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: 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 

   -vprops | -vp | -vizprops <properties file> 
                          Specify and load a visual mappings properties file (usually named vizmap.props) 

   -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

   -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 PlugI\in 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 (called ".cytoscape" and located in the users's 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 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
integer > 0
-vt
--VT
secondaryViewThreshold
2000
integer > 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
defaultWebBrowser

A path to the web browser on your system. This only needs to be specified if Cytoscape cannot find the web browser on your system.