Module:Sandbox/Jts1882/CladeN/doc
It may contain usage information, categories and other content that is not part of the original module page.
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
[edit ]{{#invoke:Sandbox/Jts1882/CladeN|main|style={{{style}}}}}
Examples
[edit ]Simple examples mimicking the clade template:
- User:Jts1882/sandbox/templates/Template:Passeroidea
- User:Jts1882/sandbox/templates/Template:Passerida
Example demonstrating more advanced features of cladeN:
Example demonstrating features available:
Template:CladeNleaf 1
leaf 2
leaf A
leaf B
(brackets)
Leaf styling
1 (default)
2
3
colorN
black (default)
red
blue
#00ff00
stateN
solid (default)
dotted
dashed
none
double
(branches) node styling
I
J
K
color
A
B
C
state
X
Y
Z
(brackets) newick
lion
jaguar
leopard
siberian
bengal
snow leopard
expanded Newick string
string
((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera
paraphyly example
x
paraphyletic group x
A cladogram illustrating cladeN features.
Technical background
[edit ]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 |
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 |
leaf1
leaf2
{{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
[edit ]| 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 |
leaf1
leaf2
{{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.
leaf1
GL1leaf2
GL2{{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
}}
}}