User:Jts1882/sandbox/templates/CladeN/doc

Description

This is a experimental version of the clade template, using a Lua module to create the tables.

Module:Sandbox/Jts1882/CladeN

Basic usage

The new template should exactly replicate the use of the Clade and cladex templates.

Clade features

• Terminal nodes (leaves) with |N=leafname
• New clades with |N=clade{{ ... }}
• Internal node labelling with labelN
• Dashed or dotted lines on branches (stateN applied to branch N)
• Different thickness on node brackets (thickness applied to the clade)

Cladex features

• Double lines on branches to denote polyphyly/paraphyly (|stateN=double)
• Coloured bars to right of taxa to indicate groups (e.g paraphyly) (barN, barbeginN, barendN)

New or extended features

Branch and clade styling

• Styling of dashed/dotted lines and thickness extended to both clade and branch levels
  • stateN and ThicknessN change just the branch
  • state and thickness change the clade (the bracket)
  • note: they apply only to a single clade level; they don't extend down the tree
• Colour option for line styling (using color and colorN)
• CSS styling of branches and clades through use of styleN or style, respectively
  • For instance, |styleN=background-color:green; adds a background color to the node or clade.
  • Because it uses CSS, the colours propagate through the table structure and changing the colour on a branch with styleN will apply the background to all subtrees.
  • You cannot used this to change the tree structure because that uses HTML border-style, border-width and border-color, which are controlled with state, thickness and color, respectively (see above)

Newick strings

• Newick strings can be used instead of clade to extend the tree, although styling options are limited with this method.
  • E.g. |newick1=(lion,tiger)panthera
  • This feature is limited to simple strings. The current parser doesn't strip out additional information (e.g. lengths after colons).
  • Beware of spaces. Don't use spaces adjacent to the newick string delimiters (parentheses, commas), although they can be used in the taxon names.
• If more options are required, the trees can be converted to the clade structure using the NewickConverter template

Caption, footer description and group labels

• Group labels to provide additional information (generally used with the bar structure)
  • use grouplabel to add the text of the label
  • use labelstyle to apply CSS styling
• Captions and a footer description can be added (similar to cladogram)
  • caption and captionstyle add a CSS styled caption to the top of diagram
  • footer and footerstyle add a CSS styled description below the diagram

Demonstration illustrating features

Template:CladeN

Demo	Node structure label1 leaf 1 label2 leaf 2 label3 label A leaf A label B leaf B leaf 3 is a transcluded cladeN structure (brackets)   Leaf styling thicknessN 1 (default) 2 3 line thickness colorN black (default) red blue  #00ff00 stateN solid (default) dotted dashed none double line styles (branches) node styling thickness I J K color A B C state X Y Z (brackets) newick subtree panthera lion jaguar leopard tiger siberian bengal snow leopard  expanded Newick string string ((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera paraphyly example  Geraniales Myrtales x Crossosomatales Picramniales Sapindales Huerteales Brassicales Malvales  paraphyletic group x
A cladogram illustrating cladeN features.

Examples

Felidae

Felidae

Panthera lineage Pantherinae Neofelis Clouded leopards Panthera Lion Jaguar Leopard Tiger Snow leopard Felinae Bay cat lineage Pardofelis Bay cat Asian golden cat Marbled cat Caracal lineage Caracal Caracal African golden cat Serval Ocelot lineage Leopardus Ocelot Margay Andean mountain cat Pampas cat Geoffroy's cat Kodkod Tigrina Lynx lineage Lynx Iberian lynx Eurasian lynx Canadian lynx Bobcat Puma lineage Acinonyx Cheetah Puma Puma (Cougar) Jaguarundi] Leopard cat lineage Otocolobus Pallas cat Prionailurus Rusty spotted cat Asian leopard cat Fishing cat Flat-headed cat Felis   Domestic cat European wild cat African wild cat Chinese desert cat Desert cat Black-footed cat Jungle cat Domestic cat lineage

More examples

User:Jts1882/sandbox/templates/Template:Passerida

User:Jts1882/sandbox/templates/Template:Passerida

User:Jts1882/sandbox/templates/Template:Passeroidea

User:Jts1882/sandbox/templates/Template:APG_III_system