Command Line Arguments and Properties

Cytoscape recognizes a number of optional command line arguments, including run-time specification of network files and expression data:

   -g | -graph <GML network filename>  (e.g., xxx.gml) 
                          Loads a network file in GML format (see 5. Building and
                          Storing Interaction Networks)
 
   -i  | -interaction
<SIF interactions filename>  (e.g., yyy.sif)
                          Loads a network file in SIF format (see 5. Building and
                          Storing Interaction Networks)
 
   -b | -BDS <bioData directory> (e.g., annotation/manifest)
                          Specifies which directory to use for the BioDataServer annotations 

   -e | -expression  <expression filename>  (e.g., zzz.pvals)
                          Loads an expression data file (see 6. Loading Gene Expression Data 

   -n | -nodeAttributes  <nodeAttributes filename>  (one or more)
                          Loads node attributes files (see 7. Node and Edge Attributes 

   -j | -edgeAttributes  <edgeAttributes filename>  (one or more)
                          Loads edge attributes files (see 7. Node and Edge Attributes 

   -s | -species     Set the default species name 

   -c | -noCanonicalization 
                          Turn off default node name canonicalization 

   -h | -help | -help | --help
                          Help: display these command line arguments 

    -p | -plugin | --JLD | --JLW | --JLL <one or more files, directories or URLs...>
                          Specify a list of plugins (jar files), directories containing plugins,
                          URLs (http://) to jar files, or URLs to manifest files listing jar files 

   -props <properties file> 
                          Specify and load a properties file 

   -headless | -noView   
                          Run in headless mode; do not create and display the GUI

   -noDialog | -suppressView
                          Do not popup informational dialog when express file is loaded

   -vt | --VT <view threshold>
                          Specify the threshold # of nodes at which views will not automatically
                          be created

   -project <project file>  
                          Specify the location of the project file

   -script | --script <script text…> -end
                          Specify script text

   -rp | -resourcePlugin <resource plugins…>      
                          Specify the list of resource plugins

Most data sets may also be loaded after Cytoscape is running. See the sections on 6. Loading Gene Expression Data and 7. Node and Edge Attributes for details.

Additional command line arguments that are not recognized by the Cytoscape core are passed to the PlugIn modules. Please refer to the documentation for each specific PlugIn for more details.

Cytoscape Properties

The Cytoscape Preferences Dialog, accessed via Edit -> Preferences..., has sections for general properties display and editing, and plugins specification via the properties mechanism.  Preferences in Cytoscape are stored in the form of Java properties specified in the cytoscape.props file located in the user's working directory, home directory or Cytoscape distribution directory. This file is automatically loaded at startup time and written upon normal exit of the application.

Cytoscape properties are displayed in the Properties section of the dialog. These properties are configurable via Add, Modify and Delete operations.

The specification of plugins to be loaded into Cytoscape at startup time is also supported in cytoscape.props and accessible in this dialog under the Plugins section. In this special case, the plugins property specifies a comma-separated list of jar files or URLs to jar files containing plugins. This property is parsed into its constituents and presented and managed in the Plugins table.

Preferences Dialog

Some common properties are described below.


Property name
Default value
Valid values
Related command line argument
defaultSpeciesName
PleaseSpecify
species names
this value must match the name in the first line of the file specified in the bioDataServer’s manifest for synonyms
e.g., for yeast synonyms, specify Saccharomyces cerevisiae
-s
-species
bioDataServer
PleaseSpecify
annotation/manifest, and other manifest file locations
-b
-BDS
viewThreshold
500
integers > 0
-vt
--VT
secondaryViewThreshold
2000
integers > 0

viewType
tabbed
tabbed

plugins

comma-separated list of jar files containing plugins, or URL’s to jar files containing plugins (e.g., http://server/my-plugin.jar) -p
-plugin
--JLD
--JLW
--JLL

Java System properties

Cytoscape also honors a new Java system property introduced in Java 1.4: java.awt.headless. This property allows the Java system to run without Graphics support; Cytoscape running in this mode allows users to run non-graphical analyses as batch jobs or on systems without keyboard/mouse/display capabilities, such as compute servers.


   -Djava.awt.headless = true | false
                         Similar to command line argument –headless | -noView;   run in headless mode,
                         do not create and display the GUI