routine want to use it in currently unanticipated ways
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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643 return (superresult)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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644 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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645
5
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646 # vim: sw=2 ts=2 et :