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<title>ploticus: proc tree</title>
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<td><br><h2>proc tree</h2></td>
<td align=right>
<small>
<a href="../doc/welcome.html"><img src="../doc/ploticus.gif" border=0></a><br>
Version 2.41 Mar2009
</small><br><a href="../doc/scripthome.html">Scripts</a>
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<title>Manual page for proc_tree(PL)</title>
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<a href="../gallery/tree1.htm">
<img src="../gallery/tree1.gif">
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<b>proc tree</b> draws a rooted tree diagram from a file of data in the Newick format.<tt> </tt>
Newick format is described <b>
<a href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">
here.<tt> </tt>
</a>
</b>
<p>
The example Newick data that created the tree1 example (above) is:
<pre>
(((CAST/EiJ:0.08377, PWD/PhJ:0.15195):0.07349, ((BTBRT+tf/J:0.03469,
(MOLF/EiJ:0.11686, (NOD/LtJ:0.01352, FVB/NJ:0.00729):0.11623):0.05377):0.09926,
(WSB/EiJ:0.07204, AKR/J:0.05425):0.06139):1.20771):0.10313, (129S1SvImJ:0.00533,
(C3H/HeJ:0.04002, BALB/cByJ:0.00089, (NZW/LacJ:0.01695, (KK/HlJ:0.03494,
A/J:0.01334):0.03618):0.02865):0.02484):0.05949, DBA/2J:0.01695)[0.1429];
</pre>
According to the spec, tokens can be delimited by whitespace and newlines, or not.<tt> </tt>
<br><br>
<h2>Notes</h2>
For this proc, a plotting area must be already set up with Y ranging from 0 to the number of leaf nodes
(eg. if you have 12 leaf nodes then use <tt>yrange: 0 12</tt>). X should range from 0 to an upper
end based on the magnitudes embedded in your newick data. Try <tt>xrange: 0 1</tt> and go from there.<tt> </tt>
<p>
This proc doesn't use data as acquired by proc getdata.<tt> </tt>
<p>
This proc is new in version 2.40.<tt> </tt>
<br><br><br>
<h2>Attributes</h2>
The <tt>newickfile</tt> attribute <b>must</b> be specified.<tt> </tt>
<br><br>
<p>
<b>newickfile</b>
<i>pathname</i>
<dl>
<dt> <dd>
File containing data for one tree represented in newick format.<tt> </tt>
The document cited above was used as the formal specification of the grammar.<tt> </tt>
There is one exception: to print a single quote (') within a label, escape it with a backslash.<tt> </tt>
<br><br>
</dl>
<p>
<b>linedetails</b>
<a href="linedetails.html">
linedetails
</a>
<dl>
<dt> <dd>
Details controlling the color, width, and dash pattern of the arc lines.<tt> </tt>
<br><br>
</dl>
<p>
<b>textdetails</b>
<a href="textdetails.html">
textdetails
</a>
<dl>
<dt> <dd>
Details controlling the color and size of the text labels.<tt> </tt>
<br><br>
</dl>
<p>
<b>squaredoff</b>
<tt>yes | no</tt>
<dl>
<dt> <dd>
Default is <tt>yes</tt> which creates arcs that are squared off.
Use <tt>no</tt> for arcs that aren't squared off.<tt> </tt>
<br><br>
</dl>
<p>
<b>rootsym</b>
<a href="symboldetails.html">
symboldetails
</a>
<dl>
<dt> <dd>
Details controlling the data point symbol drawn at the root of the tree when squared-off arcs are being done.<tt> </tt>
To omit the symbol say <tt>rootsym: none</tt>
<br><br>
</dl>
<p>
<b>mustparen</b>
<tt>yes | no</tt>
<dl>
<dt> <dd>
Default is <tt>yes</tt>, meaning that the first non-whitespace character in the newickfile must be an open parenthesis,
or else an error will result. This allows easy screening of inappropriate or garbage input. Use <tt>no</tt>
if you have a legitimate newickfile that doesn't start with an open parenthesis.<tt> </tt>
<br>
<br>
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<a href="../doc/welcome.html">
<img src="../doc/ploticus.gif" border=0></a><br><small>data display engine <br>
<a href="../doc/Copyright.html">Copyright Steve Grubb</a>
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Ploticus is hosted at http://ploticus.sourceforge.net</td><td> </td><td>
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