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author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
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13:292186c14b08 14:76e1b1b21cce
1 <tool id="plotmatrix" name="matrix-visualization">
2 <description>with sorting and clustering)</description>
3 <command interpreter="python"> plotmatrix.py $input $output $uselog $subset $reorder $color $scale $cols</command>
4 <inputs>
5 <param name="input" format="tabular" type="data" label="Data file"/>
6 <param name="cols" type="text" value="1,3,8:10" label="data columns" help="e.g.: column 1, 3, 8,9,10"/>
7 <param name="uselog" label="log transform the data" type="boolean" truevalue="uselog" falsevalue="none" checked="True"/>
8 <param name="subset" label="sample a subset if the data is too large" type="boolean" truevalue="subset" falsevalue="none" checked="True"/>
9 <param name="scale" label="normalize by row" type="boolean" truevalue="scale" falsevalue="none" checked="False"/>
10 <param name="reorder" type="select" label="reorder features (rows)">
11 <option value="none" selected="true">None</option>
12 <option value="sort_by_sum">Sort row by sum</option>
13 <option value="sort_by_center">Sort row by center </option>
14 <option value="average">Cluster rows (average)</option>
15 <option value="median">Cluster rows (median) </option>
16 <option value="centroid">Cluster rows (centroid)</option>
17 <option value="complete">Cluster rows (complete)</option>
18 <option value="single">Cluster rows (single)</option>
19 </param>
20
21 <param name="color" type="select" label="color scheme">
22 <option value="heat" selected="true">heat</option>
23 <option value="gray">gray</option>
24 <option value="rainbow">rainbow</option>
25 <option value="topo">topo</option>
26 <option value="terrain">terrain</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data format="pdf" name="output" />
31 </outputs>
32 <help>
33
34 **What it does**
35
36 This tool generates a heatmap for output from 'align' tool. Each row is the color-coded coverage of a feature, and the features are sorted by the total coverage in the interval.
37
38 **Example**
39
40 .. image:: ./static/operation_icons/heatmap.png
41
42 </help>
43 </tool>