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1 <tool id="abims_ACP" name="PCA" version="1.2">
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2
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3 <description>Principal Component Analysis using FactoMineR</description>
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4
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5 <command interpreter="Rscript">
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6 abims_acp.r file "$input" graph TRUE scale.unit "$scale_unit" sep "$sep" dec "$dec"
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7 </command>
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8
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9 <inputs>
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10 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
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11 <!--<param name="graph" type="select" label="graph" help="if FALSE no graph generated">
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12 <option value="T" selected="true">TRUE</option>
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13 <option value="F" >FALSE</option>
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14 </param>-->
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15 <param name="scale_unit" type="select" label="scale.unit" help="if FALSE no reduction of variables">
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16 <option value="T" selected="true">TRUE</option>
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17 <option value="F" >FALSE</option>
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18 </param>
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19
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20 <param name="sep" type="select" format="text" optional="true">
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21 <label>Separator of columns</label>
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22 <option value="tabulation">tabulation</option>
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23 <option value="semicolon">;</option>
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24 <option value="comma">,</option>
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25 </param>
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26 <param name="dec" type="text" label="Decimal separator" value="." help="" />
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27
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28 <!--<param name="nr_col_names" type="integer" label="names" value="2" help="number of the column with names of metabolits" />
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29 <param name="from" type="integer" label="from" value="15" help="number of the column starting peak values data (to exlude all metadata)" />
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30 <param name="to" type="integer" label="to" value="30" help="number of the column finishing peak values data (to exlude all metadata)" />
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31 <param name="gr_number" type="integer" label="gr_number" value="2" help="number of groups (conditions)" />
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32 <param name="nb_col_gr" type="text" label="nb_col_gr" value="8,8" help="number of column of each group; separate with coma as indicated; first position coresponding to the first group etc." />
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33 <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
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34
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35 </inputs>
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36
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37 <outputs>
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38 <data name="acp_zip" format="zip" from_work_dir="acp.zip" label="${input.name[:-4]}.pca.zip"/>
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39 </outputs>
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40
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41 <stdio>
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42 <exit_code range="1:" level="fatal" />
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43 </stdio>
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44
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45 <help>
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46
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47
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48 .. class:: infomark
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49
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50 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
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51
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52 ---------------------------------------------------
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53
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54 ===
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55 PCA
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56 ===
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57
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58 -----------
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59 Description
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60 -----------
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61
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62
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63 Performs **Principal Component Analysis (PCA)** with supplementary individuals, supplementary quantitative variables and supplementary categorical variables.
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64 Missing values are replaced by the column mean. This scripts uses the FactoMineR package.
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65
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66
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67 -----------
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68 Input files
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69 -----------
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70
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71 +---------------------------+------------+
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72 | Parameter : num + label | Format |
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73 +===========================+============+
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74 | 1 : Data Matrix file | Tabular |
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75 +---------------------------+------------+
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76
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77
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78
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79 ----------
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80 Parameters
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81 ----------
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82
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83 **Data Matrix file**
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84
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85 Matrix of numeric data with headers (tabular format) issued from diffreport or annotateDiffreport to make post xcms analyse .
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86
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87 **scale.unit**
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88
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89 If FALSE: no reduction of the variables
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90
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91 **Separator of columns:**
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92
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93 Type of separator for the columns
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94
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95 **Decimal separator:**
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96
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97 Type of decimal separator of the numbers in your tabular files.
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98
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99
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100
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101 ------------
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102 Output files
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103 ------------
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104
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105
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106
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107 **input_name.pca.zip**
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108
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109 | A zip file containing fours files (eigenvalue.png, percentage_of_variance.png, Rplots.pdf and Rplots1.pdf).
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110
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111
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112 ---------------------------------------------------
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113
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114
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115
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116 ---------------
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117 Working example
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118 ---------------
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119
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120
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121 Input files
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122 -----------
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123
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124 **>A part of an example of Data Matrix file input :**
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125
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126
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127 +--------+------------------+----------------+
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128 | Name | AN7 | AN8 |
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129 +========+==================+================+
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130 |M102T645| 10880.0637170802 |17207.2222120537|
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131 +--------+------------------+----------------+
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132 |M105T604| 41911.160863452 |38105.7953589089|
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133 +--------+------------------+----------------+
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134
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135
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136
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137 Parameters
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138 ----------
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139
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140 | scale.unit -> **TRUE*
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141 | Separator of columns: -> **tabulation**
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142 | Decimal separator -> **.**
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143
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144
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145
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146 Output files
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147 ------------
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148
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149
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150 **eigenvalue.png:**
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151
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152 .. image:: pca_abims_eigenvalue.png
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153
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154 **percentage_of_variance.png:**
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155
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156 .. image:: pca_abims_percentage_of_variance.png
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157
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158 **Rplots.pdf:**
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159
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160 .. image:: pca_abims_Rplots.png
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161
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162 **Rplots1.pdf:**
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163
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164 .. image:: pca_abims_Rplots1.png
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165
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166
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167
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168
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169 </help>
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170
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171 </tool>
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