Mercurial > repos > galaxyp > cardinal_classification

annotate classification.xml @ 16:eddc2ae2db80 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
author galaxyp
date Sun, 29 Aug 2021 07:26:30 +0000
parents f28ad96b76dc
children 4c177985028a
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eddc2ae2db80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
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1 <tool id="cardinal_classification" name="MSI classification" version="@VERSION@.0">
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2 <description>spatial classification of mass spectrometry imaging data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.3">r-gridextra</requirement>
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eddc2ae2db80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
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8 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
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9 </expand>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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13 @INPUT_LINKING@
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14 cat '${MSI_segmentation}' &&
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15 Rscript '${MSI_segmentation}'
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="MSI_segmentation"><![CDATA[
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23 ################################# load libraries and read file #########################
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25 library(Cardinal)
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26 library(gridExtra)
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27 library(ggplot2)
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28 library(scales)
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30 @READING_MSIDATA@
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32 msidata = as(msidata, "MSImageSet") ##coercion to MSImageSet
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35 ## remove duplicated coordinates
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36 msidata <- msidata[,!duplicated(coord(msidata))]
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38 @DATA_PROPERTIES_INRAM@
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41 ######################################## PDF ###################################
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42 ################################################################################
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43 ################################################################################
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45 Title = "Prediction"
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47 #if str( $type_cond.type_method) == "training":
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49 Title = "$type_cond.method_cond.class_method"
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50 #end if
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52 pdf("classificationpdf.pdf", fonts = "Times", pointsize = 12)
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53 plot(0,type='n',axes=FALSE,ann=FALSE)
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56 title(main=paste0(Title," for file: \n\n", "$infile.display_name"))
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59 ##################### I) numbers and control plots #############################
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60 ################################################################################
0
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62 ## table with values
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63 grid.table(property_df, rows= NULL)
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66 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){
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68 opar <- par()
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69
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70 ######################## II) Training #######################################
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71 #############################################################################
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72 #if str( $type_cond.type_method) == "training":
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73 print("training")
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76 ## load y response (will be needed in every training scenario)
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78 y_tabular = read.delim("$type_cond.annotation_file", header = $type_cond.tabular_header, stringsAsFactors = FALSE)
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80 #if str($type_cond.column_fold) == "None":
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81 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response)]
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82 #else
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83 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response, $type_cond.column_fold)]
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84 #end if
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85
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86 colnames(y_input)[1:2] = c("x", "y")
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87 ## merge with coordinate information of msidata
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88 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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89 colnames(msidata_coordinates)[3] = "pixel_index"
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90 merged_response = merge(msidata_coordinates, y_input, by=c("x", "y"), all.x=TRUE)
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91 merged_response[is.na(merged_response)] = "NA"
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92 merged_response = merged_response[order(merged_response\$pixel_index),]
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93 conditions = as.factor(merged_response[,4])
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94 y_vector = conditions
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95
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96 ## colours selection:
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97
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98 #if str($colour_conditional.colour_type) == "manual_colour"
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99 #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $colour_conditional.colours])
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100 colourvector = c($color_string)
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101
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102 #elif str($colour_conditional.colour_type) == "colourpalette"
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103 number_levels = (length(levels(conditions)))
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104 colourvector = noquote($colour_conditional.palettes)(number_levels)
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105
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106 #end if
0
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107
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108 ## plot of y vector
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109
14
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110 position_df = cbind(coord(msidata)[,1:2], conditions)
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111 y_plot = ggplot(position_df, aes(x=x, y=y, fill=conditions))+
0
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112 geom_tile() +
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113 coord_fixed()+
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114 ggtitle("Distribution of the conditions")+
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115 theme_bw()+
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116 theme(
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117 plot.background = element_blank(),
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118 panel.grid.major = element_blank(),
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119 panel.grid.minor = element_blank())+
0
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120 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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121 theme(legend.position="bottom",legend.direction="vertical")+
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122 guides(fill=guide_legend(ncol=4,byrow=TRUE))+
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123 scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)
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124 coord_labels = aggregate(cbind(x,y)~conditions, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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125 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$conditions)
0
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126 print(y_plot)
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127
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128
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129 ## plot of folds
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130
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131 #if str($type_cond.column_fold) != "None":
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132 fold_vector = as.factor(merged_response[,5])
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133
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134
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135 position_df = cbind(coord(msidata)[,1:2], fold_vector)
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136 fold_plot = ggplot(position_df, aes(x=x, y=y, fill=fold_vector))+
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137 geom_tile() +
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138 coord_fixed()+
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139 ggtitle("Distribution of the fold variable")+
14
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140 theme_bw()+
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141 theme(
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142 plot.background = element_blank(),
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143 panel.grid.major = element_blank(),
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144 panel.grid.minor = element_blank())+
0
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145 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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146 theme(legend.position="bottom",legend.direction="vertical")+
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147 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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148 coord_labels = aggregate(cbind(x,y)~fold_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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149 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$fold_vector)
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150 print(fold_plot)
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151
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152 #end if
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153
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154 ######################## PLS #############################
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155 #if str( $type_cond.method_cond.class_method) == "PLS":
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156 print("PLS")
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157
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158 ######################## PLS - CV #############################
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159 #if str( $type_cond.method_cond.analysis_cond.PLS_method) == "cvapply":
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160 print("PLS cv")
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161
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162 ## set variables for components and number of response groups
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163 components = c($type_cond.method_cond.analysis_cond.plscv_comp)
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164 number_groups = length(levels(y_vector))
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165
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166 ## PLS-cvApply:
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167 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)
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168
2
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169 ## remove msidata to clean up RAM space
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170 rm(msidata)
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171 gc()
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172
0
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173 ## create table with summary
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174 count = 1
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175 summary_plscv = list()
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176 accuracy_vector = numeric()
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177 for (iteration in components){
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178 summary_iteration = summary(msidata.cv.pls)\$accuracy[[paste0("ncomp = ", iteration)]]
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179 ## change class of numbers into numeric to round and calculate mean
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180 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
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181 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
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182 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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183 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
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184 summary_iteration4 = t(summary_iteration3)
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185 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
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186 summary_plscv[[count]] = summary_iteration5
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187 count = count+1} ## create list with summary table for each component
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188 summary_plscv = do.call(rbind, summary_plscv)
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189 summary_df = as.data.frame(summary_plscv)
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190 colnames(summary_df) = NULL
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191
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192 ## plots
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193 ## plot to find ncomp with highest accuracy
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194 plot(components, accuracy_vector, ylab = "mean accuracy",type="o", main="Mean accuracy of PLS classification")
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195 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
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196 ## one image for each sample/fold, 4 images per page
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197 minimumy = min(coord(msidata.cv.pls)[,2])
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198 maximumy = max(coord(msidata.cv.pls)[,2])
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f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
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199 image(msidata.cv.pls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(1, 1), col=colourvector)
0
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200
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201 ## print table with summary in pdf
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202 par(opar)
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203 plot(0,type='n',axes=FALSE,ann=FALSE)
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204 title(main="Summary for the different components\n", adj=0.5)
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205 ## 20 rows fits in one page:
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206 if (nrow(summary_df)<=20){
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207 grid.table(summary_df, rows= NULL)
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208 }else{
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209 grid.table(summary_df[1:20,], rows= NULL)
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210 mincount = 21
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211 maxcount = 40
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212 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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213 plot(0,type='n',axes=FALSE,ann=FALSE)
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214 if (maxcount <= nrow(summary_df)){
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215 grid.table(summary_df[mincount:maxcount,], rows= NULL)
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216 mincount = mincount+20
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217 maxcount = maxcount+20
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218 }else{### stop last page with last sample otherwise NA in table
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219 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
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220 }
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221 }
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222
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223 ## optional output as .RData
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224 #if $output_rdata:
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225 save(msidata.cv.pls, file="$classification_rdata")
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226 #end if
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227
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228
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229 ######################## PLS - analysis ###########################
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230 #elif str( $type_cond.method_cond.analysis_cond.PLS_method) == "PLS_analysis":
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231 print("PLS analysis")
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232
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233 ## set variables for components and number of response groups
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234 component = c($type_cond.method_cond.analysis_cond.pls_comp)
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235 number_groups = length(levels(y_vector))
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236
4
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237 ### stop if multiple values for PLS components are selected what sets component to 0
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238 tryCatch(
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239 {
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240
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241 if (component==0)
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242 {
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243 stop(call.=FALSE)
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244 }
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245 },
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246 error=function(cond) {
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247 ## in case user used multiple inputs for component - this is only possible in cv apply
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248 message("Error during PLS training")
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249 message("Possible problems: Multiple values for component were selected - this is only possible in cvapply but not for PLS analysis or component was set to 0 but minimum for component is 1)")
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250 stop(call.=FALSE)
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251 }
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252 )
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253
0
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254 ### pls analysis and coefficients plot
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255 msidata.pls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.analysis_cond.pls_scale)
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256 plot(msidata.pls, main="PLS coefficients per m/z", col=colourvector)
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257
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258 ### summary table of PLS
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259 summary_table = summary(msidata.pls)\$accuracy[[paste0("ncomp = ",component)]]
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260 summary_table2 = round(as.numeric(summary_table), digits=2)
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261 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
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262 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
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263 summary_table4 = t(summary_table3)
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264 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
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265 plot(0,type='n',axes=FALSE,ann=FALSE)
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266 grid.table(summary_table5, rows= NULL)
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267
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268 ### image of the best m/z
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269 minimumy = min(coord(msidata)[,2])
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270 maximumy = max(coord(msidata)[,2])
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271 print(image(msidata, mz = topFeatures(msidata.pls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), smooth.image="gaussian", main="best m/z heatmap"))
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272
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273 ### m/z and pixel information output
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274 pls_classes = data.frame(msidata.pls\$classes[[1]])
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275 ## pixel names and coordinates
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276 ## to remove potential sample names and z dimension, split at comma and take only x and y
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277 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
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278 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
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279 x_coordinates = gsub("x = ","",x_coords)
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280 y_coordinates = gsub(" y = ","",y_coords)
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281 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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282
2
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283 ## remove msidata to clean up RAM space
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284 rm(msidata)
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285 gc()
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286 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)
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287 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")
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288 pls_toplabels = topFeatures(msidata.pls, n=Inf)
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289 pls_toplabels[,4:6] <-round(pls_toplabels[,4:6],6)
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290 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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291 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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292
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293 ## image with predicted classes
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294 prediction_df = cbind(coord(msidata.pls)[,1:2], pls_classes)
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295 colnames(prediction_df) = c("x", "y", "predicted_classes")
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296
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297 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
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298 geom_tile() +
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299 coord_fixed()+
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300 ggtitle("Predicted condition for each pixel")+
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301 theme_bw()+
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302 theme(
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303 plot.background = element_blank(),
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304 panel.grid.major = element_blank(),
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305 panel.grid.minor = element_blank())+
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306 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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307 theme(legend.position="bottom",legend.direction="vertical")+
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308 guides(fill=guide_legend(ncol=4,byrow=TRUE))+
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309 scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)
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310 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
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311 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
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312 print(prediction_plot)
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313
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314 ### optional output as .RData
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315 #if $output_rdata:
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316 save(msidata.pls, file="$classification_rdata")
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317 #end if
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318
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319 #end if
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320
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321 ######################## OPLS #############################
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322 #elif str( $type_cond.method_cond.class_method) == "OPLS":
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323 print("OPLS")
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324
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325 ######################## OPLS -CV #############################
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326 #if str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_cvapply":
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327 print("OPLS cv")
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328
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329 ## set variables for components and number of response groups
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330 components = c($type_cond.method_cond.opls_analysis_cond.opls_cvcomp)
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331 number_groups = length(levels(y_vector))
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332
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333 ## OPLS-cvApply:
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334 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components)
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335 ## for use to reduce msidata: keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv
0
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336
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
337 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
338 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
339 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
340
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
341 ## create table with summary
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
342 count = 1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
343 summary_oplscv = list()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
344 accuracy_vector = numeric()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
345 for (iteration in components){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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346
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
347 summary_iteration = summary(msidata.cv.opls)\$accuracy[[paste0("ncomp = ", iteration)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
348 ## change class of numbers into numeric to round and calculate mean
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
349 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
350 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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351 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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352 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
353 summary_iteration4 = t(summary_iteration3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
354 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
355 summary_oplscv[[count]] = summary_iteration5
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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356 count = count+1} ## create list with summary table for each component
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
357 summary_oplscv = do.call(rbind, summary_oplscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358 summary_df = as.data.frame(summary_oplscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
359 colnames(summary_df) = NULL
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
360
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
361 ## plots
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362 ## plot to find ncomp with highest accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
363 plot(components, accuracy_vector, ylab = "mean accuracy", type="o", main="Mean accuracy of OPLS classification")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
364 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 ## one image for each sample/fold, 4 images per page
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366 minimumy = min(coord(msidata.cv.opls)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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367 maximumy = max(coord(msidata.cv.opls)[,2])
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
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diff changeset
368 image(msidata.cv.opls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(1, 1), col=colourvector)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
369
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
370 ## print table with summary in pdf
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
371 par(opar)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
372 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
373 title(main="Summary for the different components\n", adj=0.5)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
374 ## 20 rows fits in one page:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 if (nrow(summary_df)<=20){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376 grid.table(summary_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
378 grid.table(summary_df[1:20,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 mincount = 21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 maxcount = 40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
383 if (maxcount <= nrow(summary_df)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 grid.table(summary_df[mincount:maxcount,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
385 mincount = mincount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
386 maxcount = maxcount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
387 }else{### stop last page with last sample otherwise NA in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
388 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
389 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
391
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
392 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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393 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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394 save(msidata.cv.opls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
396
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
397
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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398 ######################## OPLS -analysis ###########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
399 #elif str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_analysis":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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400 print("OPLS analysis")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 component = c($type_cond.method_cond.opls_analysis_cond.opls_comp)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
405
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
406 ### stop if multiple values for OPLS components are selected what sets component to 0
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
407 tryCatch(
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
408 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
409
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
410 if (component==0)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
411 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
412 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
413 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
414 },
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
415 error=function(cond) {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
416 ## in case user used multiple inputs for component - this is only possible in cv apply
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
417 message("Error during OPLS training")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
418 message("Possible problems: Multiple values for component were selected - this is only possible in cvapply but not for OPLS analysis or component was set to 0 but minimum for component is 1)")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
419 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
420 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
421 )
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 ### opls analysis and coefficients plot
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
424 msidata.opls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.opls_analysis_cond.opls_scale)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
425 ## to reduce msidata: keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
426 plot(msidata.opls, main="OPLS coefficients per m/z", col=colourvector)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
428
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 ### summary table of OPLS
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 summary_table = summary(msidata.opls)\$accuracy[[paste0("ncomp = ",component)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 summary_table2 = round(as.numeric(summary_table), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 summary_table4 = t(summary_table3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 grid.table(summary_table5, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 ### image of the best m/z
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440 minimumy = min(coord(msidata)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 maximumy = max(coord(msidata)[,2])
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
442 print(image(msidata, mz = topFeatures(msidata.opls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 opls_classes = data.frame(msidata.opls\$classes[[1]])
3
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
445 ## pixel names and coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
446 ## to remove potential sample names and z dimension, split at comma and take only x and y
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
447 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
448 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
449 x_coordinates = gsub("x = ","",x_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
450 y_coordinates = gsub(" y = ","",y_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
451 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
452
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
456 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
457 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
458 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
459
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
460 opls_toplabels = topFeatures(msidata.opls, n=Inf)
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 opls_toplabels[,4:6] <-round(opls_toplabels[,4:6],6)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 ## image with predicted classes
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 prediction_df = cbind(coord(msidata.opls)[,1:2], opls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 colnames(prediction_df) = c("x", "y", "predicted_classes")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 geom_tile() +
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 coord_fixed()+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 ggtitle("Predicted condition for each pixel")+
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
473 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
474 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
475 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
476 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
477 panel.grid.minor = element_blank())+
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 theme(text=element_text(family="ArialMT", face="bold", size=15))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 theme(legend.position="bottom",legend.direction="vertical")+
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
480 guides(fill=guide_legend(ncol=4,byrow=TRUE))+
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
481 scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 print(prediction_plot)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 save(msidata.opls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 ######################## SSC #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 #elif str( $type_cond.method_cond.class_method) == "spatialShrunkenCentroids":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 print("SSC")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 ######################## SSC - CV #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 #if str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_cvapply":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 print("SSC cv")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 ## SSC-cvApply:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
507 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
508 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
509 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
510
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
511 ## create table with summary
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 count = 1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 summary_ssccv = list()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514 accuracy_vector = numeric()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 iteration_vector = character()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 for (iteration in names(msidata.cv.ssc@resultData[[1]][,1])){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 summary_iteration = summary(msidata.cv.ssc)\$accuracy[[iteration]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 ## change class of numbers into numeric to round and calculate mean
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 summary_iteration4 = t(summary_iteration3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 summary_iteration5 = cbind(c(iteration, colnames(summary_iteration)), summary_iteration4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 summary_ssccv[[count]] = summary_iteration5
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527 iteration_vector[count] = unlist(strsplit(iteration, "[,]"))[3]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 count = count+1} ## create list with summary table for each component
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 summary_ssccv = do.call(rbind, summary_ssccv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 summary_df = as.data.frame(summary_ssccv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 colnames(summary_df) = NULL
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 ## plot to find parameters with highest accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534 plot(c($type_cond.method_cond.ssc_s),accuracy_vector[!duplicated(iteration_vector)], type="o",ylab="Mean accuracy", xlab = "Shrinkage parameter (s)", main="Mean accuracy of SSC classification")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535 best_params = names(msidata.cv.ssc@resultData[[1]][,1])[which.max(accuracy_vector)] ## find parameters with max. accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 r_value = as.numeric(substring(unlist(strsplit(best_params, ","))[1], 4))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 s_value = as.numeric(substring(unlist(strsplit(best_params, ","))[3], 5)) ## remove space
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 minimumy = min(coord(msidata.cv.ssc)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 maximumy = max(coord(msidata.cv.ssc)[,2])
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
540 image(msidata.cv.ssc, model = list( r = r_value, s = s_value ), ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout=c(1,1), col=colourvector)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
542 #if $type_cond.method_cond.ssc_analysis_cond.write_best_params:
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
543 write.table(r_value, file="$best_r", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
544 write.table(s_value, file="$best_s", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
545 #end if
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
546
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 ## print table with summary in pdf
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548 par(opar)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550 title(main="Summary for the different parameters\n", adj=0.5)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551 ## 20 rows fits in one page:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552 if (nrow(summary_df)<=20){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553 grid.table(summary_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555 grid.table(summary_df[1:20,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
556 mincount = 21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557 maxcount = 40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560 if (maxcount <= nrow(summary_df)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 grid.table(summary_df[mincount:maxcount,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
562 mincount = mincount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563 maxcount = maxcount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564 }else{### stop last page with last sample otherwise NA in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
568
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571 save(msidata.cv.ssc, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574 ######################## SSC -analysis ###########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575 #elif str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_analysis":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576 print("SSC analysis")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
581 ## SSC analysis and plot
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
582 msidata.ssc <- spatialShrunkenCentroids(msidata, y = y_vector,
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
583 r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
584 plot(msidata.ssc, mode = "tstatistics", model = list("r" = c($type_cond.method_cond.ssc_r), "s" = c($type_cond.method_cond.ssc_s)),
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
585 col=colourvector, lwd=2)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
586
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
587 ### summary table SSC
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
588 ##############summary_table = summary(msidata.ssc)
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
589
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
590 ### stop if multiple values for r and s were used as input
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
591 tryCatch(
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
592 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
593
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
594 if (length(names(msidata.ssc@resultData))>1)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
595 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
596 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
597 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
598 },
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
599 error=function(cond) {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
600 ## in case user used multiple inputs for r or s stop - this is only possible in cv apply
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
601 message("Error during SSC training")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
602 message("Possible problem: multiple values for r or s selected - this is only possible in cvapply but not for spatial shrunken centroid analysis)")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
603 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
604 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
605 )
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
606
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607 summary_table = summary(msidata.ssc)\$accuracy[[names(msidata.ssc@resultData)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 summary_table2 = round(as.numeric(summary_table), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
609 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
610 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
611 summary_table4 = t(summary_table3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
612 summary_table5 = cbind(c(names(msidata.ssc@resultData),colnames(summary_table)), summary_table4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
613 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
614 grid.table(summary_table5, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
615
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
616 ### image of the best m/z
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
617 minimumy = min(coord(msidata)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
618 maximumy = max(coord(msidata)[,2])
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
619 print(image(msidata, mz = topFeatures(msidata.ssc)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
620
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
621 ## m/z and pixel information output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
622 ssc_classes = data.frame(msidata.ssc\$classes[[1]])
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
623 ssc_probabilities = data.frame(msidata.ssc\$probabilities[[1]])
3
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
624
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
625 ## pixel names and coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
626 ## to remove potential sample names and z dimension, split at comma and take only x and y
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
627 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
628 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
629 x_coordinates = gsub("x = ","",x_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
630 y_coordinates = gsub(" y = ","",y_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
631 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
632
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
633
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
634 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
635 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
636 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
637
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
638 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes, ssc_probabilities)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
639 colnames(ssc_classes2) = c("pixel names", "x", "y","predicted condition", levels(msidata.ssc\$classes[[1]]))
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
640 ssc_toplabels = topFeatures(msidata.ssc, n=Inf)
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
641 ssc_toplabels[,6:9] <-round(ssc_toplabels[,6:9],6)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
642 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
643 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
644
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
645 image(msidata.ssc, model=list(r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s)), ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
646 col=colourvector, mode="classes", layout=c(1,1), main="Class Prediction")
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
647 image(msidata.ssc, model=list(r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s)), ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
648 col=colourvector, mode="probabilities", layout=c(1,1), main="Class probabilities")
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
649
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
650
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
651 ## image with right and wrong classes:
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
652 prediction_df = cbind(coord(msidata.ssc)[,1:2], ssc_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
653 colnames(prediction_df) = c("x", "y", "predicted_classes")
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
654 comparison_df = cbind(prediction_df, y_vector)
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
655 comparison_df\$correct<- ifelse(comparison_df\$predicted_classes==comparison_df\$y_vector, T, F)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
656 correctness = round(sum(comparison_df\$correct)/length(comparison_df\$correct)*100,2)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
657
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
658 correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
659 geom_tile() +
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
660 coord_fixed()+
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
661 ggtitle(paste0("Correctness of classification: ",correctness, "%"))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
662 scale_fill_manual(values = c("TRUE" = "orange","FALSE" = "darkblue"))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
663 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
664 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
665 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
666 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
667 panel.grid.minor = element_blank())+
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
668 theme(text=element_text(family="ArialMT", face="bold", size=15))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
669 theme(legend.position="bottom",legend.direction="vertical")+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
670 guides(fill=guide_legend(ncol=2,byrow=TRUE))
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
671 ## coord_labels = aggregate(cbind(x,y)~correct, data=comparison_df, mean, na.rm=TRUE, na.action="na.pass")
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
672 ##coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
673 print(correctness_plot)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
674
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
675 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
676 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
677 save(msidata.ssc, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
678 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
679
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
680 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
681 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
682
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
683
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
684
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
685 ######################## II) Prediction #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
686 #############################################################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
687
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
688 #elif str($type_cond.type_method) == "prediction":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
689 print("prediction")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
690
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
691 training_data = loadRData("$type_cond.training_result")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
692
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
693 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
694 print("new response")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
695
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
696 new_y_tabular = read.delim("$type_cond.new_y_values_cond.new_response_file", header = $type_cond.new_y_values_cond.new_tabular_header, stringsAsFactors = FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
697 new_y_input = new_y_tabular[,c($type_cond.new_y_values_cond.column_new_x, $type_cond.new_y_values_cond.column_new_y, $type_cond.new_y_values_cond.column_new_response)]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
698 colnames(new_y_input)[1:2] = c("x", "y")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
699 ## merge with coordinate information of msidata
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
700 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
701 colnames(msidata_coordinates)[3] = "pixel_index"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
702 merged_response = merge(msidata_coordinates, new_y_input, by=c("x", "y"), all.x=TRUE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
703 merged_response[is.na(merged_response)] = "NA"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
704 merged_response = merged_response[order(merged_response\$pixel_index),]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
705 new_y_vector = as.factor(merged_response[,4])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
706 prediction = predict(training_data,msidata, newy = new_y_vector)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
707
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
708 ##numbers of levels for colour selection
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
709 number_levels = length(levels(new_y_vector))
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
710
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
711 ## Summary table prediction
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
712 summary_table = summary(prediction)\$accuracy[[names(prediction@resultData)]]
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
713 summary_table2 = round(as.numeric(summary_table), digits=2)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
714 summary_matrix = matrix(summary_table2, nrow=4, ncol=ncol(summary_table))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
715 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
716 summary_table4 = t(summary_table3)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
717 summary_table5 = cbind(c(names(prediction@resultData),colnames(summary_table)), summary_table4)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
718 plot(0,type='n',axes=FALSE,ann=FALSE)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
719 grid.table(summary_table5, rows= NULL)
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
720
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721 #else
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
722 prediction = predict(training_data,msidata)
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
723 number_levels = length(levels(training_data\$y[[1]]))
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
724 #end if
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
725
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
726 ## colours selection:
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
727
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
728 #if str($colour_conditional.colour_type) == "manual_colour"
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
729 #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $colour_conditional.colours])
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
730 colourvector = c($color_string)
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
731
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
732 #elif str($colour_conditional.colour_type) == "colourpalette"
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
733 colourvector = noquote($colour_conditional.palettes)(number_levels)
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
734
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
735 #end if
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
736
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
737 ## m/z and pixel information output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
738 predicted_classes = data.frame(prediction\$classes[[1]])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
739 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
740 pixel_names = gsub(" = ", "y_", pixel_names)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
741 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
742 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
743 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
744 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition")
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
745 predicted_toplabels = topFeatures(prediction, n=Inf)
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
746 if (colnames(predicted_toplabels)[4] == "coefficients"){
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
747 predicted_toplabels[,4:6] <-round(predicted_toplabels[,4:6],5)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
748 }else{
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
749 predicted_toplabels[,6:9] <-round(predicted_toplabels[,6:9],5)}
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
750
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
751 ##predicted classes
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
752 prediction_df = cbind(coord(prediction)[,1:2], predicted_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
753 colnames(prediction_df) = c("x", "y", "predicted_classes")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
754
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
755 #if str($type_cond.classification_type) == "SSC_classifier":
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
756 ## this seems to work only for SSC, therefore overwrite tables
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
757 predicted_probabilities = data.frame(prediction\$probabilities[[1]])
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
758 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes, predicted_probabilities)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
759 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition", levels(prediction\$classes[[1]]))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
760 ## also image modes are specific to SSC
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
761 image(prediction, mode="classes", layout=c(1,1), main="Class", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), col=colourvector)
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
762 image(prediction, mode="probabilities", layout=c(1,1), main="Class probabilities",ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), col=colourvector)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
763
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
764 #else
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
765
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
766 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
767 geom_tile()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
768 coord_fixed()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
769 ggtitle("Predicted condition for each spectrum")+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
770 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
771 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
772 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
773 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
774 panel.grid.minor = element_blank())+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
775 theme(text=element_text(family="ArialMT", face="bold", size=15))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
776 theme(legend.position="bottom", legend.direction="vertical")+
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
777 guides(fill=guide_legend(ncol=4, byrow=TRUE))+
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
778 scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
779 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
780 coord_labels\$file_number = gsub( "_.*§", "", coord_labels\$predicted_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
781 print(prediction_plot)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
782 #end if
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
783
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
784 write.table(predicted_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
785 write.table(predicted_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
786
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
787
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
788
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
789
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
790 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
791 ## image with right and wrong classes:
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
792
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
793 comparison_df = cbind(prediction_df, new_y_vector)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
794 comparison_df\$correct<- ifelse(comparison_df\$predicted_classes==comparison_df\$new_y_vector, T, F)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
795 correctness = round(sum(comparison_df\$correct)/length(comparison_df\$correct)*100,2)
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
796
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
797 correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
798 geom_tile()+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
799 scale_fill_manual(values = c("TRUE" = "orange","FALSE" = "darkblue"))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
800 coord_fixed()+
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
801 ggtitle(paste0("Correctness of classification: ",correctness, "%"))+
9
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
802 theme_bw()+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
803 theme(text=element_text(family="ArialMT", face="bold", size=15))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
804 theme(legend.position="bottom",legend.direction="vertical")+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
805 guides(fill=guide_legend(ncol=2,byrow=TRUE))
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 8
diff changeset
806 print(correctness_plot)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
807 #end if
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
808
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
809 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
810 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
811 msidata = prediction
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
812 save(msidata, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
813 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
814
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
815 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
816
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
817 dev.off()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
818
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
819 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
820 print("Inputfile has no intensities > 0 or contains NA values")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
821 dev.off()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
822 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
823
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
824
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
825 ]]></configfile>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
826 </configfiles>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
827 <inputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
828 <expand macro="reading_msidata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
829 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
830 <param name="type_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
831 <option value="training" selected="True">training</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
832 <option value="prediction">prediction</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
833 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
834 <when value="training">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
835
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
836 <param name="annotation_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and their classes"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
837 help="Three or four columns: x values, y values, response values, optionally fold values"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
838 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
839 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
840 <param name="column_response" data_ref="annotation_file" label="Column with response (condition) values" type="data_column" help="This is the condition (pixel group) which will be classified"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
841 <param name="column_fold" data_ref="annotation_file" optional="True" label="Column with fold values - only neccessary for cvapply" type="data_column" help="Each fold must contain pixels of all response groups and is used for cross validation"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
842 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
843
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
844 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
845 <param name="class_method" type="select" label="Select the method for classification">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
846 <option value="PLS" selected="True">PLS-DA</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
847 <option value="OPLS">OPLS-DA</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
848 <option value="spatialShrunkenCentroids">spatial shrunken centroids</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
849 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
850 <when value="PLS">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
851
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
852 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
853 <param name="PLS_method" type="select" label="Crossvalidation or analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
854 <option value="cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
855 <option value="PLS_analysis">PLS-DA analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
856 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
857 <when value="cvapply">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
858 <param name="plscv_comp" type="text" value="1:2"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
859 label="The number of PLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5). Mininum is 1.">
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
860 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
861 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
862 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
863 <when value="PLS_analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
864 <param name="pls_comp" type="integer" value="5"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
865 label="The optimal number of PLS-DA components as indicated by cross-validations (minimum is 1)" help="Run cvApply first to optain optimal number of PLS-DA components"/>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
866 <param name="pls_scale" type="boolean" label="Data scaling" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
867 <param name="pls_toplabels" type="integer" value="100"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
868 label="Number of toplabels (m/z features) which should be written in tabular output"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
869 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
870 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
871 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
872
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
873 <when value="OPLS">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
874
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
875 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
876 <param name="opls_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
877 <option value="opls_cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
878 <option value="opls_analysis">OPLS-DA analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
879 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
880
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
881 <when value="opls_cvapply">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
882 <param name="opls_cvcomp" type="text" value="1:2"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
883 label="The number of OPLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5). Minimum is 1.">
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
884 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
885 </param>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
886 <!--param name="xnew_cv" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
887 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
888
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
889 <when value="opls_analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
890 <param name="opls_comp" type="integer" value="5"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
891 label="The optimal number of OPLS-DA components as indicated by cross-validations (minimum is 1)" help="Run cvApply first to optain optimal number of OPLS-DA components"/>
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
892 <!--param name="xnew" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
893 <param name="opls_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Data scaling"/>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
894 <!--param name="opls_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
895 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
896 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
897 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
898 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
899
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
900 <when value="spatialShrunkenCentroids">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
901 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
902 <param name="ssc_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
903 <option value="ssc_cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
904 <option value="ssc_analysis">spatial shrunken centroids analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
905 </param>
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
906 <when value="ssc_cvapply">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
907 <param name="write_best_params" type="boolean" label="Write out best r and s values" help="Can be used to generate automatic classification workflow"/>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
908 </when>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
909 <when value="ssc_analysis">
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
910 <!--param name="ssc_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
911 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
912 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
913 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
914 <param name="ssc_r" type="text" value="2"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
915 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="For cvapply multiple values are allowed (e.g. 0,1,2,3 or 2:5)">
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
916 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
917 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
918 <param name="ssc_s" type="text" value="2"
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
919 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)." help="For cvapply multiple values are allowed (e.g. 0,1,2 or 2:5)">
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
920 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
921 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
922 <param name="ssc_kernel_method" type="select" display="radio" label = "The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
923 <option value="gaussian">gaussian</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
924 <option value="adaptive" selected="True">adaptive</option>
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
925 </param>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
926 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
927 </conditional>
8
277dc652246e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
928
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
929 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
930
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
931 <when value="prediction">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
932 <param name="training_result" type="data" format="rdata" label="Result from previous classification training"/>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
933 <!--param name="predicted_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
934 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
935 <param name="classification_type" type="select" display="radio" optional="False" label="Which classification method was used">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
936 <option value="PLS_classifier" selected="True" >PLS classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
937 <option value="OPLS_classifier">OPLS classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
938 <option value="SSC_classifier">SSC_classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
939 </param>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
940 <conditional name="new_y_values_cond">
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
941 <param name="new_y_values" type="select" label="Load annotations (optional, but allows accuracy calculations)">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
942 <option value="no_new_response" selected="True">no</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
943 <option value="new_response">use annotations</option>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
944 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
945 <when value="no_new_response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
946 <when value="new_response">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
947 <param name="new_response_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and the new response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
948 <param name="column_new_x" data_ref="new_response_file" label="Column with x values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
949 <param name="column_new_y" data_ref="new_response_file" label="Column with y values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
950 <param name="column_new_response" data_ref="new_response_file" label="Column with new response values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
951 <param name="new_tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
952 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
953 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
954 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
955 </conditional>
15
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
956 <conditional name="colour_conditional">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
957 <param name="colour_type" type="select" label="Choose a colour scheme">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
958 <option value="colourpalette" selected="True" >Colour palette</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
959 <option value="manual_colour">Manual selection</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
960 </param>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
961 <when value="manual_colour">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
962 <repeat name="colours" title="Colours for the plots" min="1" max="50">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
963 <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
964 <sanitizer>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
965 <valid initial="string.letters,string.digits">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
966 <add value="#" />
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
967 </valid>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
968 </sanitizer>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
969 </param>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
970 </repeat>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
971 </when>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
972 <when value="colourpalette">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
973 <param name="palettes" type="select" display="radio" label="Select a colourpalette">
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
974 <option value="hue_pal()" selected="True">hue</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
975 <option value="rainbow">rainbow</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
976 <option value="heat.colors">heat colors</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
977 <option value="terrain.colors">terrain colors</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
978 <option value="topo.colors">topo colors</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
979 <option value="cm.colors">cm colors</option>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
980 </param>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
981 </when>
f28ad96b76dc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89-dirty"
galaxyp
parents: 14
diff changeset
982 </conditional>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
983 <param name="output_rdata" type="boolean" label="Results as .RData output" help="Can be used to generate a classification prediction on new data"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
984 </inputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
985 <outputs>
2
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
986 <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
987 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
988 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
989 <data format="txt" name="best_r" label="${tool.name} on ${on_string}:best r">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
990 <filter>type_cond['type_method'] == 'training' and type_cond['method_cond']['class_method'] == 'spatialShrunkenCentroids' and type_cond['method_cond']['ssc_analysis_cond']['ssc_method'] == 'ssc_cvapply' and type_cond['method_cond']['ssc_analysis_cond']['write_best_params']</filter>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
991 </data>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
992 <data format="txt" name="best_s" label="${tool.name} on ${on_string}:best s">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
993 <filter>type_cond['type_method'] == 'training' and type_cond['method_cond']['class_method'] == 'spatialShrunkenCentroids' and type_cond['method_cond']['ssc_analysis_cond']['ssc_method'] == 'ssc_cvapply' and type_cond['method_cond']['ssc_analysis_cond']['write_best_params']</filter>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
994 </data>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
995 <data format="rdata" name="classification_rdata" label="${tool.name} on ${on_string}: results.RData">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
996 <filter>output_rdata</filter>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
997 </data>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
998 </outputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
999 <tests>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1000 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1001 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1002 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1003 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1004 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1005 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1006 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1007 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1008 <param name="column_fold" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1009 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1010 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1011 <param name="class_method" value="PLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1012 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1013 <param name="PLS_method" value="cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1014 <param name="plscv_comp" value="2:4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1015 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1016 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1017 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1018 <output name="mzfeatures" file="features_test1.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1019 <output name="pixeloutput" file="pixels_test1.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1020 <output name="classification_images" file="test1.pdf" compare="sim_size" delta="2000"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1021 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1022
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1023 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1024 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1025 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1026 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1027 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1028 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1029 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1030 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1031 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1032 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1033 <param name="class_method" value="PLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1034 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1035 <param name="PLS_method" value="PLS_analysis"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1036 <param name="pls_comp" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1037 <param name="pls_scale" value="TRUE"/>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1038 <!--param name="pls_toplabels" value="100"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1039 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1040 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1041 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1042 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1043 <output name="mzfeatures" file="features_test2.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1044 <output name="pixeloutput" file="pixels_test2.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1045 <output name="classification_images" file="test2.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1046 <output name="classification_rdata" file="test2.rdata" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1047 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1048
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1049 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1050 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1051 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1052 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1053 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1054 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1055 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1056 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1057 <param name="column_fold" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1058 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1059 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1060 <param name="class_method" value="OPLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1061 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1062 <param name="opls_method" value="opls_cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1063 <param name="opls_cvcomp" value="1:2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1064 <param name="xnew_cv" value="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1065 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1066 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1067 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1068 <output name="mzfeatures" file="features_test3.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1069 <output name="pixeloutput" file="pixels_test3.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1070 <output name="classification_images" file="test3.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1071 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1072
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1073 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1074 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1075 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1076 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1077 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1078 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1079 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1080 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1081 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1082 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1083 <param name="class_method" value="OPLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1084 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1085 <param name="opls_method" value="opls_analysis"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1086 <param name="opls_comp" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1087 <param name="xnew" value="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1088 <param name="opls_scale" value="FALSE"/>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1089 <!--param name="opls_toplabels" value="100"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1090 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1091 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1092 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1093 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1094 <output name="mzfeatures" file="features_test4.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1095 <output name="pixeloutput" file="pixels_test4.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1096 <output name="classification_images" file="test4.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1097 <output name="classification_rdata" file="test4.rdata" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1098 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1099
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1100 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1101 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1102 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1103 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1104 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1105 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1106 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1107 <param name="column_response" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1108 <param name="column_fold" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1109 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1110 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1111 <param name="class_method" value="spatialShrunkenCentroids"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1112 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1113 <param name="ssc_method" value="ssc_cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1114 <param name="ssc_r" value="1:2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1115 <param name="ssc_s" value="2:3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1116 <param name="ssc_kernel_method" value="adaptive"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1117 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1118 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1119 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1120 <output name="mzfeatures" file="features_test5.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1121 <output name="pixeloutput" file="pixels_test5.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1122 <output name="classification_images" file="test5.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1123 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1124
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1125 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1126 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1127 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1128 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1129 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1130 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1131 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1132 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1133 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1134 <param name="class_method" value="spatialShrunkenCentroids"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1135 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1136 <param name="ssc_method" value="ssc_analysis"/>
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1137 <!--param name="ssc_toplabels" value="20"/-->
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1138 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1139 <param name="ssc_r" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1140 <param name="ssc_s" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1141 <param name="ssc_kernel_method" value="adaptive"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1142 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1143 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1144 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1145 <output name="mzfeatures" file="features_test6.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1146 <output name="pixeloutput" file="pixels_test6.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1147 <output name="classification_images" file="test6.pdf" compare="sim_size"/>
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
1148 <output name="classification_rdata" file="test6.rdata" compare="sim_size" delta="15000"/>
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1149 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1150
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1151 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1152 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1153 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1154 <param name="type_method" value="prediction"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1155 <param name="training_result" value="test2.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1156 <conditional name="new_y_values_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1157 <param name="new_y_values" value="new_response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1158 <param name="new_response_file" value="pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1159 <param name="column_new_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1160 <param name="column_new_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1161 <param name="column_new_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1162 <param name="new_tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1163 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1164 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1165 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1166 <output name="mzfeatures" file="features_test7.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1167 <output name="pixeloutput" file="pixels_test7.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1168 <output name="classification_images" file="test7.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1169 <output name="classification_rdata" file="test7.rdata" compare="sim_size" />
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1170 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1171 </tests>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1172 <help>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1173 <![CDATA[
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1174
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1175
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1176 @CARDINAL_DESCRIPTION@
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1177
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1178 -----
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1179
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1180 This tool provides three different Cardinal functions for supervised classification of mass-spectrometry imaging data.
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1181
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1182 @MSIDATA_INPUT_DESCRIPTION@
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1183 - NA intensities are not allowed
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1184 - duplicated coordinates will be removed
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1185
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1186 - For training: tabular file with condition and fold for each pixel: Two columns for pixel coordinates (x and y values); one column with the condition for the pixel, which will be used for classification; for the cross validation (cvapply) another column with a fold is necessary, each fold must contain pixels of all response groups and is used for cross validation. Condition and fold columns are treated as factor to perform discriminant analysis (also when numeric values are provided).
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1187
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1188 ::
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1189
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1190 x_coord y_coord condition fold
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1191 1 1 A f1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1192 2 1 A f2
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1193 3 1 A f3
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1194 1 2 B f1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1195 2 2 B f2
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1196 3 2 B f3
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1197 ...
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1198 ...
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1199
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1200
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1201 - For prediction: RData output from previous classification run is needed as input, optionally new response values can be loaded with a tabular file containing x values, y values and the response
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1202
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1203
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1204 **Options**
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1205
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1206 - PLS-DA: partial least square discriminant analysis
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1207 - O-PLS-DA: Orthogonal partial least squares discriminant analysis
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1208 - Spatial shrunken centroids (more details in `Bemis et al. <https://doi.org/10.1074/mcp.O115.053918>`_)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1209 - training and prediction
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1210
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1211 - training can be done with cvapply that uses cross validation to find the best value for s, this requires not only a condition for each spectrum but also a fold (each fold should contain spectra of all conditions)
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
1212 - training with the best value for r and s gives the top m/z features for each condition and the predicted classification group for each spectrum
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1213 - training result can be saved as RData file that can be reused for prediction of further samples
14
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
galaxyp
parents: 9
diff changeset
1214 - prediction can calculate accuracies when the annotations are known and provided
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1215
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1216
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1217 .. image:: $PATH_TO_IMAGES/classification_overview.png
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1218 :width: 1000
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1219 :height: 465
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1220
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1221
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1222
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1223 **Tips**
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1224
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1225 - The classification function will only run on files with valid intensity values (NA are not allowed)
4
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1226 - Only a single input file is accepted, several files have to be combined previously, for example with the MSI combine tool.
0
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1227
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1228
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1229 **Output**
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1230
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1231 - Pdf with the heatmaps and plots for the classification
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1232 - Tabular file with information on m/z features and pixels: toplabels/classes
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1233 - Optional: RData output that can be used to predict new data or to explore the results more deeply with the Cardinal package in R
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1234
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1235 ]]>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1236 </help>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1237 <expand macro="citations"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1238 </tool>
7
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
1239