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<body>
<div class="document" id="last-dotplot">
<h1 class="title">last-dotplot</h1>

<p>This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise sequence
alignments in MAF or LAST tabular format.  It requires the Python
Imaging Library to be installed.  It can be used like this:</p>
<pre class="literal-block">
last-dotplot my-alignments my-plot.png
</pre>
<p>The output can be in any format supported by the Imaging Library:</p>
<pre class="literal-block">
last-dotplot alns alns.gif
</pre>
<p>To get a nicer font, try something like:</p>
<pre class="literal-block">
last-dotplot -f /usr/share/fonts/truetype/freefont/FreeSans.ttf alns alns.png
</pre>
<p>If the fonts are located somewhere different on your computer, change
this as appropriate.</p>
<div class="section" id="choosing-sequences">
<h2>Choosing sequences</h2>
<p>If there are too many sequences, the dotplot will be very cluttered,
or the script might give up with an error message.  You can exclude
sequences with names like &quot;chrUn_random522&quot; like this:</p>
<pre class="literal-block">
last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png
</pre>
<p>Option &quot;-1&quot; selects sequences from the 1st genome, and &quot;-2&quot; selects
sequences from the 2nd genome.  'chr[!U]*' is a <em>pattern</em> that
specifies names starting with &quot;chr&quot;, followed by any character except
U, followed by anything.</p>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="74%" />
</colgroup>
<tbody valign="top">
<tr><td>Pattern</td>
<td>Meaning</td>
</tr>
<tr><td><tt class="docutils literal">*</tt></td>
<td>zero or more of any character</td>
</tr>
<tr><td><tt class="docutils literal">?</tt></td>
<td>any single character</td>
</tr>
<tr><td><tt class="docutils literal">[abc]</tt></td>
<td>any character in abc</td>
</tr>
<tr><td><tt class="docutils literal">[!abc]</tt></td>
<td>any character not in abc</td>
</tr>
</tbody>
</table>
<p>If a sequence name has a dot (e.g. &quot;hg19.chr7&quot;), the pattern is
compared to both the whole name and the part after the dot.</p>
<p>You can specify more than one pattern, e.g. this gets sequences with
names starting in &quot;chr&quot; followed by one or two characters:</p>
<pre class="literal-block">
last-dotplot -1 'chr?' -1 'chr??' alns alns.png
</pre>
</div>
<div class="section" id="options">
<h2>Options</h2>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>
<td>Show a help message, with default option values, and exit.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-1 <var>PATTERN</var></span>, <span class="option">--seq1=<var>PATTERN</var></span></kbd></td>
<td>Which sequences to show from the 1st genome.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-2 <var>PATTERN</var></span>, <span class="option">--seq2=<var>PATTERN</var></span></kbd></td>
<td>Which sequences to show from the 2nd genome.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-x <var>WIDTH</var></span>, <span class="option">--width=<var>WIDTH</var></span></kbd></td>
<td>Maximum width in pixels.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-y <var>HEIGHT</var></span>, <span class="option">--height=<var>HEIGHT</var></span></kbd></td>
<td>Maximum height in pixels.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-f <var>FILE</var></span>, <span class="option">--fontfile=<var>FILE</var></span></kbd></td>
<td>TrueType or OpenType font file.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-s <var>SIZE</var></span>, <span class="option">--fontsize=<var>SIZE</var></span></kbd></td>
<td>TrueType or OpenType font size.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-c <var>COLOR</var></span>, <span class="option">--forwardcolor=<var>COLOR</var></span></kbd></td>
<td>Color for forward alignments.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-r <var>COLOR</var></span>, <span class="option">--reversecolor=<var>COLOR</var></span></kbd></td>
<td>Color for reverse alignments.</td></tr>
</tbody>
</table>
</blockquote>
<div class="section" id="unsequenced-gap-options">
<h3>Unsequenced gap options</h3>
<p>Note: these &quot;gaps&quot; are <em>not</em> alignment gaps (indels): they are regions
of unknown sequence.</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">--gap1=<var>FILE</var></span></kbd></td>
<td>Read unsequenced gaps in the 1st genome from an agp or gap file.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--gap2=<var>FILE</var></span></kbd></td>
<td>Read unsequenced gaps in the 2nd genome from an agp or gap file.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--bridged-color=<var>COLOR</var></span></kbd></td>
<td>Color for bridged gaps.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--unbridged-color=<var>COLOR</var></span></kbd></td>
<td>Color for unbridged gaps.</td></tr>
</tbody>
</table>
</blockquote>
<p>An unsequenced gap will be shown only if it covers at least one whole
pixel.</p>
</div>
</div>
</div>
</body>
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