Documentation

Global

Type Definitions

InitialData

An object describing the tree. Either nodes and links or nwk or nexus are the only required properties,the rest will be set as default
Type:
  • Object
Properties:
Name Type Description
nodes list A list of node names ['ST131','ST11']
links list A list of objects containing source,target and distance , where source and targets are indexes to the nodes list e.g. [{source:0,target:1,distance:10},...]
nwk string A tree in newick format
nexus string A tree in nexus format
layout_algorithm string The initial algorithm to work out node positions. Can be either 'force' or 'greedy'. Default is 'greedy'
layout_data LayoutData Data describing the layout. If none is supplied default values will be supplied and the specified algorithm will calculate the initial layout
metadata object The metadata for the tree - see D3MSTree#addMetadata
initial_category string The initial category to display in the tree - see D3MSTree#changeCategory

LayoutData

Type:
  • Object
Properties:
Name Type Description
node_positions object A dictionary of node id to an array of x,y co-ordinate e.g. {node_a:[23,76],node_b:[65,75]}
node_links object a dictionary of the following
  • max_link_length The maxiumum length of a link . Any link over this distance will be corrected to this length and displayed as dotted.
  • max_link_scale Controls the length that each link is displayed. The links will be scaled (in pixels) between this value and 0
  • log_link_scale If true - link length will be altered to the power of 0.8. Default is false
  • link_font_size The size in pixels of link labels. Default is 10
  • show_link_labels Determines whether the distance labels on links are present. Default is false
  • hide_link_length All links over this length will not be displayed. Default is infinity
  • base_node_size The base size of the nodes. Default is 10
  • show_node_labels Determines whether node labels are present. Default true
  • node_font_size Controls the size (in pixels) of node labels. Default is 14
  • node_text_value The category to display on the node label. Default is none (node id is shown)
  • size_power Controls the size of the nodes. Nodes, will have a radius which equal to number of items associated with the node to the power of size_power multiplied by base_node_size Default value is 0.5
  • show_individual_segments If true then every single component of the node will have its own 'wedge' even those in the same category (although they will be the same colour). Default is false.
  • node_collapsed_value Nodes connecting by links with a distance equal or below this value will be collapsed. Default is 0
  • custom_colours A dictionary of categories to value/colour pairs e.g. {category1:{value_1:"blue",value_2:"red",..},"category_2":{....},...}
  • scale The scale factor (1.0 being normal size)
  • translate The offset of the tree an array of x.y co-ordinate e.g. [30.-20]