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

Module:Sandbox/Jts1882/CladeN

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

  • 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)
  • 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

[mali niŋ | mali mi di yibu sheena n-niŋ]

Branch and clade styling

[mali niŋ | mali mi di yibu sheena n-niŋ]
  • 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 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
[mali niŋ | mali mi di yibu sheena n-niŋ]
  • 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

[mali niŋ | mali mi di yibu sheena n-niŋ]
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.

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    








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