|
11
|
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>
|
