PhyD3

A phylogenetic tree viewer.

Installation

Using npm:

npm install @vibbioinfocore/phyd3

Using yarn:

yarn add @vibbioinfocore/phyd3

Usage

import{makeCompatTable,phyloxml}from"@vibbioinfocore/phyd3-parser-compat";import{build}from"@vibbioinfocore/phyd3";constxml="<phyloxml><phylogeny rooted='true'><clade><name>A</name></clade></phylogeny></phyloxml>";constparser=newDOMParser();constdoc=parser.parseFromString(xml,"text/xml");constsvg=build(makeCompatTable(phyloxml.parse(doc)));// insert svg.node() somewhere in your document

Options

Parsing

PhyD3 does not perform any parsing. You can use a compatible parser such as Phylio or phyd3-parser-compat or use any another parser. If you use another parser you will have to transform the result into a structure that PhyD3 expects. This is described below. As an example, see phyd3-parser-compat/makeCompatTable().

{"metadata": Array<Metadata>,// A metadata structure for each phylogeny (there may only be one)"nodes": Array<Node>,// All nodes in all phylogenies"edges": Array<Edge>// All edges between nodes (this will form a disconnected graph)}

This is what a metadata structure looks like:

{name: string|undefined,// The name of this phylogenydescription: string|undefined,// A description of this phylogenyparent: number,// The unique numeric identifier of the root node for this phylogenyrooted: boolean// Whether this phylogeny is rooted or not}

An edge looks like this:

{source: number,// The unique identifier of the starting node for this edgesink: number,// The unique numeric identifier of the ending node for this edgelength: number// The length of the edge}

And finally, this is a node.

{name: string,event: "Clade"|"Taxa"|"Hybrid"|"LateralGeneTransfer"|"Recombination",ref: number,// The unique identifier for this nodeattributes: Map<string,Attribute>// A set of attributes}

Attributes may either be scalar values, lists, or sub-mappings:

typeAttribute={tag: "numeric",value: number}|{tag: "text",value: string}|{tag: "bool",value: boolean}|{tag: "list",value: Array<Attribute>}|{tag: "mapping",value: Map<string,Attribute>}

Citation

When using PhyD3, please cite:

Kreft, L; Botzki, A; Coppens, F; Vandepoele, K; Van Bel, M

"PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization"

Bioinformatics (2017) PMID 28525531 doi:10.1093/bioinformatics/btx324.