Table of Contents

• TidyTree
  • Parameters
  • setData
    • Parameters
  • setTree
    • Parameters
  • draw
    • Parameters
  • redraw
  • recenter
  • setLayout
    • Parameters
  • setColorOptions
    • Parameters
  • setMode
    • Parameters
  • setType
    • Parameters
  • setRotation
    • Parameters
  • setHStretch
    • Parameters
  • setVStretch
    • Parameters
  • setAnimation
    • Parameters
  • setBranchNodes
    • Parameters
  • eachBranchNode
    • Parameters
  • setBranchLabels
    • Parameters
  • eachBranchLabel
    • Parameters
  • setBranchDistances
    • Parameters
  • eachBranchDistance
    • Parameters
  • setLeafNodes
    • Parameters
  • eachLeafNode
    • Parameters
  • setEquidistantLeaves
    • Parameters
  • setLeafLabels
    • Parameters
  • eachLeafLabel
    • Parameters
  • setRuler
    • Parameters
  • getNodeGUIDs
    • Parameters
  • search
    • Parameters
  • on
    • Parameters
  • off
    • Parameters
  • trigger
    • Parameters
  • destroy
  • validLayouts
  • validTypes
  • validModes
  • validNodeColorModes
  • validBranchColorModes
• circularPoint
  • Parameters
• findNodeColor
  • Parameters
• findBranchColor
  • Parameters
• getAllLeaves
  • Parameters

TidyTree

This class function creates a TidyTree object.

Parameters

• data
• options Object A Javascript object containing options to set up the tree
• events
• newick String A valid newick string

setData

Update the TidyTree’s underlying data structure There are two contexts in which you should call this: 1. You wish to replace the tree with a completely different tree, given by a different newick string 2. Your underlying tree data has changed (e.g. the tree has been re-rooted)

Parameters

• data Object A patristic.Branch object

Returns Object the TidyTree object

setTree

Update the TidyTree’s underlying data structure There are two contexts in which you should call this: 1. You wish to replace the tree with a completely different tree, given by a different newick string 2. Your underlying tree data has changed (e.g. the tree has been re-rooted)

Parameters

• newick String A valid newick string

Returns Object the TidyTree object

draw

Draws a Phylogenetic on the element referred to by selector

Parameters

• selector String A CSS selector

Returns TidyTree the TidyTree object

redraw

Redraws the links and relocates the nodes accordingly

Returns TidyTree The TidyTree Object

recenter

Recenters the tree in the center of the view

Returns TidyTree The TidyTree object

setLayout

Set the TidyTree’s layout

Parameters

• newLayout String The new layout

Returns TidyTree The TidyTree Object

setColorOptions

Set the TidyTree’s colorOptions

Parameters

• newColorOptions Object The new colorOptions

Returns TidyTree The TidyTree Object

setMode

Set the TidyTree’s mode

Parameters

• newMode String The new mode

Returns TidyTree The TidyTree object

setType

Set the TidyTree’s type

Parameters

• newType Boolean The new type

Returns TidyTree the TidyTree object

setRotation

Set the TidyTree’s rotation

Parameters

• degrees Number The new number of degrees by which to rotate the tree

Returns TidyTree the TidyTree object

setHStretch

Set the TidyTree’s Horizontal Stretch

Parameters

• proportion Number The new proportion by which to stretch the tree

Returns TidyTree the TidyTree object

setVStretch

Set the TidyTree’s Vertical Stretch

Parameters

• proportion Number The new proportion by which to stretch the tree

Returns TidyTree the TidyTree object

setAnimation

Set the TidyTree’s animation time. Note that this does not trigger a redraw.

Parameters

• time number The desired duration of an animation, in ms. Set to 0 to turn animations off completely.

Returns TidyTree The TidyTree object

setBranchNodes

Shows or hides the Branch Nodes

Parameters

• show Boolean Should Branch nodes be shown?

Returns TidyTree the TidyTree object

eachBranchNode

Restyles Leaf Nodes

Parameters

• styler Function A function that restyles each node. styler receives a reference to the DOM node to be styled, and an associated data object.

Returns TidyTree the TidyTree Object

setBranchLabels

Set the TidyTree’s branchLabels

Parameters

• show Boolean Should the TidyTree show branchLabels?

Returns TidyTree the TidyTree Object

eachBranchLabel

Restyles Branch Label

Parameters

• styler Function A function that restyles each node. styler receives a reference to the DOM node to be styled, and an associated data object.

Returns TidyTree the TidyTree Object

setBranchDistances

Shows or hides the TidyTree’s branch labels

Parameters

• show Boolean Should the TidyTree show branch distances?

Returns TidyTree The TidyTree Object

eachBranchDistance

Restyles Branch Distances

Parameters

• styler Function A function that restyles each node. styler receives a reference to the DOM node to be styled, and an associated data object.

Returns TidyTree the TidyTree Object

setLeafNodes

Shows or Hides the Leaf Nodes

Parameters

• show Boolean Should leaf nodes be visible?

Returns TidyTree The TidyTree Object

eachLeafNode

Restyles Leaf Nodes

Parameters

• styler Function A function that restyles each node. styler receives a reference to the DOM node to be styled, and an associated data object.

Returns TidyTree the TidyTree Object

setEquidistantLeaves

Set the TidyTree’s leaves to be equidistant

Parameters

• isEquidistant

setLeafLabels

Shows or Hides the TidyTree’s Leaf Labels

Parameters

• show Boolean Should the TidyTree show leafLabels?

Returns TidyTree the TidyTree Object

eachLeafLabel

Restyles Leaf Labels

Parameters

• styler Function A function that restyles each node. styler receives a reference to the DOM node to be styled, and an associated data object.

Returns TidyTree the TidyTree Object

setRuler

Shows or hides the TidyTree’s branch labels

Parameters

• show Boolean Should the TidyTree show branchLabels?

Returns TidyTree The TidyTree Object

getNodeGUIDs

Retrieves the GUIDs of the nodes in the TidyTree instance.

Parameters

• leavesOnly boolean Whether to retrieve GUIDs only for leaf nodes.
• predicate function A function that returns true if the node should be included

Returns Array An array of GUIDs of the nodes.

search

Searches the tree, returns Search Results

Parameters

• test Function A function which takes a Branch and returns a Truthy or Falsy value.

Returns Array The array of results

on

Attaches a new event listener Please note that this is not yet functioning.

Parameters

• events String A space-delimited list of event names
• callback Function The function to run when one of the events occurs.

Returns TidyTree The TidyTree on which this method was called.

off

Removes all event listeners from the given events

Parameters

• events String A space-delimited list of event names

Returns TidyTree The TidyTree on which this method was called.

trigger

Forces the tree to respond as though an event has occurred

Parameters

• events String space-delimited list of names of events to trigger.
• args Spread Any arguments which should be passed to the event handler(s).

Returns any The output of the callback run on event

destroy

Destroys the TidyTree

Returns undefined

validLayouts

The available layouts for rendering trees.

Type: Array

validTypes

The available types for rendering branches.

Type: Array

validModes

The available modes for rendering branches.

Type: Array

validNodeColorModes

The available color modes for rendering nodes.

Type: Array

validBranchColorModes

The available color modes for rendering branches.

Type: Array

circularPoint

Calculate the coordinates of a point transformed onto a circle.

Parameters

• x number The x-coordinate of the center of the point.
• y number The y-coordinate of the center of the point.

Returns Array<number> The new x and y coordinates of the point on the circle.

findNodeColor

Finds the color of a given node based on the color options provided.

Parameters

• node Object The node for which to find the color.
• colorOptions Object The color options object containing the color mode, node list, default color, and highlight color.

Returns string The color of the node.

findBranchColor

Find the color of a given link based on the provided color options.

Parameters

• link string The link for which to find the color.
• colorOptions object The options for different link colors.

Returns string The color of the link.

getAllLeaves

Returns an array of all the child leaf nodes of the given node in a tree.

Parameters

• node Object A node of the tree.
• includeSelf boolean Whether to include the given node itself as a leaf node. Defaults to false.

Returns Array An array of leaf nodes.