Module:Sandbox/Jts1882/CladeN/doc

This is the documentation page for Module:Sandbox/Jts1882/CladeN

This module is rated as beta, and is ready for widespread use. It is still new and should be used with some caution to ensure the results are as expected.

This module uses TemplateStyles:

This module is designed to be used with the CladeN template to draw phylogenetic trees or cladograms. The new template-module combination extends the feature available with the clade and cladex templates. As it replicates the behaviour of the clade and cladex templates it should be suitable for replacing them.

Additionally, the module as the code for a prototype [User:Jts1882/sandbox/templates/NewickConverter|NewickConverter] template, which converts Newick strings into clade structure. This is not to be used in wikipedia articles, but is a utility to help construct cladograms for inclusion in articles.

Usage

{{#invoke:Sandbox/Jts1882/CladeN|main|style={{{style}}}}}

Examples

Simple examples mimicking the clade template:

Example demonstrating more advanced features of cladeN:

User:Jts1882/sandbox/test/Felidae

Example demonstrating features available:

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

	Brassicales

	Malvales

paraphyletic group x

A cladogram illustrating cladeN features.

Technical background

The clade template has many features for customising the appearance. Using them optimally requires some understanding of how the template works. The cladogram is a table and the lines of the cladogram are borders of the cells.

Description Table cell structure Cladogram Code using clade template

A simple clade structure with a single child node (or leaf).

This is an HTML table with two rows and two columns. The upper and lower cells in the left column hold the labels provided by |label= and |sublabel= parameters, respectively. The the cells of the righthand column are merged using the rowspan attribute.

labelA	Leaf A
sublabelA

labelA	LeafA
sublabelA

{{cladeN |thickness=3
|label1=labelA
|sublabel1=sublabelA
|1=LeafA
}}

To build the cladogram, a the text in LeafA can be replaced with another clade structure.

Hence a second HTML table is placed inside a the right-hand cell of the outer table.

labelA

label1	leaf1
sublabel1
label2	leaf2
sublabel2

sublabelA

labelA

label1	leaf1
sublabel1
label2	leaf2
sublabel2

sublabelA

{{cladeN |thickness=3
|label1=labelA
|sublabel1=sublabelA
|1={{cladeN |thickness=3
   |label1=label1
   |sublabel1=sublabel1
   |1=leaf1
   |label2=label2
   |sublabel2=sublabel2
   |2=leaf2
   }}
}}

Add right hand labels with grouplabel

Description

Table cell structure

Cladogram

Code using clade template

Bar adds a solid line to the right of the column containing the leaves.

Group label adds an third column to the basic 2x2 clade structure. As with the leaf the two cells are merged using the rowspan attribute.

labelA	Leaf A	Grouplabel A
sublabelA

labelA	Leaf A	Grouplabel A
sublabelA

{{cladeN |thickness=3
|label1=labelA
|sublabel1=sublabelA
|1=Leaf A
|bar1=blue
|grouplabel1=Grouplabel A
}}

To build the cladogram, the text in LeafA can be replaced with another clade structure.

Hence a second HTML table is placed inside a the right-hand cell of the outer table.

labelA

label1	leaf1
sublabel1
label2	leaf2
sublabel2

Grouplabel A

sublabelA

labelA

label1	leaf1
sublabel1
label2	leaf2
sublabel2

Grouplabel A

sublabelA

{{cladeN |thickness=3
|label1=labelA |sublabel1=sublabelA
|grouplabel1=Grouplabel A
|bar1=blue
|1={{cladeN |thickness=3
   |label1=label1
   |sublabel1=sublabel1
   |1=leaf1 
   |label2=label2
   |sublabel2=sublabel2
   |2=leaf2 
   }}
}}

Grouplabels can be applied at any level.

labelA

label1	leaf1	GL1
sublabel1
label2	leaf2	GL2
sublabel2

Grouplabel A

sublabelA

labelA

label1	leaf1	GL1
sublabel1
label2	leaf2	GL2
sublabel2

Grouplabel A

sublabelA

{{cladeN |thickness=3
|label1=labelA |sublabel1=sublabelA
|grouplabel1=Grouplabel A
|bar1=blue
|1={{cladeN |thickness=3
   |label1=label1
   |sublabel1=sublabel1
   |grouplabel1=GL1
   |bar1=orange
   |1= leaf1 
   |label2=label2
   |sublabel2=sublabel2
   |grouplabel2=GL2
   |bar2=purple
   |2= leaf2 
   }}
}}