Template:Cladex/doc

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< Template:Cladex
Revision as of 12:05, 21 June 2011 by imported>Peter coxhead
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This template is an eXtended version of {{Clade}}, hence the name. Both templates are for drawing branching trees with the nodes and base labels being clickable links. Such diagrams are especially suited to represent evolutionary trees.

Most of the documentation is the same as the parent template, {{Clade}}, and is included below for convenience. Unless the two extra features of {{Cladex}} are needed, you are advised to use {{Clade}}.

The two extra features of {{Cladex}} 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 paraphyletic groups to be identified. See #Bracketting nodes. Note that this feature only works with a cladograms with a very limited set of shapes.

{{Clade}} and {{Cladex}} can be freely mixed, so if only one clade requires either of the extra features, only this one need be specified using {{Cladex}}.

Basic features

Usage


{{cladex
|label1=Base
|1=Node
}}

produces

Base

Node


{{cladex
|1={{cladex
   |label1=[[Subtree1]]
   |1=Leaf1
   |label2=Subtree2
   |2=[[Leaf2]]
   }}
}}

produces

Subtree1 

Leaf1

Subtree2 

Leaf2


{{cladex| style=font-size:75%;line-height:75%
|1={{cladex
   |label1=Subtree1
   |1=Leaf1
   |label2=Subtree2
   |2=Leaf2
   }}
}}

produces

Subtree1

Leaf1

Subtree2

Leaf2


{{cladex
|1={{cladex
   |1={{cladex | thickness=3
      |1=Leaf1
      |2=Leaf2
      }}
   |2=Leaf3
   }}
}}

produces

Leaf1

Leaf2

Leaf3

To replace the solid line with a dashed line, use |stateN=dashed:


{{cladex
|1={{cladex
   |1={{cladex
      |1=Leaf1|state1=dashed
      |2=Leaf2
      }}
   |2=Leaf3
   }}
}}

produces

Leaf1

Leaf2

Leaf3

{{Cladex}} only. To replace a single line leading to the Nth child by a double line, use |stateN=double:


{{cladex
|1={{cladex
   |1={{cladex
      |1=Leaf1
      |2=Leaf2|state2=double
      }}
   |2=Leaf3
   }}
}}

produces

Leaf1

Leaf2

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.

  1. Start with Newick format ((a,b),(c,d))
  2. Replace "(" with "{{cladex|"
  3. Replace ")" with "}}"
  4. Edit to replace commas with pipes and numbers
  5. Edit clade labels if needed

{{cladex
 |1={{cladex
    |1=a
    |2=b
    }}
 |2={{cladex
    |1=c
    |2=d
    }}
}}

Example Perl script to automate the conversion:

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/\(\Q$clade\E\)/${\join('','{{cladex',N,map(T.'|'.($_+1).'='.$branches[$_].N,0..$#branches),T.'}}')}/; # substitute
	}
	pos($tree)=0;
}
$tree=~s/(\t*)\t\}\}/$1\}\}/g; # lazy fix

print $tree;

Using a box

You can nest the templates and use links around the text. You may use non-breaking spaces (&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.

Example
Neornithes  
Paleognathae

 

 Neognathae 
 

Other birds

Galloanserae 

Anseriformes

    

Galliformes

Craciformes

Sample of Template:Cladogram
{{cladogram|title=Example
|caption=Sample of Template:Cladogram
|clades={{cladex| style=font-size:75%;line-height:75%
|label1=[[Neornithes]]  
|1={{cladex
	|label1=[[Paleognathae]]
	|1= 
	|label2= [[Neognathae]] 
	|2={{cladex
	   |1=Other birds
	   |label1= 
	   |label2=[[Galloanserae]] 
	   |2={{cladex
	       |1=[[Anseriformes]]
		   |label2=    
		   |2={{cladex
		      |1=[[Galliformes]]
		      |2=[[Craciformes]]
		      }}
	      }}
	   }}
       }}
  }}
}}

Bracketting nodes

{{Cladex}} only.

To insert a coloured 'bracket' around a set of leaf nodes which follow one another in the generated cladogram:

  • Add barbeginN=colour for the first node, where N is its order as a child and colour is the required colour.
  • Add barN=colour for the remaining nodes other than the last (note that N must be the order of that node as a child of its parent).
  • Add barendN=colour for the last node.

{{cladex
|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
         }}
      }}
   }}
}}

produces

Leaf A

Leaf B

Leaf C

Leaf D

Leaf E

Leaf F

Leaf G

Leaf H

The horizontal lines can be omitted by using |barN=colour throughout. Thus


{{cladex
|1=Leaf A
|2={{cladex
   |1=Leaf B|bar1=midnightblue
   |2=Leaf C|bar2=midnightblue
   }}
|3=Leaf D|bar3=midnightblue 
}}

produces

Leaf A

Leaf B

Leaf C

Leaf D

Note that brackets or bars must only be applied to leaf nodes. In the example above, it may be tempting to write


{{cladex
|1=Leaf A
|bar2=midnightblue
|2={{cladex
   |1=Leaf B
   |2=Leaf C
   }}
|3=Leaf D|bar3=midnightblue
}}

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 colour names, the three or six hex digit notations, such as #FC3 or #F3C630, or the rgb() notation.

Limitations, work-arounds

{{Cladex}} like {{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.

{{Cladex}} is at the very limits of what is possible using table drawing algorithms to produce cladograms. In some cases, extra space has to be added to the name of one of the leaves. Consider the following example. (Note the use of {{Clade}} for the clades which don't have any brackets/bars.)


{{clade
|1={{clade
   |1=Leaf A
   |2={{cladex
      |1=Leaf B|barbegin1=purple
      |2={{cladex
         |1=Leaf C|bar1=purple
         |2={{cladex
            |1=Leaf E|barend1=purple
            |2=Leaf F
            }}
         }}
      }}
   }}
}}

This produces

Leaf A

Leaf B

Leaf C

Leaf E

Leaf F

However, if the name of either Leaf B or Leaf C is sufficiently long so that it extends beyond the end of the name of Leaf E, the bar is not drawn correctly:

Leaf A

Leaf B

Leaf C with a long name

Leaf E

Leaf F

The work-around is that the name of the leaf which would be furthest to the right if all the names were of equal length must be padded, e.g. by adding repeats of &nbsp;. In this case, 22 repetitions of &nbsp; after "Leaf E" produced the following cladogram.

Leaf A

Leaf B

Leaf C with a long name

Leaf E                       

Leaf F

(An alternative technique is to pad out the name of this leaf to make it the same length as the longest by adding hidden text, using e.g. Leaf E<span style="visibility:hidden"> with a long name</span>.)

{{Cladex}} does not work if the bracket or bar includes a clade other than at the very beginning or end of the bracket or bar. Thus the following does not display correctly.


{{clade
|1={{clade
   |1=Leaf A
   |2={{cladex
      |1=Leaf B|barbegin1=purple
      |2={{cladex
         |1={{cladex
            |1=Leaf C1|bar1=purple
            |2=Leaf C2|bar1=purple
            }}
         |2={{cladex
            |1=Leaf E has a long name|barend1=purple
            |2=Leaf F
            }}
         }}
      }}
   }}
}}

Leaf A

Leaf B

Leaf C1

Leaf C2

Leaf E has a long name

Leaf F

As of 21 June 2011, there is no reliable work-around for this issue. (Adding repetitions of &nbsp; to e.g. "Leaf C2" may appear to make the bars line up for one particular font and font size, but this does not work more generally.)

Size limitations

Both {{Clade}} and {{Cladex}} 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 {{Clade}} will not handle the entire cladogram. Because {{Cladex}} 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.