#Phenogrid installation

Please see the instructions in index.html to see how to install the Phenogrid widget.

#Phenogrid configuration

The phenogrid can be configured via a variety of options contained in the ./js/phenogrid_config.js file. This file must be loaded as a separate Javascript file in every page that uses the phenogrid. Please be sure that this file is loaded before the main ./js/phenogrid.js file.

Options that can be modified include

• serverURL - the base url of the server/site from which the widget will be served. Should usually left to be null, in which case the server url be inferred from the code.

• selectedCalculation: an integer value describing the initial similarity measure that will be used. Other values can always be selected via the appropriate pulldown. Possible values include:

  • 0 - for Similarity (default)
  • 1 - Ratio (q)
  • 2 - Uniqueness
  • 3 - Ratio (t)

• selectedSort - the initial sort order. As with the calculation, these choices may be adjusted via a pulldown. Values include Frequency, Alphabetic, and Frequency and Rarity. Frequency is the default.

• targetSpeciesList - a list of "name", "taxon" pairs indicating the organisms to be shown in the phenogrid. "Name" should be the traditional latin name, while "taxon" should be the NCBI taxon number. Default value includes Homo sapiens, Mus musculus, Danio rerio, and Drosophila melanogaster

• targetSpeciesName The initial species name to be displayed, or "Overview" if the multi-species overview is desired. Must be one of the species included in the targetSpeciesList. Default is "overview".

• refSpecies the reference species that provides the comparison point for similarity scoring. Must be one of the species included in the targetSpeciesList. Defaults to "Homo sapiens".

The Phenogrid is implemented as a jQuery UI Widget. However, due to the overhead of refresh, we do not automatically update when options are set. If you wish to set options using the configuration file, those options will be read and processed upon initialization. For any other changes, you should be able to use setOption or setOptions followed by a manual call to the reDraw method.