Module:Clade/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 clade template to draw phylogenetic trees or cladograms. The new template-module combination extends the feature available with the clade and cladex templates, while replicating the behaviour of the older templates written with the template language. This module is copied from the test version Module:Sandbox/Jts1882/CladeN, which was used with the template Template:CladeN to test the features during development.
Additionally, the module has the code for template {{clade newick converter }}, which is a basic utility to convert Newick strings into nested clade structures. This is not to be used in wikipedia articles, but is a tool to help construct cladograms for inclusion in articles.
The diagram below gives an overview of the features. See the template documentation for a more detailed description of how to use the templates.
Usage
[edit ]{{#invoke:Clade|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:
leaf 1
leaf A
leaf B
leaf 3
|label1=Node structure |sublabel1=(brackets) |style1=background-color:#ffdddd; |1={{Clade |label1=label1 |1=leaf 1 |label2=label2 |grouplabel2= leaf 2 is a nested clade structure |2={{Clade |style=background-color:#ffaaaa; |label1=label A |1=leaf A |label2=label B |2=leaf B |bar1=purple |bar2=purple }} |label3=label3 |sublabel3=sublabel3 |3=leaf 3 }}
1 (default)
2
line thickness3
black (default)
red
blue
#00ff00
solid (default)
dotted
dashed
line stylesnone
double
|label3=Leaf styling |sublabel3=(branches) |style3=background-color:#eeeeee; |3={{Clade |label1=thicknessN |1={{Clade |1=1 (default) |thickness1=1 |barbegin1=blue |2=2 |thickness2=2 |bar2=blue |barlabel2= line thickness |3=3 |thickness3=3 |barend3=blue }} |label2=colorN |2={{Clade |1=black (default) |color1=black |2=red |color2=red |3=blue |color3=blue |4= #00ff00 |color4=#00ff00 }} |label3=stateN |3={{Clade |1=solid (default) |state1=solid |barbegin1=purple |2=dotted |state2=dotted |bar2=purple |3=dashed |state3=dashed |bar3=purple |barlabel3= line styles |4=none |state4=none |bar4=purple |5=double |state5=double |barend5=purple }} }}
I
J
K
A
B
C
X
Y
Z
|label4=node styling |sublabel4=(brackets) |style4=background-color:#ffffee; |4={{Clade |label1=thickness |1={{Clade |thickness=3 |1=I |2=J |3=K }} |label2=color |2={{Clade |color=red |1=A |2=B |3=C }} |label3=state |3={{Clade |state=dashed |1=X |2=Y |3=Z }} }}
((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera
lion
jaguar
leopard
siberian
bengal
snow leopard
|label6=newick |style6=background-color:#ddffdd; |6={{Clade |label1=string |1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera |label2=subtree |grouplabel2= expanded Newick string |grouplabelstyle2=vertical-align: middle; |2={{Clade |style=background-color:#ccffcc; |newick1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera |1=Leaf1 (redundant if newick1 set) }} }}
|label7=paraphyly example |style7=background-color:#ffeeff; |7={{Clade |1={{Clade |1=[[Geraniales]] |2=[[Myrtales]] }} |grouplabel2= label a paraphyletic group within a clade |label2=clade |style2=background-color:#ffddff; |2={{Clade |1=[[Crossosomatales]] |barbegin1=purple |2={{Clade |1=[[Picramniales]] |bar1=purple |2={{Clade |1=[[Sapindales]] |bar1=purple |2={{Clade |1=[[Huerteales]] |bar1=purple |2={{Clade |1=[[Brassicales]] |barend1=purple |2=[[Malvales]] |style2=background-color:#ff99ff; }} }} }} }} }} }}
A cladogram illustrating clade features.