USAGE.html

<h2>Using the cadnano plugin interface:</h2>
<p>The plugin interface has two tabs in addition to the &quot;Usage help&quot; tab.</p>
<p>One control tab where you do the plotting, and another where you specify what to plot. The former is the simplest: Press the &quot;Process and plot!&quot; button to plot according to the directives provided in the &quot;Specify plots&quot; tab. You can then save the plot or data if you'd like.</p>
<p>The &quot;Specify plots&quot; tab has a big text area, which is used to specify how to analyze the design and how the result should be plotted and/or printed.</p>
<p>The input format is in yaml. You will need to know a bit of yaml as well as standard python datastructs to feel really comfortable editing the input. However, even without prior knowledge, you can probably figure out a lot by immitating and modifying the examples.</p>
<p>The yaml input in the text area takes the form of a dict with keys:</p>
<p><code>figure</code> : specify figure format (optional)</p>
<p><code>statspecs</code> : a list of dicts, where each 'statspecs' dict specifies a statistical analysis method, including how to plot and/or print the data/statistics.</p>
<p>A <code>statspec</code> dict in the <code>statspecs</code> list can contain the following elements:</p>
<ul>
<li><code>scoremethod</code> : A way to score the design. See statutils.py.</li>
<li><code>scoremethod_kwargs</code> : This is passed to the scoremethod as **kwargs.</li>
<li><code>plot_frequencies</code> : Whether to plot frequency histogram, rather than individual items. Default=True.</li>
<li><code>plotspec</code> : a dict specifying how to plot the results of this scoring method.</li>
<li><code>printspec</code> : a dict specifynig how to output the results of this scoring method.</li>
</ul>
<p>The plotspec dict can have the following elements:</p>
<ul>
<li><code>plot_kwargs</code> : a dict which is passed to the plotting method (currently pyplot.vlines).</li>
<li><code>label</code> : What label to use for this plot. The label appears in e.g. the legend.</li>
<li><code>label_fmt</code> : can be used to automatically format the label.</li>
<li><code>xlabel</code> : label ON THE X-AXIS.</li>
<li><code>subplot</code> : subplot specification (where to plot the graph within the figure, as n-rows, n-cols, plot-number).</li>
<li><code>xlim</code> : two-item list of [xmin, xmax].</li>
<li><code>ylim</code> : two-item list of [ymin, ymax].</li>
<li><code>title</code> : What title to use for the plot.</li>
<li><code>title_fmt</code> : Can be used to automatically format the title.</li>
<li><code>legend</code> : dict. Will be passed as pyplot.legend(**legend)</li>
</ul>
<p>The <code>printspec</code> element is currently just a kwargs dict, which gets passed to <code>staplestatter.get_highest_scores()</code>.</p>
<p>Regarding scoremethod_kwargs: {margin: 0}</p>
<ul>
<li>'margin' is currently only keyword argument. This is set at a per-plot level. It is not used by all scoring methods.</li>
</ul>
<p>If you want to plot statistics for multiple cadnano designs in the same figure, you can set the <code>figure.newfigure</code> option to <code>false</code>. This will re-use the old figure instead of creating a new figure every time you press &quot;Process and plot!&quot; button. Now, just load the designs one by one, plotting each design with the &quot;Process and plot!&quot; button.</p>
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