Widgets

There are several widgets available on the InterMine list analysis page, and they are configured in webconfig-model.xml.

There are three categories of widget: table, graph, and enrichment widgets.

widget type	purpose	requirements
table	displays the counts from the list for the collection specified	update config file
graph	displays a chart based on a dataset you specify	update config file, query written in java
enrichment	displays the p-values of objects that appear in your list	update config file, query written in java

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Table widgets

Table widgets display objects and the counts of related objects in your list.

To create a table widget, follow these two steps:

1. Configure the widget in webconfig-model.xml

attribute	purpose	example
id	unique id used by javascript only	unique_id
pathStrings	which collection to use in the widget	Gene.proteins
exportField	which field from the objects in your list to export	primaryIdentifier
typeClass	types of lists that should display this widget	org.flymine.model.genomic.Gene

optional attributes

attribute	purpose
title	appears at the top of the widget
description	description of the widget
displayFields	which fields from the objects in the collection (in the above example, Gene.proteins) to display, eg. primaryAccession
columnTitle	heading for the "count" column
externalLink	link displayed next to first column, identifier will be appended to link
externalLinkLabel	label for external link
link	what query to run when the user clicks on the widget (see below)

2. Create a Java class for links from the widget (optional)
   • Create new java class, eg EmployeeURLQuery.java
   • Update generatePathQuery() method with the correct paths
   • Add name of new class to config as link, eg link="org.intermine.model.testmodel.web.widget.EmployeeURLQuery"

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Graph widgets

Graph widgets display datasets in graphical format.

To create a graph widget, follow these two steps:

1. Configure the widget in webconfig-model.xml

attribute	purpose	example
id	unique id used by javascript only	unique_id
dataSetLoader	Java class that retrieves the data displayed in the chart	org.flymine.web.widget.FlyAtlasDataSetLdr
typeClass	types of lists that should display this widget	org.flymine.model.genomic.Gene

optional attributes

attribute	purpose	example
title	appears at the top of the widget	Chromosome Distribution
description	description of the widget	Actual: number of items in this list found on each chromosome. Expected: given the total number ...
domainLabel	Label displayed on x-axis	Chromosome
rangeLabel	Label displayed on y-axis	Count
graphType	which type of chart to render	BarChart (default) or StackedBarChart
link	what query to run when the user clicks on the widget	org.flymine.web.widget.FlyAtlasGraphURLGenerator
extraAttributeClass	currently only used to add organism	org.intermine.bio.web.logic.BioUtil

2. Write Java classes

class	purpose	example
DataSetLoader	Retrieves the data to be rendered in the chart.	org.flymine.web.widget.FlyAtlasDataSetLdr
URLGenerator (optional)	Generates the URLs assigned to each bar on the chart	org.flymine.web.widget.FlyAtlasGraphURLGenerator

NOTE: The graphs use a Java library called JFreeChart. Currently only BarCharts and StackedBarCharts are supported.

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Enrichment widgets

Enrichment widgets display the p-values of objects that appear in your list. See EnrichmentWidgets for more information on how the p-value is calculated.

To create an enrichment widget, follow these two steps:

1. Configure the widget in webconfig-model.xml

attribute	purpose	example
id	unique id used by javascript only	unique_id
typeClass	types of lists that should display this widget	org.flymine.model.genomic.Gene
dataSetLoader	Java class that retrieves the data displayed in the widget	org.intermine.bio.web.widget.PublicationLdr

optional attributes

attribute	purpose
title	appears at the top of the widget
description	description of the widget
label	heading for the column
externalLink	link displayed next to first column
externalLinkLabel	label for external link
filters	extra filters to add to the display
filterLabel	label for filter form field
link	what query to run when the user clicks on the widget

2. Write Java classes.

class	purpose	example
DataLoader	This class generates the queries needed for the statistical analysis.	org.intermine.bio.web.widget.PublicationLdr
URLQuery (optional)	This class generates the queries used to generate results when a user clicks on a specific data point.	org.intermine.bio.web.widget.PublicationURLQuery

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