Utility Plugins

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Description

These plugins provide some relatively discrete functionality that can be useful. Some of thse are relatively constrained (e.g. EdgeLister) and some provide more significant functionality such as the Dynamic Expression Plugin.

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Add Parent Neighbors Plugin

This simple plugin allows you to extend a child network by adding the neighbors of a selected node in the parent network. This can be useful when you have a large, complex network and you want to focus in on some portion of it. For example, if you create a child network of p53 interaction partners from a larger network of all Human protein-protein interactions. If you find an interesting interaction partner to p53, and want to see its interaction partners, you can select the partner in the child network and select Plugins→Add neighbors from parent to add all of the interaction partners of that node in the parent network to this network.

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Batch Tool Plugin

batchTool provides a very rudimentary command processing interface to Cytoscape to allow a limited amount of automation. In general, you would create a "command" file with a series of batchTool comments. You would then startup Cytoscape providing the name of the batch file.

Commands

• apply vizmap
• Apply vizmap map vizmap to the current network
• destroy network
• Destroys the network and the network view for network
• exit
• Exit Cytoscape
• export [vizmap|node attributes|edge attributes] to filename
• Export the vizmap and node or edge attributes to a file
• export network as [XGMML, PSI-MI, GML, SIF, PDF, SVG, PNG, GIF, JPG] to filename
• Export a network as either a network data file or a graphics file
• import [network|node attributes|edge attribute] filename
• Import a network or attribute data
• layout layout-algorithm tunable1=value1 tunable2=value2 etc.
• Layout the network using the layout layout-algorithm with the tunables set to the appropriate values
• open sessionfile
• Open a session file
• save as filename
• Save a Cytoscape session file
• set property=value
• Set a cytoscape property (e.g. a linkout) to a specific value

Example (test.com)

import network pte.xgmml
import node attributes subgroup.noa
layout force-directed
export network as pdf to test.pdf zoom=10
exit

You would execute this file by executing Cytoscape with the "-S" flag:

cytoscape.sh -S test.com

Layout Tunables

force-directed (Force Directed)
Tunable Name	Tunable Description
defaultSpringCoefficient	Default Spring Coefficient
defaultSpringLength	Default Spring Length
defaultNodeMass	Default Node Mass
numIterations	Number of Iterations
min_weight	The minimum edge weight to consider
max_weight	The maximum edge weight to consider
integrator	Integration algorithm to use
selected_only	Only layout selected nodes
edge_attribute	The edge attribute that contains the weights

fruchterman-rheingold (Biolayout)
Tunable Name	Tunable Description
partition	Partition graph before layout
randomize	Randomize graph before layout
min_weight	The minimum edge weight to consider
max_weight	The maximum edge weight to consider
selected_only	Only layout selected nodes
edge_attribute	The edge attribute that contains the weights
repulsion_multiplier	Multiplier to calculate the repulsion force
attraction_multiplier	Divisor to calculate the attraction force
gravity_multiplier	Multiplier to calculate the gravity force
iterations	Number of iterations
temperature	Initial temperature
spread_factor	Amount of extra room for layout
update_iterations	Number of iterations before updating display
conflict_avoidance	Constant force applied to avoid conflicts
max_distance_factor	Percent of graph used for node repulsion calculations

kamada-kawaii (Spring Embedded
Tunable Name	Tunable Description
partition	Partition graph before layout
randomize	Randomize graph before layout
min_weight	The minimum edge weight to consider
max_weight	The maximum edge weight to consider
selected_only	Only layout selected nodes
edge_attribute	The edge attribute that contains the weights
iterations_pernode	Number of iteratations for each node
layout_passes	Number of layout passes
distance_strength	Spring strength
rest_length	Spring rest length
disconnected_strength	Strength of a 'disconnected' spring
disconnected_rest_length	Rest length of a 'disconnected' spring
anticollisionStrength	Strength to apply to avoid collisions

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Dynamic Expression Plugin

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Edge Length Plugin

The Edge Length Plugin is a simple plugin that was written to support the paper "Network Validation...". The plugin adds a new attribute, length to each edge. This attribute is the actual length of the edge measured as the Euclidean distance between the source node and the target node. This can be used to determine the accuracy of edge weighted layout algorithms and estimate the "edge frustration" as it was called in the paper, where edge frustration is defined as the actual layout and a perfect layout. A perfect layout is defined as one in which all of the edge lengths are proportional to their weights, which is only possible in the general case in n dimensions, where n is the number of nodes - 1. To add the new edge attribute, the plugin adds a new menu: Plugins→Calculate Edge Lengths. This is not a dynamic attribute, so the plugin will need to be called after each layout change.

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Edge Lister Plugin

The Edge Lister Plugin is a simple plugin that provides the functionality to name a set of edges for later action. The plugin registers the Edge Memory submenu under the Plugins menu. The Edge Memory has five submenus, which are discussed below.

Figure 1. The Enter Edge List Name dialog is shown to allow users to name the selected group of edges.

Remember selected edges...

Initially, all of the submenu items will be greyed out (unselectable) except for this one. Once a group of edges have been selected, that selection may be named (remembered) by selecting this menu item. A dialog will appear (see Figure 1) to allow the user to name the selection. Once there is a named selection, the other menu items will be selectable and can be used to operate on any named selection.

Hide edges→

Underneath this menu will be a submenu for each named selection. Choosing a named selection will cause that group of edges to be hidden (removed from the network), even if they are not currently selected.

Remove list→

Removes the named selection from the list of named selections. If there are any edges hidden, they will be restored before the named selection is removed.

Restore edges→

If the edges for this named selection are hidden, they will be restored.

Select edges→

Select the edges associated with this named selection.

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