PathVisio Plugins

  1. PathVisio Plugins
  2. Visualizing and analyzing experimental data
    1. Experimental data plugin
    2. Visualization plugin
    3. Zscore plugin
    4. GSEA plugin
  3. Pathway Building and Formatting
    1. MAPPBuilder plugin
    2. Putative Pathway Parts
    3. GO plugin
    4. SBGN
    5. Molecular Interaction Maps (MIM)
  4. Import / Export to different File Formats
    1. BioPAX level 3
    2. Html Export
    3. SBML Export
  5. Other
    1. Chempaint
    2. Groovy Console
    3. Advanced Identifier Mapping plugin

Note Webstart security model prevents plugins from local disk to be added to them. If you want to run one of these plugins, either run PathVisio from your IDE, or install PathVisio using one of the methods described in AlternativeInstallation.

If you want to try a plugin that is currently in Beta, or if you simply wish to know more, please ask about it by sending a message to our MailingLists

Once you obtained a plugin, you should create a directory under your user directory named ~/.PathVisio/plugins, and place the jar file there. To see if a plugin was installed succesfully, check under Help->Plugin Manager. If the plugin is listed under "Active", it is installed correctly. If it's not, there may be an error message under "errors" that can help you figure out what the problem is.

Visualizing and analyzing experimental data

Experimental data plugin

This plug-in lets the user import any tab-delimited datafile. It doesn't matter if the data contains transcriptomic, metabolomic or other data, as long as it is a matrix with samples as columns and reporters (genes, proteins or metabolites) as rows.

Visualization plugin

Visualizing experimental data on pathways, by coloring the genes. Two types of visualization are included: block coloring and numeric representation.

Zscore plugin

This plugin ranks pathways using Z-score, based on the hypergeometric distribution.

GSEA plugin

This plugin uses the "Gene Set Enrichment Analysis" method to rank pathways based on experimental data.

Pathway Building and Formatting

MAPPBuilder plugin

MAPPBuilder lets you get started quickly on creating a pathway. All you need is a list of gene identifiers, and MAPPBuilder will build a prototype pathway for you.

Putative Pathway Parts

Putative Pathway Parts queries databases for potential links between biological entities, and can make suggestions for you on what biological entities are related to the ones currently in your Pathway. You can use this plug-in to improve a Pathway, or to find references on existing links.

GO plugin

Lets the user create a pathway based on all genes from a single GO category.

SBGN

Status: work in progress

Molecular Interaction Maps (MIM)

Status: work in progress

Import / Export to different File Formats

BioPAX level 3

Import / Export pathways in BioPAX format.

Html Export

Export a pathway as a hyperlinked html page. The pathway itself is a PNG embedded in the html, using an image map to link each element to external information.

SBML Export

Status: planned

Other

Chempaint

Displays chemical structures for annotated metabolites.

Source code:  http://svn.bigcat.unimaas.nl/pvplugins/trunk/chempaint/

Groovy Console

Programmatic access to the pathway model while PathVisio is running

  • Completion Status: Beta

Advanced Identifier Mapping plugin

The Standard PathVisio distribution gives you access to only a small subset of the possibilities of the BridgeDb Identifier Mapping Framework. Use this plugin to get the full power of BridgeDb in PathVisio

  • Completion Status: Beta