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Class Biojs.KEGGViewer


Version 1.0.0_beta.

Extends Biojs.

Defined in: Biojs.KEGGViewer.js.

Class Summary
Constructor Attributes Constructor Name and Description
 
Biojs.KEGGViewer(options)
Component that renders a KEGGML file and displays a KEGG pathway.
Field Summary
Field Attributes Field Name and Description
<inner>  
Array containing the supported event names
<inner>  
opt
Default values for the options
Method Summary
Method Attributes Method Name and Description
 
constructor(options)
Methods borrowed from class Biojs:
addListener, extend, getId, listen, raiseEvent, removeListener, setEventHandlers, setOptions
Class Detail
Biojs.KEGGViewer(options)
Component that renders a KEGGML file and displays a KEGG pathway. It highlights pathway genes according to defined expression values for each experimental condition and allows users to change the threshold parameters for down and up-regulation.
Author: José Villaveces.
var instance = new Biojs.KEGGViewer({
     target: 'YourOwnDivId',
		pathId: 'hsa04910',
     proxyUrl: '../biojs/dependencies/proxy/proxy.php',
     expression:{
         upColor:'red',
         downColor:'blue',
         genes: ['hsa:7248', 'hsa:51763', 'hsa:2002', 'hsa:2194'],
         conditions: [
             {
                 name: 'condition 1',
                 values: [-1, 0.5, 0.7, -0.3]
             },
             {
                 name: 'condition 2',
                 values: [0.5, -0.1, -0.2, 1]
             },
             {
                 name: 'condition 3',
                 values: [0, 0.4, -0.2, 0.5]
             }
           ]
     }     

});
Parameters:
{Object} options
An object with the options for this component.
Options detailed:
{string} target
id of the div where the component should be displayed
{string} pathId
KEGG pathway ID
{string} proxyUrl
url of the proxy to use.
{Object} expression
expression values to highloght in the pathway.
{string} upColor
Prefered color for upregulated genes.
{string} downColor
Prefered color for downregulated genes.
{string[]} genes
Array containing the KEGG id of the genes to highlight.
{Object[]} conditions
Array containing the different conditions.
{string} name
Condition name.
{string[]} values
Array containing the gene expression values for the particular condition.
Requires:
jQuery 1.9.1
jQuery-UI 1.10.3
Cytoscape.js v2.0.2
Field Detail
<inner> eventTypes
Array containing the supported event names

<inner> opt
Default values for the options
Method Detail
constructor(options)
Parameters:
options

Documentation generated by JsDoc Toolkit 2.3.2 on Thu Apr 17 2014 17:42:43 GMT+0100 (BST)