- Phylotree
An instance of a phylotree. Sets event listeners, parses tags, and creates links that represent branches.
- getBranchLengths() ⇒
Array Returns branch lengths
- setBranchLength(attr) ⇒
Object Get or set branch length accessor.
- normalize()
Normalizes branch lengths
- scale(function)
Scales branch lengths
- branchName(attr) ⇒
Get or set branch name accessor.
- mrca() ⇒
Return most recent common ancestor of a pair of nodes.
- deleteANode(The) ⇒
Delete a given node.
- getTips() ⇒
Array Get the tips of the tree
- getInternals() ⇒
Array Get the internal nodes of the tree
- getRootNode() ⇒
Get the root node.
- getNodes() ⇒
Array Get an array of all nodes.
- getNodeByName(name) ⇒
Node Get a node by name.
- assignAttributes(attributes)
Add attributes to nodes. New attributes will be placed in the
annotationskey of any nodes that are matched.- isLeafNode(A) ⇒
Bool Determine if a given node is a leaf node.
- updateKeyName(old_key, new_key) ⇒
Update a given key name in each node.
- reroot(node, if) ⇒
Phylotree Reroot the tree on the given node.
- leftChildRightSibling(tree) ⇒
Object Traverses a tree that represents left-child right-sibling
- clusterPicker(tree, bootstrap_thresold, diameter_threshold, root_node, missing_bootstrap_value) ⇒
Implements a linear time / space version of the Cluster picker algorithm
- newickParser(nwk_str) ⇒
Object Parses a Newick string into an equivalent JSON representation that is suitable for consumption by
hierarchy.Optionally accepts bootstrap values. Currently supports Newick strings with or without branch lengths, as well as tagged trees such as
(a,(b{TAG},(c{TAG},d{ANOTHERTAG})))- getNewick(annotator) ⇒
String Return Newick string representation of a phylotree.
- loadAnnotations(tree, NEXUS) ⇒
Object Loads annotations from a nexus-formatted buffer and annotates existing tree nodes appropriately.
- computeMidpoint(tree) ⇒
Object Compute midpoint of a phylogenetic tree
- toggleCollapse(node) ⇒
Phylotree Toggle collapsed view of a given node. Either collapses a clade into a smaller blob for viewing large trees, or expands a node that was previously collapsed.
- modifySelection(node_selecter, attr, place, skip_refresh, mode) ⇒
Modify the current selection, via functional programming.
- getSelection() ⇒
Array Get nodes which are currently selected.
- selectAllDescendants(node, terminal, internal) ⇒
Array Select all descendents of a given node, with options for selecting terminal/internal nodes.
- selectionCallback(callback) ⇒
Getter/setter for the selection callback. This function is called every time the current selection is modified, and its argument is an array of nodes that make up the current selection.
- nodeSpan(attr) ⇒
Get or set the current node span. If setting, the argument should be a function of a node which returns a number, so that node spans can be determined dynamically. Alternatively, the argument can be the string
"equal", to give all nodes an equal span.- nodeLabel(attr) ⇒
Get or set nodeLabel accessor.
- nodeBubbleSize(A) ⇒
Float Return the bubble size of the current node.
- selectionLabel(attr) ⇒
Getter/setter for the selection label. Useful when allowing users to make multiple selections.
- nodeSpan(attr) ⇒
Get or set the current node span. If setting, the argument should be a function of a node which returns a number, so that node spans can be determined dynamically. Alternatively, the argument can be the string
"equal", to give all nodes an equal span.- selectionCallback(callback) ⇒
Getter/setter for the selection callback. This function is called every time the current selection is modified, and its argument is an array of nodes that make up the current selection.
An instance of a phylotree. Sets event listeners, parses tags, and creates links that represent branches.
Returns: Phylotree - phylotree - itself, following the builder pattern.
| Param | Type | Description |
|---|---|---|
| nwk | Object |
A Newick string, PhyloXML string, or hierarchical JSON representation of a phylogenetic tree. |
| options | Object |
- boostrap_values - type - format type |
Returns branch lengths
Kind: global function
Returns: Array - array of branch lengths
Get or set branch length accessor.
Kind: global function
Returns: Object - The branch length accessor if getting, or the current this if setting.
| Param | Type | Description |
|---|---|---|
| attr | function |
Empty if getting, or new branch length accessor if setting. |
Normalizes branch lengths
Scales branch lengths
Kind: global function
| Param | Type | Description |
|---|---|---|
| function | function |
that scales the branches |
Get or set branch name accessor.
Kind: global function
Returns: The nodeLabel accessor if getting, or the current this if setting.
| Param | Type | Description |
|---|---|---|
| attr | function |
(Optional) If setting, a function that accesses a branch name from a node. |
Return most recent common ancestor of a pair of nodes.
Kind: global function
Returns: An array of strings, comprising each tag that was read.
Delete a given node.
Kind: global function
Returns: The current phylotree.
| Param | Type | Description |
|---|---|---|
| The | Node |
node to be deleted, or the index of such a node. |
Get the tips of the tree
Kind: global function
Returns: Array - Nodes in the current phylotree.
Get the internal nodes of the tree
Kind: global function
Returns: Array - Nodes in the current phylotree.
Get the root node.
Kind: global function
Returns: the current root node of the phylotree.
Get an array of all nodes.
Kind: global function
Returns: Array - Nodes in the current phylotree.
Get a node by name.
Kind: global function
Returns: Node - Desired node.
| Param | Type | Description |
|---|---|---|
| name | String |
Name of the desired node. |
Add attributes to nodes. New attributes will be placed in the
annotations key of any nodes that are matched.
Kind: global function
| Param | Type | Description |
|---|---|---|
| attributes | Object |
An object whose keys are the names of nodes to modify, and whose values are the new attributes to add. |
Determine if a given node is a leaf node.
Kind: global function
Returns: Bool - Whether or not the node is a leaf node.
| Param | Type | Description |
|---|---|---|
| A | Node |
node in a tree. |
Update a given key name in each node.
Kind: global function
Returns: The current this.
| Param | Type | Description |
|---|---|---|
| old_key | String |
The old key name. |
| new_key | String |
The new key name. |
reroot(node, if) ⇒ Phylotree
Reroot the tree on the given node.
Kind: global function
Returns: Phylotree - The current phylotree.
| Param | Type | Description |
|---|---|---|
| node | Node |
Node to reroot on. |
| if | fraction |
specified, partition the branch not into 0.5 : 0.5, but according to the specified fraction |
TODO add the option to root in the middle of a branch
Kind: inner property of reroot
Traverses a tree that represents left-child right-sibling
Kind: global function
Returns: Object - An edge list that represents the original multi-way tree
| Param | Type | Description |
|---|---|---|
| tree | Object |
- the phylotree.js tree object |
Implements a linear time / space version of the Cluster picker algorithm
Kind: global function
Returns: an array of clusters, where cluster =
{
'root' : [root node of cluster],
'members' : [list of leaf. nodes],
'diameter' : max distance in the cluster,
'bootstrap' : bootstrap support at the root node
}
| Param | Description |
|---|---|
| tree | - the tree object |
| bootstrap_thresold | - value in [0,1] that sets the stringency of bootstrap support |
| diameter_threshold | - value >=0 that defines the maximum allowable pairwise distance in a cluster |
| root_node | - if specified, traverse the tree starting here (useful for only looking at parts of the tree), tree root by default |
| missing_bootstrap_value | - if a branch is missing bootstrap support value, use this value instead (1.0 by default) |
Parses a Newick string into an equivalent JSON representation that is
suitable for consumption by hierarchy.
Optionally accepts bootstrap values. Currently supports Newick strings with or without branch lengths,
as well as tagged trees such as
(a,(b{TAG},(c{TAG},d{ANOTHERTAG})))
Kind: global function
Returns: Object - An object with keys json and error.
| Param | Type | Description |
|---|---|---|
| nwk_str | String |
A string representing a phylogenetic tree in Newick format. |
| bootstrap_values. | Object |
Return Newick string representation of a phylotree.
Kind: global function
Returns: String - newick - Phylogenetic tree serialized as a Newick string.
| Param | Type | Description |
|---|---|---|
| annotator | function |
Function to apply to each node, determining what label is written (optional). |
Loads annotations from a nexus-formatted buffer and annotates existing tree nodes appropriately.
Kind: global function
Returns: Object - Annotations
| Param | Type | Description |
|---|---|---|
| tree | Object |
Instatiated phylotree |
| NEXUS | String |
string |
Compute midpoint of a phylogenetic tree
Kind: global function
Returns: Object - the calculated midpoint to root on
{ location: root_node, breakpoint: 0 }
| Param | Type | Description |
|---|---|---|
| tree | Object |
- the phylotree.js tree object |
toggleCollapse(node) ⇒ Phylotree
Toggle collapsed view of a given node. Either collapses a clade into a smaller blob for viewing large trees, or expands a node that was previously collapsed.
Kind: global function
Returns: Phylotree - The current phylotree.
| Param | Type | Description |
|---|---|---|
| node | Node |
The node to toggle. |
Modify the current selection, via functional programming.
Kind: global function
Returns: The current this.
| Param | Type | Description |
|---|---|---|
| node_selecter | function |
A function to apply to each node, which determines whether they become part of the current selection. Alternatively, if restricted-selectable mode is enabled, a string describing one of the pre-defined restricted-selectable options. |
| attr | String |
(Optional) The selection attribute to modify. |
| place | Boolean |
(Optional) Whether or not placenodes should be called. |
| skip_refresh | Boolean |
(Optional) Whether or not a refresh is called. |
| mode | String |
(Optional) Can be "toggle", "true", or "false". |
Get nodes which are currently selected.
Kind: global function
Returns: Array - An array of nodes that match the current selection.
Select all descendents of a given node, with options for selecting terminal/internal nodes.
Kind: global function
Returns: Array - An array of selected nodes.
| Param | Type | Description |
|---|---|---|
| node | Node |
The node whose descendents should be selected. |
| terminal | Boolean |
Whether to include terminal nodes. |
| internal | Boolean |
Whther to include internal nodes. |
Getter/setter for the selection callback. This function is called every time the current selection is modified, and its argument is an array of nodes that make up the current selection.
Kind: global function
Returns: The current selectionCallback if getting, or the current this if setting.
| Param | Type | Description |
|---|---|---|
| callback | function |
(Optional) The selection callback function. |
Get or set the current node span. If setting, the argument should
be a function of a node which returns a number, so that node spans
can be determined dynamically. Alternatively, the argument can be the
string "equal", to give all nodes an equal span.
Kind: global function
Returns: The nodeSpan if getting, or the current phylotree if setting.
| Param | Type | Description |
|---|---|---|
| attr | function |
Optional; if setting, the nodeSpan function. |
Get or set nodeLabel accessor.
Kind: global function
Returns: The nodeLabel accessor if getting, or the current this if setting.
| Param | Type | Description |
|---|---|---|
| attr | function |
(Optional) If setting, a function that accesses a branch name from a node. |
Return the bubble size of the current node.
Kind: global function
Returns: Float - The size of the bubble associated to this node.
| Param | Type | Description |
|---|---|---|
| A | Node |
node in the phylotree. |
Getter/setter for the selection label. Useful when allowing users to make multiple selections.
Kind: global function
Returns: The current selection label if getting, or the current phylotree if setting.
| Param | Type | Description |
|---|---|---|
| attr | String |
(Optional) If setting, the new selection label. |
Get or set the current node span. If setting, the argument should
be a function of a node which returns a number, so that node spans
can be determined dynamically. Alternatively, the argument can be the
string "equal", to give all nodes an equal span.
Kind: global function
Returns: The nodeSpan if getting, or the current phylotree if setting.
| Param | Type | Description |
|---|---|---|
| attr | function |
Optional; if setting, the nodeSpan function. |
Getter/setter for the selection callback. This function is called every time the current selection is modified, and its argument is an array of nodes that make up the current selection.
Kind: global function
Returns: The current selectionCallback if getting, or the current this if setting.
| Param | Type | Description |
|---|---|---|
| callback | function |
(Optional) The selection callback function. |