This directory contains plugins which are loaded when Cytoscape starts
up. Adding plugin .jar files to this directory will cause them to be
automatically loaded whenever Cytoscape is run.

The current version of Cytoscape comes preconfigured with the following
plugin files in this directory:

HierarchicalLayout.jar
----------------------
This plugin adds a choice to the Layout menu labelled "Apply Hierarchical
Layout". Choosing this item causes the graph nodes to be repositioned in
an approximately optimal configuration for a tree-like directed graph.
As much as possible, nodes will be positioned in layers so as to minimize
the number of edges which point upwards. If the graph is acyclic, no edges
should point upwards. Also, connected components are separated, and some
effort is made to reduce the number of edge crossings (the method seeks
to acheive fair quality with minimal runtime complexity). This method
can also be applied to a selected subset of nodes (>1), which will be
layed out separately from the rest of the graph.

MCODE.jar
---------
This plugin adds a choice to the Plugins menu labelled "MCODE". Through
this menu you can access the MCODE analysis routines ("Molecular Complex
Detection"), that detect densely connected regions in large networks.
Depending on the type of network, clusters may mean different things.
For instance, clusters in a protein-protein interaction network have
been shown to be protein complexes and parts of pathways. Clusters
in a protein similarity network represent protein families. The
method is based on vertex weighting by local neighborhood
density and outward traversal from a locally dense seed protein to isolate
the dense regions according to given parameters. The algorithm has the
advantage over other graph clustering methods of having a directed mode
that allows fine-tuning of clusters of interest without considering the
rest of the network and allows examination of cluster interconnectivity,
which is relevant for protein networks.

SigAttributes.jar
-----------------
This plugin add a choice to the Plugins menu labelled "Find Enriched
Attributes". This item allows you to scan for significant attributes
loaded onto the network. The scan can be performed by Attribute
or by Annotation, and is based on a group of selected nodes.

control.jar
-----------
This plugin add a choice to the Layout menu labelled "Align". This item
will display a toolbar which allow you to align and distribute selected
nodes relative to each other (Align/Distribute horizontal
left/center/right, Align/Distribute vertical top/center/bottom)

diff.jar
--------
This plugin add a choice to the Data menu labelled "Diff". In order for
this plugin to function properly, the plugin in "filter.jar" must also
be loaded. The "Diff" menu item allows the user to compare two networks,
and will display differences found. Filters that have been created can
also be applied during the comparison.

filter.jar
----------
This plugin adds a new menu named "Filters", a toolbar button to
access the "Use Filters" function, and a menu item labelled "Attribute
Browser if passed Filter" to the Data menu. Through these controls, the
user can define a set of conditions which define a subset of the graph.
These sets of conditions can be used to select, browse, or compare
subsets of the currently viewed network.

jgraphLayout.jar
----------------
This plugin adds a new choice to the Layout menu labelled "JGraph".
Through this submenu, the user can apply several layout algorithms
to the currently viewed network. Circle (all nodes in a single circle),
Radial (nodes in concentric circles), Spring (embedded spring energy
minimization), and Sugiyama (layered hierarchical) are possible
choices.

layout.jar
----------
This plugin adds several new layout choices to the Layout menu: 
ISOM (spring embedded), Radial (polar coordinates), Circle (all nodes
in a single circle), Spring (local spring embedded optimization)

yLayouts.jar
------------
This plugin add a new choice to the Layout menu labelled "yFiles".
Through this submenu, the user can apply several layout algorithms
and view transforms including Circular, Organic, Scale, Hierarchic,
Random, Tree, MirrorX, MirrorY, Rotate, and Orthogonal.

yeast-context.jar
-----------------
This plugin adds a context sensitive menu to Cytoscape that enables
links to Saccharomyces cerevisiae web resources. It can be accessed by
right-clicking on any node, but is only relevant for budding yeast networks.
