Difference between revisions of "User talk:RobertBuels"

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(Configuring Faceted Track Selection)
(Configuring the Track Selector)
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== Configuring the Track Selector ==
 
== Configuring the Track Selector ==
  
To enable the faceted track selector, set <code>trackSelector.type</code> to <code>Faceted</code> in the JBrowse configuration.
+
To enable the faceted track selector, set <code>trackSelector.type</code> to <code>Faceted</code> in the JBrowse configuration.  The <code>Faceted</code> track selector takes all sources of track metadata, aggregates them, and makes the tracks searchable using this metadata.  By default, tracks only have three metadata facets, all of which come from the track's configuration itself: ''Name'' - the track's human-readable name, ''Category'' - the track's category, if that is defined in its configuration, and ''Label'' - the track's unique label.  Faceted track selector users will usually want to add much more metadata, see [[#Defining Track Metadata]] below.
  
 
There are some other configuration variables that can be used to customize operation of the track selector:
 
There are some other configuration variables that can be used to customize operation of the track selector:
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       renameFacets: { 'developmental-stage': 'Conditions', submission: 'Submission ID' }
 
       renameFacets: { 'developmental-stage': 'Conditions', submission: 'Submission ID' }
 
   }
 
   }
 
  
 
== Defining Track Metadata ==
 
== Defining Track Metadata ==

Revision as of 17:58, 12 June 2012

(add on JBrowse)

JBrowse Configuration Guide

Anonymous Usage Statistics

JBrowse instances report usage statistics to the JBrowse developers. This data is very important to the JBrowse project, since it is used to make the case to grant agencies for continuing to fund JBrowse development. No research data is transmitted, the data collected is limited to standard Google Analytics, along with a count of how many tracks the JBrowse instance has, how many reference sequences are present, their average length, and what types of tracks (wiggle, feature, etc) are present. Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.

Configuring Faceted Track Selection

Starting with version 1.4.0, JBrowse has an advanced "faceted" track selector tailored for sites with hundreds or thousands of tracks in a single JBrowse instance. This track selector allows users to interactively search for the tracks they are interested in using metadata that is associated with each track.

An example of a faceted track selector in action with about 1,800 tracks can be seen here. This is an example installation containing a snapshot of modENCODE track metadata. Note that the track data and reference sequences in this example are not real (they are actually all just copies of the same volvox test track), this is just an example of the faceted track selector in action.

Configuring the Track Selector

To enable the faceted track selector, set trackSelector.type to Faceted in the JBrowse configuration. The Faceted track selector takes all sources of track metadata, aggregates them, and makes the tracks searchable using this metadata. By default, tracks only have three metadata facets, all of which come from the track's configuration itself: Name - the track's human-readable name, Category - the track's category, if that is defined in its configuration, and Label - the track's unique label. Faceted track selector users will usually want to add much more metadata, see #Defining Track Metadata below.

There are some other configuration variables that can be used to customize operation of the track selector:

Option Value
trackSelector.displayColumns Array of which facets should be displayed as columns in the track list. Columns are displayed in the order given. If not provided, all facets will be displayed as columns, in lexical order.
trackSelector.renameFacets Object containing "display names" for some or all of the facet names. For example, setting this to { 'developmental-stage': 'Conditions' } would display "Conditions" as the name of the developmental-stage facet.

Example

 trackSelector: {
     type: 'Faceted',
     displayColumns: ['key', 'organism', 'technique', 'target', 'factor', 'developmental-stage','principal_investigator','submission' ],
     renameFacets: { 'developmental-stage': 'Conditions', submission: 'Submission ID' }
 }

Defining Track Metadata

Searchable Names

generate-names.pl

This script makes it possible to search for features by label (the visible name below a feature in JBrowse) and/or by alias (a secondary name that is not visible in the web browser, but may be present in the JSON used by the JBrowse client). For tracks that are added using flatfile-to-json.pl or biodb-to-json.pl, searchability depends on how the 'autocomplete' option is used. If a track is input with the autocomplete option set to 'alias', for instance, features will be searchable by alias after generate-names.pl is run (provided that alias names are present in the original data source). For tracks added using ucsc-to-json.pl, features will be searchable by label after running generate-names.pl.

To search for a term, use the text box at the top of the JBrowse window.

Basic syntax:

bin/generate-names.pl [options]

Note that generate-names.pl does not require any arguments. However, some options are available:

Option Value
dir A path to the output directory (default is 'data/names' in the current directory).
thresh A lower-bound on the Patricia trie chunk size. Specifically, the lowest possible chunk size is (thresh + 1). The default value is 200. In this context, a chunk is a group of connected Patricia trie nodes that can be visualized as a single entity, and the chunk size is the total number of genomic features contained in a chunk. The lower the value of thresh, the more chunks there will be.
verbose This setting causes information about the division of nodes into chunks to be printed to the screen.