Module:Clade/doc

This is a documentation subpage for Module:Clade.
It may contain usage information, categories and other content that is not part of the original module page.

This Lua module is used on approximately 8,500 pages and changes may be widely noticed. Test changes in the module's /sandbox or /testcases subpages, or in your own module sandbox. Consider discussing changes on the talk page before implementing them.

This module uses TemplateStyles:

Template:Clade/styles.css (sandbox)

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

{{#invoke:Clade|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:Clade

Node structure

label1

leaf 1

label2

label A	leaf A

label B	leaf B

leaf 2 is a nested clade structure

label3

leaf 3

sublabel3

|label1=Node structure  |sublabel1=(brackets)
|style1=background-color:#ffdddd;
|1={{Clade
   |label1=label1  
   |1=leaf 1             
   |label2=label2
   |grouplabel2=&nbsp;leaf 3 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           
   }}

(brackets)

Leaf styling

thicknessN

	1 (default)

	2	line thickness

	3

colorN

	black (default)

	red

	blue

	#00ff00

stateN

	solid (default)

	dotted

	dashed	line styles

	none

	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=&nbsp;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=&nbsp;#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=&nbsp;line styles
      |4=none            |state4=none   |bar4=purple
      |5=double          |state5=double |barend5=purple 
      }}
   }}

(branches)

node styling

thickness

	I

	J

	K

color

	A

	B

	C

state

	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        
   }} }}

(brackets)

newick

string

((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera

subtree

panthera

	lion

	jaguar

	leopard

tiger

	siberian

	bengal

snow leopard

expanded Newick string

|label6=newick  
|style6=background-color:#ddffdd;
|6={{Clade
   |label1=string
   |1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera         
   |label2=subtree 
   |grouplabel2=&nbsp;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)        
      }}
   }}

paraphyly example

	Geraniales

	Myrtales

clade

	Brassicales

	Malvales

label a paraphyletic group within a clade

|label7=paraphyly example&nbsp; |style7=background-color:#ffeeff;
|7={{Clade
   |1={{Clade
      |1=[[Geraniales]]          
      |2=[[Myrtales]]            
      }}
   |grouplabel2=&nbsp;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.

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