phyloviz_bundle v0.1.2

PHYLOViZ BUNDLE

This package allows integration of PHYLOViZ Online tree visualization and associated features in a HTML canvas element. It combines a range of packages that perform individual tasks in PHYLOViZ Online and that are also available at npm.

goeburst - link

phyloviz_graph - link

phyloviz_input - link

phyloviz_metadata_link - link

#INPUT

The package uses as input a graph object defined in PHYLOViZ Online as the following:

graph_PHYLOViZ_Object = {
	name: "datasetName", //Name for the data set
	key:"ID", //Key used to link metadata to profiles
	data_type: "profile", //type of data used
	profiles: [{"ID": "ST1","A":"1","B":"3"},{"ID": "ST2","A":"2", "B":"1"}], //profiles format. One ID per profile and the 
	schemegenes: ["ID","A","B"], //ID of profiles and id of each position of the profile
	metadata: ["ID", "From"], //ID of each metadata and each field of the metadata
	isolates: [{"ID":"ST1", "From":"Japan"}, {"ID":"ST2", "From":"USA"}, {"ID":"ST2", "From":"Portugal"}], //information to link to the tree. 
	newick: undefined, //used for newick visualization. undefined by default
	linkMethod: 'isolates', //link method that is being used. By profile or by isolates
	propertyIndex: 1 //Index of the field in metadata that is being used to link colours to the tree.
}

#Usage example

var divCanvasID = 'canvasDiv'; //Div where the canvas element will be placed.

phyloviz_graph(graph_PHYLOViZ_Object, canvasID, function(PHYLOViZgraph_Object){
	console.log(PHYLOViZgraph_Object); //PHYLOViZ Online object
});