Mercurial > repos > xuebing > sharplabtool
comparison tools/multivariate_stats/kpca.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.0"> | |
2 <description> </description> | |
3 <command interpreter="python"> | |
4 kpca.py | |
5 --input=$input1 | |
6 --output1=$out_file1 | |
7 --output2=$out_file2 | |
8 --var_cols=$var_cols | |
9 --kernel=$kernelChoice.kernel | |
10 --features=$features | |
11 #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot": | |
12 --sigma=$kernelChoice.sigma | |
13 --degree="None" | |
14 --scale="None" | |
15 --offset="None" | |
16 --order="None" | |
17 #elif $kernelChoice.kernel == "polydot": | |
18 --sigma="None" | |
19 --degree=$kernelChoice.degree | |
20 --scale=$kernelChoice.scale | |
21 --offset=$kernelChoice.offset | |
22 --order="None" | |
23 #elif $kernelChoice.kernel == "tanhdot": | |
24 --sigma="None" | |
25 --degree="None" | |
26 --scale=$kernelChoice.scale | |
27 --offset=$kernelChoice.offset | |
28 --order="None" | |
29 #elif $kernelChoice.kernel == "besseldot": | |
30 --sigma=$kernelChoice.sigma | |
31 --degree=$kernelChoice.degree | |
32 --scale="None" | |
33 --offset="None" | |
34 --order=$kernelChoice.order | |
35 #elif $kernelChoice.kernel == "anovadot": | |
36 --sigma=$kernelChoice.sigma | |
37 --degree=$kernelChoice.degree | |
38 --scale="None" | |
39 --offset="None" | |
40 --order="None" | |
41 #else: | |
42 --sigma="None" | |
43 --degree="None" | |
44 --scale="None" | |
45 --offset="None" | |
46 --order="None" | |
47 #end if | |
48 </command> | |
49 <inputs> | |
50 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> | |
51 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > | |
52 <validator type="no_options" message="Please select at least one column."/> | |
53 </param> | |
54 <param name="features" size="10" type="integer" value="2" label="Number of principal components to return" help="To return all, enter 0"/> | |
55 <conditional name="kernelChoice"> | |
56 <param name="kernel" type="select" label="Kernel function"> | |
57 <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option> | |
58 <option value="polydot">Polynomial</option> | |
59 <option value="vanilladot">Linear</option> | |
60 <option value="tanhdot">Hyperbolic</option> | |
61 <option value="laplacedot">Laplacian</option> | |
62 <option value="besseldot">Bessel</option> | |
63 <option value="anovadot">ANOVA Radial Basis Function</option> | |
64 <option value="splinedot">Spline</option> | |
65 </param> | |
66 <when value="vanilladot" /> | |
67 <when value="splinedot" /> | |
68 <when value="rbfdot"> | |
69 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> | |
70 </when> | |
71 <when value="laplacedot"> | |
72 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> | |
73 </when> | |
74 <when value="polydot"> | |
75 <param name="degree" size="10" type="integer" value="1" label="degree" /> | |
76 <param name="scale" size="10" type="integer" value="1" label="scale" /> | |
77 <param name="offset" size="10" type="integer" value="1" label="offset" /> | |
78 </when> | |
79 <when value="tanhdot"> | |
80 <param name="scale" size="10" type="integer" value="1" label="scale" /> | |
81 <param name="offset" size="10" type="integer" value="1" label="offset" /> | |
82 </when> | |
83 <when value="besseldot"> | |
84 <param name="sigma" size="10" type="integer" value="1" label="sigma" /> | |
85 <param name="order" size="10" type="integer" value="1" label="order" /> | |
86 <param name="degree" size="10" type="integer" value="1" label="degree" /> | |
87 </when> | |
88 <when value="anovadot"> | |
89 <param name="sigma" size="10" type="integer" value="1" label="sigma" /> | |
90 <param name="degree" size="10" type="integer" value="1" label="degree" /> | |
91 </when> | |
92 </conditional> | |
93 </inputs> | |
94 <outputs> | |
95 <data format="input" name="out_file1" metadata_source="input1" /> | |
96 <data format="pdf" name="out_file2" /> | |
97 </outputs> | |
98 <requirements> | |
99 <requirement type="python-module">rpy</requirement> | |
100 </requirements> | |
101 <tests> | |
102 <test> | |
103 <param name="input1" value="iris.tabular"/> | |
104 <param name="var_cols" value="1,2,3,4"/> | |
105 <param name="kernel" value="polydot"/> | |
106 <param name="features" value="2"/> | |
107 <param name="offset" value="0"/> | |
108 <param name="scale" value="1"/> | |
109 <param name="degree" value="2"/> | |
110 <output name="out_file1" file="kpca_out1.tabular"/> | |
111 <output name="out_file2" file="kpca_out2.pdf"/> | |
112 </test> | |
113 </tests> | |
114 <help> | |
115 | |
116 | |
117 .. class:: infomark | |
118 | |
119 **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* | |
120 | |
121 ----- | |
122 | |
123 .. class:: infomark | |
124 | |
125 **What it does** | |
126 | |
127 This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Principal Component Analysis (kPCA) on the input data. It outputs two files, one containing the summary statistics of the performed kPCA, and the other containing a scatterplot matrix of rotated values reported by kPCA. | |
128 | |
129 *Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis (2004). kernlab - An S4 Package for Kernel Methods in R. Journal of Statistical Software 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/* | |
130 | |
131 ----- | |
132 | |
133 .. class:: warningmark | |
134 | |
135 **Note** | |
136 | |
137 This tool currently treats all variables as continuous numeric variables. Running the tool on categorical variables might result in incorrect results. Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. | |
138 | |
139 </help> | |
140 </tool> |