view mds_plot.xml @ 0:fe542273784f draft default tip

author bgruening
date Thu, 15 Aug 2013 03:39:14 -0400
line wrap: on
line source

<tool id="ctb_mds_plot" name="MDS Scatter Plot" version="0.1">
    <description>of molecule similarity</description>
        <requirement type="package" version="0.13.1">scikit_learn</requirement>
        <requirement type="package" version="1.2.1">matplotlib</requirement>
    <command interpreter='python'>
            -i $infile
            --oformat $oformat
            -o $outfile
        <param name="infile" type="data" format="binary" label="Similarity Matrix"/>
        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
            <option value='png'>PNG</option>
            <option value='svg'>SVG</option>
        <data type="data" format="png" name="outfile" label="${} on ${on_string}"></data>
            <param name="infile" ftype="tabular" value="sm.dat" />
            <output ftype="png" name="outfile" file='mds_plot_on_sm_dat.png' />

**Note**. You need an NxN similarity matrix as input. Use the NxN Clustering tool to generate one.

**What it does**

Scatter plot of similarity matrix after embeding in 2D coordinates using Multidimensional Scaling (MDS).



* input::
    Similarity Matrix

* output::

	Scatter plot

.. image:: $PATH_TO_IMAGES/mds_plot.png