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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 <a class="reference external" href="https://pillow.readthedocs.io/">Python
Imaging Library</a> 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>
<div class="section" id="terminology">
<h2>Terminology</h2>
<p>last-dotplot shows alignments of one set of sequences against another
set of sequences.  This document calls a &quot;set of sequences&quot; a
&quot;genome&quot;, though it need not actually be a genome.</p>
</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">-v</span>, <span class="option">--verbose</span></kbd></td>
<td>Show progress messages &amp; data about the plot.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-x <var>INT</var></span>, <span class="option">--width=<var>INT</var></span></kbd></td>
<td>Maximum width in pixels.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-y <var>INT</var></span>, <span class="option">--height=<var>INT</var></span></kbd></td>
<td>Maximum height in pixels.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-m <var>M</var></span>, <span class="option">--maxseqs=<var>M</var></span></kbd></td>
<td>Maximum number of horizontal or vertical sequences.  If there
are &gt;M sequences, the smallest ones (after cutting) will be
discarded.</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 (horizontal) 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 (vertical) genome.</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>
<tr><td class="option-group">
<kbd><span class="option">--alignments=<var>FILE</var></span></kbd></td>
<td>Read secondary alignments.  For example: we could use primary
alignment data with one human DNA read aligned to the human
genome, and secondary alignment data with the whole chimpanzee
versus human genomes.  last-dotplot will show the parts of the
secondary alignments that are near the primary alignments.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--sort1=<var>N</var></span></kbd></td>
<td>Put the 1st genome's sequences left-to-right in order of: their
appearance in the input (0), their names (1), their lengths (2),
the top-to-bottom order of (the midpoints of) their alignments
(3).  You can use two colon-separated values, e.g. &quot;2:1&quot; to
specify 2 for primary and 1 for secondary alignments.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--sort2=<var>N</var></span></kbd></td>
<td>Put the 2nd genome's sequences top-to-bottom in order of: their
appearance in the input (0), their names (1), their lengths (2),
the left-to-right order of (the midpoints of) their alignments
(3).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--strands1=<var>N</var></span></kbd></td>
<td>Put the 1st genome's sequences: in forwards orientation (0), in
the orientation of most of their aligned bases (1).  In the
latter case, the labels will be colored (in the same way as the
alignments) to indicate the sequences' orientations.  You can
use two colon-separated values for primary and secondary
alignments.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--strands2=<var>N</var></span></kbd></td>
<td>Put the 2nd genome's sequences: in forwards orientation (0), in
the orientation of most of their aligned bases (1).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--max-gap1=<var>FRAC</var></span></kbd></td>
<td>Maximum unaligned gap in the 1st genome.  For example, if two
parts of one DNA read align to widely-separated parts of one
chromosome, it's probably best to cut the intervening region
from the dotplot.  FRAC is a fraction of the length of the
(primary) alignments.  You can specify &quot;inf&quot; to keep all
unaligned gaps.  You can use two comma-separated values,
e.g. &quot;0.5,3&quot; to specify 0.5 for end-gaps (unaligned sequence
ends) and 3 for mid-gaps (between alignments).  You can use two
colon-separated values (each of which may be comma-separated)
for primary and secondary alignments.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--max-gap2=<var>FRAC</var></span></kbd></td>
<td>Maximum unaligned gap in the 2nd genome.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--pad=<var>FRAC</var></span></kbd></td>
<td>Length of pad to leave when cutting unaligned gaps.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--border-pixels=<var>INT</var></span></kbd></td>
<td>Number of pixels between sequences.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--border-color=<var>COLOR</var></span></kbd></td>
<td>Color for pixels between sequences.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--margin-color=<var>COLOR</var></span></kbd></td>
<td>Color for the margins.</td></tr>
</tbody>
</table>
</blockquote>
<div class="section" id="text-options">
<h3>Text options</h3>
<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">-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">--labels1=<var>N</var></span></kbd></td>
<td>Label the displayed regions of the 1st genome with their:
sequence name (0), name:length (1), name:start:length (2),
name:start-end (3).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--labels2=<var>N</var></span></kbd></td>
<td>Label the displayed regions of the 2nd genome with their:
sequence name (0), name:length (1), name:start:length (2),
name:start-end (3).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--rot1=<var>ROT</var></span></kbd></td>
<td>Text rotation for the 1st genome: h(orizontal) or v(ertical).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--rot2=<var>ROT</var></span></kbd></td>
<td>Text rotation for the 2nd genome: h(orizontal) or v(ertical).</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="annotation-options">
<h3>Annotation options</h3>
<p>These options read annotations of sequence segments, and draw them as
colored horizontal or vertical stripes.  This looks good only if the
annotations are reasonably sparse: e.g. you can't sensibly view 20000
gene annotations in one small dotplot.</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">--bed1=<var>FILE</var></span></kbd></td>
<td>Read <a class="reference external" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED-format</a>
annotations for the 1st genome.  They are drawn as stripes, with
coordinates given by the first three BED fields.  The color is
specified by the RGB field if present, else pale red if the
strand is &quot;+&quot;, pale blue if &quot;-&quot;, or pale purple.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--bed2=<var>FILE</var></span></kbd></td>
<td>Read BED-format annotations for the 2nd genome.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--rmsk1=<var>FILE</var></span></kbd></td>
<td>Read repeat annotations for the 1st genome, in RepeatMasker .out
or rmsk.txt format.  The color is pale purple for &quot;low
complexity&quot; and &quot;simple repeats&quot;, else pale red for &quot;+&quot; strand
and pale blue for &quot;-&quot; strand.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--rmsk2=<var>FILE</var></span></kbd></td>
<td>Read repeat annotations for the 2nd genome.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="gene-options">
<h3>Gene options</h3>
<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">--genePred1=<var>FILE</var></span></kbd></td>
<td>Read gene annotations for the 1st genome in <a class="reference external" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format9">genePred format</a>.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--genePred2=<var>FILE</var></span></kbd></td>
<td>Read gene annotations for the 2nd genome.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--exon-color=<var>COLOR</var></span></kbd></td>
<td>Color for exons.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--cds-color=<var>COLOR</var></span></kbd></td>
<td>Color for protein-coding regions.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<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 class="section" id="choosing-sequences">
<h2>Choosing sequences</h2>
<p>For example, 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 (horizontal) genome, and
&quot;-2&quot; selects sequences from the 2nd (vertical) 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>
<p>You can also specify a sequence range; for example this gets the first
1000 bases of chr9:</p>
<pre class="literal-block">
last-dotplot -1 chr9:0-1000 alns alns.png
</pre>
</div>
<div class="section" id="text-font">
<h2>Text font</h2>
<p>You can improve the font quality by increasing its size, e.g. to 20
points:</p>
<blockquote>
last-dotplot -s20 my-alignments my-plot.png</blockquote>
<p>last-dotplot tries to find a nice font on your computer, but may fail
and use an ugly font.  You can specify a font like this:</p>
<pre class="literal-block">
last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png
</pre>
</div>
<div class="section" id="colors">
<h2>Colors</h2>
<p>Colors can be specified in <a class="reference external" href="http://effbot.org/imagingbook/imagecolor.htm">various ways described here</a>.</p>
</div>
</div>
</body>
</html>