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<title>ploticus: proc tree</title>
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  <table cellpadding=2 width=550><tr>
  <td><br><h2>proc tree</h2></td>
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  <small>
  <a href="../doc/welcome.html"><img src="../doc/ploticus.gif" border=0></a><br>
  Version 2.40 Jan'08
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.>>

.TH proc_tree PL "15-JAN-2008   PL ploticus.sourceforge.net"

.ig >>
<center>
<a href="../gallery/tree1.htm">
<img src="../gallery/tree1.gif">
</a>
</center>
.>>

\fBproc tree\fR draws a rooted tree diagram from a file of data in the Newick format.
Newick format is described  \fB
.ig >>
<a href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">
.>>
\0here.
.ig >>
</a>
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\fR  
.LP
The example Newick data that created the tree1 example (above) is:
.nf
(((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];
.fi
According to the spec, tokens can be delimited by whitespace and newlines, or not.

.ig >>
<br><br>
.>>
.SH Notes
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 \fCyrange: 0 12\fR).  X should range from 0 to an upper
end based on the magnitudes embedded in your newick data.  Try \fCxrange: 0 1\fR and go from there.
.LP
This proc doesn't use data as acquired by proc getdata.
.LP
This proc is new in version 2.40.


.ig >>
<br><br><br>
.>>

.SH Attributes
The \fCnewickfile\fR attribute \fBmust\fR be specified.

.ig >>
<br><br>
.>>

.LP
\fBnewickfile\fR 
.ig >>
&nbsp; &nbsp;
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\fIpathname\fR
.IP \0
File containing data for one tree represented in newick format.
The document cited above was used as the formal specification of the grammar.
There is one exception: to print a single quote (') within a label, escape it with a backslash.

.ig >>
<br><br>
.>>

.LP
\fBlinedetails\fR
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&nbsp; &nbsp;
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<a href="linedetails.html">
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\0linedetails
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</a>
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.IP \0
Details controlling the color, width, and dash pattern of the arc lines.

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<br><br>
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.LP
\fBtextdetails\fR
.ig >>
&nbsp; &nbsp;
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.ig >>
<a href="textdetails.html">
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\0textdetails
.ig >>
</a>
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.IP \0
Details controlling the color and size of the text labels.

.ig >>
<br><br>
.>>
.LP
\fBsquaredoff\fR
.ig >>
&nbsp; &nbsp;
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\fCyes | no\fR
.IP \0
Default is \fCyes\fR which creates arcs that are squared off.  
Use \fCno\fR for arcs that aren't squared off.


.ig >>
<br><br>
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.LP
\fBrootsym\fR
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&nbsp; &nbsp;
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<a href="symboldetails.html">
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\0symboldetails
.ig >>
</a>
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.IP \0
Details controlling the data point symbol drawn at the root of the tree when squared-off arcs are being done.
To omit the symbol say \fCrootsym: none\fR

.ig >>
<br><br>
.>>
.LP
\fBmustparen\fR
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&nbsp; &nbsp;
.>>
\fCyes | no\fR
.IP \0
Default is \fCyes\fR, 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 \fCno\fR
if you have a legitimate newickfile that doesn't start with an open parenthesis.


.ig >>
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