PHYLOViZ INPUT
This package allows creation of PHYLOViZ graph input object that is then used in phyloviz_graph
#INPUT
The package uses as input an object that is returned after computation of links between profiles using goeBURST. It has the following attributes:
PHYLOViZ_prev_graph = {
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.
distanceMatrix: [[0,1]] //distances between profiles,
links: [{source:"ST1", target:"ST2", value: 2}]
positions:{}
}
#Usage example
var phyloviz_input = require('phyloviz_input');
phyloviz_input(PHYLOViZ_prev_graph, function(PHYLOViZ_to_graph){
console.log(PHYLOViZ_to_graph); //Object to construct the graph
});