Difference between revisions of "Template:Cladex/doc"

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{{Documentation subpage}}
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#REDIRECT [[Template:Clade/doc]]
<!---PLEASE ADD METADATA TO THE <includeonly> SECTION AT THE BOTTOM OF THIS PAGE -->
 
 
 
This template is an eXtended version of {{tl|Clade}}, hence the name. Both templates are for drawing branching trees with the node and base labels being clickable links. Such diagrams are especially suited to represent evolutionary trees (cladograms).
 
 
 
Most of the documentation is the same as the parent template, {{tl|Clade}}, and is included below for convenience. Unless the two extra features of <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> are needed, you are advised to use {{tl|Clade}}.
 
 
 
The two extra features of <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> are:
 
* Double lines leading to a node can be used as easily as dotted lines.
 
* Brackets or bars of a chosen colour can be placed to the right of a set of leaf nodes in the cladogram, thus allowing [[Paraphyly|paraphyletic]] groups to be identified. See [[#Bracketting nodes]].
 
 
 
{{tl|Clade}} and <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> can be freely mixed, so if only some clades require either of the extra features, only these need be specified using <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki>.
 
 
 
==Basic features==
 
 
 
'''Use {{tl|Clade}} unless the extra features of {tl|Cladex}} are needed.'''
 
 
 
=== Usage ===
 
 
 
<pre>
 
<nowiki>
 
{{clade
 
|label1=Base
 
|1=Node
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
 
 
{{clade
 
|label1=Base
 
|1=Node
 
}}
 
 
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{clade
 
  |label1=[[Subtree1]]
 
  |1=Leaf1
 
  |label2=Subtree2
 
  |2=[[Leaf2]]
 
  }}
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
 
 
{{clade
 
|1={{clade
 
  |label1=[[Subtree1]]&nbsp;
 
  |1=Leaf1
 
  |label2=Subtree2&nbsp;
 
  |2=[[Leaf2]]
 
  }}
 
}}
 
 
 
<pre>
 
<nowiki>
 
{{clade| style=font-size:75%;line-height:75%
 
|1={{clade
 
  |label1=Subtree1
 
  |1=Leaf1
 
  |label2=Subtree2
 
  |2=Leaf2
 
  }}
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
 
 
{{clade| style=font-size:75%;line-height:75%
 
|1={{clade
 
  |label1=Subtree1
 
  |1=Leaf1
 
  |label2=Subtree2
 
  |2=Leaf2
 
  }}
 
}}
 
 
 
Note that the order of the parameters does not matter. Exactly the same output is produced by
 
<pre>
 
<nowiki>
 
{{clade| style=font-size:75%;line-height:75%
 
|1={{clade
 
  |1=Leaf1
 
  |2=Leaf2
 
  |label2=Subtree2
 
  |label1=Subtree1
 
  }}
 
}}</nowiki>
 
</pre>
 
 
 
{{clade| style=font-size:75%;line-height:75%
 
|1={{clade
 
  |1=Leaf1
 
  |2=Leaf2
 
  |label2=Subtree2
 
  |label1=Subtree1
 
  }}
 
}}
 
 
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{clade
 
  |1={{clade | thickness=3
 
      |1=Leaf1
 
      |2=Leaf2
 
      }}
 
  |2=Leaf3
 
  }}
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
 
 
{{clade
 
|1={{clade
 
  |1={{clade | thickness=3
 
      |1=Leaf1
 
      |2=Leaf2
 
      }}
 
  |2=Leaf3
 
  }}
 
}}
 
 
 
To replace the solid line with a dashed line, use |stateN=dashed.
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{clade
 
  |1={{clade
 
      |1=Leaf1|state1=dashed
 
      |2=Leaf2
 
      }}
 
  |2=Leaf3
 
  }}
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
{{clade
 
|1={{clade
 
  |1={{clade
 
      |1=Leaf1|state1=dashed
 
      |2=Leaf2
 
      }}
 
  |2=Leaf3
 
  }}
 
}}
 
 
 
'''<nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> only.''' To replace a single line leading to the Nth child by a double line, use <tt>|stateN=double</tt>.  Notice that <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> has only been used for the (sub)clade where the double line is wanted. The outermost clade should always be specified with {tl|Clade}} unless its style is altered – see below.
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{clade
 
  |1={{cladex
 
      |1=Leaf1
 
      |2=Leaf2|state2=double
 
      }}
 
  |2=Leaf3
 
  }}
 
}}
 
</nowiki>
 
</pre>
 
 
 
produces
 
{{clade
 
|1={{clade
 
  |1={{cladex
 
      |1=Leaf1
 
      |2=Leaf2|state2=double
 
      }}
 
  |2=Leaf3
 
  }}
 
}}
 
 
 
=== Tips ===
 
 
 
An easy way of creating larger cladograms is to use the Newick format and proceed to edit it using a suitable text editor to produce the markup.
 
 
 
# Start with [[Newick format]] ((a,b),(c,d))
 
# Replace "(" with <nowiki>"{{clade|"</nowiki>
 
# Replace ")" with <nowiki>"}}"</nowiki>
 
# Edit to replace commas with pipes and numbers
 
# Edit clade labels if needed
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{clade
 
    |1=a
 
    |2=b
 
    }}
 
|2={{clade
 
    |1=c
 
    |2=d
 
    }}
 
}}
 
</nowiki>
 
</pre>
 
 
 
Example Perl script to automate the conversion:
 
<source lang="perl">
 
use constant N=>"\n";
 
use constant T=>"\t";
 
 
 
my $tree='((a,b),(c,d));'; # get sequence
 
$tree=~s/[\n\r]//g; # loose those spaces
 
$tree=~ s/\:[\.\d]+//g; # loose those lengths
 
while ($tree=~ m/\(/) {
 
foreach my $clade ($tree=~ m/\(([^\(\)]+)\)/g) {
 
my @branches=split /\,/,$clade;
 
s/(\t+)/$1\t/g for @branches;
 
die 'ERROR: degenerate/empty node!'.N if $#branches<1;
 
$tree=~ s/\(\Q$clade\E\)/${\join('','{{clade',N,map(T.'|'.($_+1).'='.$branches[$_].N,0..$#branches),T.'}}')}/; # substitute
 
}
 
pos($tree)=0;
 
}
 
$tree=~s/(\t*)\t\}\}/$1\}\}/g; # lazy fix
 
 
 
print $tree;
 
</source>
 
 
 
=== Using a box ===
 
 
 
You can nest the templates and use links around the text. You may use non-breaking spaces (&amp;nbsp;) to obtain spaces or to have labels that have spaces.
 
 
 
The entire cladogram can be placed in a box so that text flows nicely around it.
 
Use within [[Template:Cladogram]].
 
{{cladogram|title=Example
 
|caption=Sample of Template:Cladogram
 
|clades={{clade| style=font-size:75%;line-height:75%
 
|label1=[[Neornithes]]&nbsp;&nbsp;
 
|1={{clade
 
|label1=[[Paleognathae]]
 
|1=&nbsp;
 
|label2=&nbsp;[[Neognathae]]&nbsp;
 
|2={{clade
 
  |1=Other birds
 
  |label1=&nbsp;
 
  |label2=[[Galloanserae]]&nbsp;
 
  |2={{clade
 
      |1=[[Anseriformes]]
 
  |label2=&nbsp;&nbsp;&nbsp;&nbsp;
 
  |2={{clade
 
      |1=[[Galliformes]]
 
      |2=[[Craciformes]]
 
      }}
 
      }}
 
  }}
 
      }}
 
  }}
 
}}<pre>
 
{{cladogram|title=Example
 
|caption=Sample of Template:Cladogram
 
|clades={{clade| style=font-size:75%;line-height:75%
 
|label1=[[Neornithes]]&nbsp;&nbsp;
 
|1={{clade
 
|label1=[[Paleognathae]]
 
|1=&nbsp;
 
|label2=&nbsp;[[Neognathae]]&nbsp;
 
|2={{clade
 
  |1=Other birds
 
  |label1=&nbsp;
 
  |label2=[[Galloanserae]]&nbsp;
 
  |2={{clade
 
      |1=[[Anseriformes]]
 
  |label2=&nbsp;&nbsp;&nbsp;&nbsp;
 
  |2={{clade
 
      |1=[[Galliformes]]
 
      |2=[[Craciformes]]
 
      }}
 
      }}
 
  }}
 
      }}
 
  }}
 
}}</pre>
 
 
 
==Bracketting nodes==
 
'''<nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> only.'''
 
 
 
To insert a coloured 'bracket' around a set of leaf nodes which follow one another in the generated cladogram:
 
* Add <tt>barbeginN=''colour''</tt> for the first leaf node, where N is the order of that leaf node within ''its'' clade, and ''colour'' is the required colour.
 
* Add <tt>barN=''colour''</tt> for the remaining nodes other than the last (note that N must be the order of that node within ''its'' clade).
 
* Add <tt>barendN=''colour''</tt> for the last node.
 
 
 
Either the outermost clade must be specified by {{tl|Clade}} or if <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> is needed there, <tt>|style=width:auto</tt> must be present.
 
 
 
<pre>
 
<nowiki>
 
{{clade
 
|1={{cladex
 
  |1=Leaf A
 
  |2=Leaf B|barbegin2=green
 
  |3=Leaf C|bar3=green
 
  |4={{cladex
 
      |1=Leaf D|barend1=green
 
      |2=Leaf E
 
      |3=Leaf F|barbegin3=purple 
 
      |4={{cladex
 
        |1=Leaf G|bar1=purple
 
        |2=Leaf H|barend2=purple
 
        }}
 
      }}
 
  }}
 
}}
 
</nowiki>
 
</pre>
 
 
 
produces
 
{{clade
 
|1={{cladex
 
  |1=Leaf A
 
  |2=Leaf B|barbegin2=green
 
  |3=Leaf C|bar3=green
 
  |4={{cladex
 
      |1=Leaf D|barend1=green
 
      |2=Leaf E
 
      |3=Leaf F|barbegin3=purple 
 
      |4={{cladex
 
        |1=Leaf G|bar1=purple
 
        |2=Leaf H|barend2=purple
 
        }}
 
      }}
 
  }}
 
}}
 
 
 
The horizontal lines can be omitted by using <tt>|barN=''colour''</tt> throughout. Thus the following (note the use of <tt>|style=width:auto</tt> since the outermost clade uses the extra features of <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki>):
 
 
 
<pre>
 
<nowiki>
 
{{cladex|style=width:auto
 
|1=Leaf A
 
|2={{cladex
 
  |1=Leaf B|bar1=midnightblue
 
  |2=Leaf C|bar2=midnightblue
 
  }}
 
|3=Leaf D|bar3=midnightblue
 
}}</nowiki>
 
</pre>
 
 
 
produces
 
{{cladex|style=width:auto
 
|1=Leaf A
 
|2={{cladex
 
  |1=Leaf B|bar1=midnightblue
 
  |2=Leaf C|bar2=midnightblue
 
  }}
 
|3=Leaf D|bar3=midnightblue
 
}}
 
 
 
''Note that brackets or bars must only be applied to leaf nodes.'' In the example above, it may be tempting to write
 
 
 
<pre>
 
<nowiki>
 
{{clade
 
|1=Leaf A
 
|bar2=midnightblue
 
|2={{cladex
 
  |1=Leaf B
 
  |2=Leaf C
 
  }}
 
|3=Leaf D|bar3=midnightblue
 
}}</nowiki>
 
</pre>
 
 
 
with the expectation that the bar will be to the right of the whole of the clade containing Leaf B and Leaf C. This does not work!
 
 
 
===Specifying colours===
 
 
 
You can use any of the ways in which colours can be specified in HTML; e.g. the standard [http://www.w3schools.com/html/html_colornames.asp colour names], the three or six hex digit notations, such as #FC3 or #F3C630, or the <tt>rgb()</tt> notation.
 
 
 
===Limitations, debugging===
 
 
 
<nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> like {{tl|Clade}} uses the browser's (user agent's) algorithms for drawing tables. As these differ from browser to browser, the cladograms produced will not look the same on all browsers.
 
 
 
The bracket/bar drawing part of <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> is probably close to the limits of what is possible using table drawing algorithms to produce cladograms. The vertical bar is always drawn at the very right-hand edge of the (hidden) outermost table which <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> and {{tl|Clade}} produce, which is often not how it would be drawn manually. {{As of|2011|June|21}}, there is no known way round this.
 
 
 
If your cladogram doesn't display brackets/bars as you expected, check that:
 
* You understand the numbering system for the parameters <tt>barN<tt>, etc. The N must be the same as the number of the child within the clade. Thus typically you should write <tt>N=''label for leaf''|barN=''colour for bar''</tt>.
 
* You have only attempted to apply brackets/bars to ''leaf'' nodes.
 
* Either the outermost clade uses {{tl|Clade}} or if it has to use <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki>, then <tt>|style=width:auto</tt> is present.
 
 
 
==Size limitations==
 
 
 
Both {{tl|Clade}} and <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> have some size limitations.
 
* Both currently allow only a maximum of 17 children per node. It may seem that this could easily be increased by editing the templates, but see the next point.
 
* Both will only expand a cladogram up to a certain level of complexity. The cladogram at [[APG_III_system#Phylogeny]] has had to be broken into two parts, because {{tl|Clade}} will not handle the entire cladogram. Because <nowiki>{{</nowiki>Cladex<nowiki>}}</nowiki> has more complex internal code, it runs out of the allowed resources for template expansion sooner, and will only handle templates which are slightly smaller. ''Any change to either of these templates could result in larger cladograms failing to display correctly.''
 
<includeonly>
 
<!-- Categories and interwikis go here: -->
 
 
 
[[Category:Genealogy formatting templates|{{PAGENAME}}]]
 
[[Category:Wikipedia formatting and function templates|{{PAGENAME}}]]
 
 
 
</includeonly>
 

Latest revision as of 13:17, 29 January 2020

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