Mercurial > repos > xuebing > matrix_visualization
comparison matrix_visualization.xml @ 0:71c64aa187ec
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| author | xuebing |
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| date | Sat, 31 Mar 2012 23:08:31 -0400 |
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| -1:000000000000 | 0:71c64aa187ec |
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| 1 <tool id="plotmatrix" name="matrix-visualization"> | |
| 2 <description>with sorting and clustering)</description> | |
| 3 <command interpreter="python"> matrix_visualization.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> |