Class Biojs.ExpressionAtlasBaselineSummary

Version 1.0.3.

Extends Biojs.

Defined in: Biojs.ExpressionAtlasBaselineSummary.js.

Class Summary
Constructor Attributes	Constructor Name and Description
	Biojs.ExpressionAtlasBaselineSummary(options) This is the ExpressionAtlas component for displaying baseline expression of genes based on RNA-seq experiments in the ExpressionAtlas database.

Field Summary
Field Attributes	Field Name and Description
<inner>	constructor Constructor to initialize the component
<inner>	eventTypes Array containing the supported event names
<inner>	opt Default values for the options

Method Summary
Method Attributes	Method Name and Description
	constructor(options)
	setQuery(geneQuery, propertyType, geneSetMatch) Set ENSEMBL gene ids or UniProt ids.

Methods borrowed from class Biojs:: addListener, extend, getId, listen, raiseEvent, setEventHandlers, setOptions

Event Summary
Event Attributes	Event Name and Description
	onError(actionPerformed)

Class Detail

Biojs.ExpressionAtlasBaselineSummary(options)

This is the ExpressionAtlas component for displaying baseline expression of genes based on RNA-seq experiments in the ExpressionAtlas database.
Author: ExpressionAtlas Team.

   var instance = new Biojs.ExpressionAtlasBaselineSummary({
     geneQuery:"ENSG00000187003+ENSG00000185264",
     propertyType:"bioentity_identifier",
     geneSetMatch:false,
     target : "YourOwnDivId"
   });

Parameters:
{Object} options: An object with the options for ExpressionAtlasBaselineSummary component.

Options detailed:
{string} [featuresUrl='http://www-test.ebi.ac.uk/gxa/widgets/heatmap/protein']: The query URL pointing to the ExpressionAtlas for retrieving gene page results displayed as part of this widget. It is usually composed to include the identifier of the gene you are interested in, see example.
{string} geneQuery: ENSEMBL gene ids or UniProt ids. If more than one identifier follow this format "P00846+P99999"
{string} [propertyType='']: To narrow to search scope of a query term, please provide a type.
{string} [geneSetMatch=false]: If true collapse multiple returned gene profiles into one single line of average expression.
{string} target: Identifier of the DIV tag where the component should be displayed.
{string} [rootContext='../biojs/dependencies/proxy/proxy.php?url%3dhttp://www-test.ebi.ac.uk/gxa']: Specifies the root context path to be used by the widget content, i.e. this is the location of the content proxy pointing to ExpressionAtlas
{string} [proxyUrl='../biojs/dependencies/proxy/proxy.php']: This component needs to request data from a web service. To bypass the same origin policy (http://en.wikipedia.org/wiki/Same_origin_policy) this component needs a proxy. You could use your own proxy by modifying this value or one of the BioJS proxies: '../biojs/dependencies/proxy/proxy.php' or '../biojs/dependencies/proxy/proxy.jsp'

Requires:: jQuery Core 1.9.1

Field Detail

<inner> constructor

Constructor to initialize the component

<inner> eventTypes

Array containing the supported event names

<inner> opt

Default values for the options

Method Detail

constructor(options)

Parameters:
options

setQuery(geneQuery, propertyType, geneSetMatch)

Set ENSEMBL gene ids or UniProt ids.

instance.setQuery("ENSG00000187003+ENSG00000185264","bioentity_identifier",false);

instance.setQuery("Q61171","",false);

instance.setQuery("P37173+Q9UER7+P10600+P35243+Q93074+P16234","",false);

instance.setQuery("ENSG000000000000","bioentity_identifier",false);

Parameters:
{string} geneQuery: ENSEMBL gene ids or UniProt ids. If more than one identifier follow this format "P00846+P99999".
{string} propertyType: Property to narrow to search scope of a query term, please provide a type.
{boolean} geneSetMatch: If true collapse multiple returned gene profiles into one single line of average expression.

Event Detail

onError(actionPerformed)

instance.onError(
   function( error ) {
      alert( error.message );
   }
);

Parameters:
{function} actionPerformed: A function which receives a Biojs.Event object as argument.

Event object data:
{string} message: Error message in case of result be 'failure'.
{Object} jqXHR: XMLHttpRequest object
{string} textStatus: It describes the type of error that occurred and an optional exception object, if one occurred
{string} errorThrown: When an HTTP error occurs, errorThrown receives the textual portion of the HTTP status, such as "Not Found" or "Internal Server Error."

Classes

Class Biojs.ExpressionAtlasBaselineSummary