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Utility Plugins


Description

These apps 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.


Enhanced Graphics App

Figure 2. The sample network galFiltered with nodes painted with a pie graph representing the significance of the expression difference for each experimental condition as expressed in the attributes "gal1RGsig (red), gal4RGsig (yellow), and gal80Rsig (green)". This was created with the command: nodecharts pie nodelist="all" attributelist="gal1RGsig,gal4RGsig,gal80Rsig" colorlist="contrasting"

The Node chart plugin exports commands that can be used by users (via the Command Tool) or by plugin developers who can call the commands using the Cytoscape CyCommandHandler mechanism. In either case, node charts provides a simple way to paint bar, line, or pie graphs onto nodes. These graphics are preserved as part of the session, and are rendered as objects, providing excellent graphics stability. The capabilities of the renderings are limited, so users with more complex charting needs should look at the GoogleCharts plugin, which links to the Cytoscape 2.8 formula capability.

Here are the list of commands supported by the nodeCharts plugin:

nodecharts bar
Paints a bar chart onto the node, according to the arguments provided. The valuelist and either node or nodelist arguments are required.
Arguments:
attributelist
If the values are going to be specified by node attributes, this list provides the attribute or attributes to be used as a comma-separated list.
colorlist
The list of colors, one for each bar. colorlist also supports the following keywords:
  • contrastingSelect colors base on a contrasting color scheme
  • modulatedSelect colors base on a modulated rainbow color scheme
  • rainbowSelect colors base on the rainbow color scheme
  • randomSelect colors randomly
  • up:colorUse color if the value is positive
  • down:colorUse color if the value is negative
labellist
This list provides the labels to be associated with each bar, point, or pie slice on the resulting graph. The values should contain a comma-separated list of labels, one for each value.
network
The network that this command refers to. Note that this is optional -- if it's not provided the current network is used.
node
The specific node that this command refers to
nodelist
The list of nodes that this command refers to. To have the command take effect for all of the currently selected nodes, the keyword selected is provided. To have it take effect for all nodes, use the all keyword
position
The position of the graphic relative to the center of the node. This can be expressed as either an "x,y" pair, or using the main compas points: north, northeast, east, southeast, south, southwest, west, northwest or center.
separation
The separation between any two bars
valuelist
The list of values (as a comma-separated list) for each point, bar, or pie slice.

nodecharts clear
Clears the node chart graphic from a node or list of nodes.
Arguments (hyperlinked arguments are the same as described above):

node
The specific node that this command refers to
nodelist
The list of nodes that this command refers to. To have the command take effect for all of the currently selected nodes, the keyword selected is provided. To have it take effect for all nodes, use the all keyword

nodecharts line
This chart type displays the values passed as arguments as a line chart on the node.
Arguments (hyperlinked arguments are the same as described above):
attributelist
color
The color of the line to be plotted
labellist
network
node
nodelist
position
valuelist

nodecharts list
This is a simple command that returns a list of the available chart types

nodecharts pie
This chart type displays the values passed as arguments as a pie chart on the node.
Arguments (hyperlinked arguments are the same as described above):
arcstart
The angle in degrees to start the pie. 0° points east, 90° points south, etc.
attributelist
colorlist
labellist
network
node
nodelist
position
valuelist

nodecharts stripe
This chart type displays the values passed as arguments as a series of stripes on the node.
Arguments (hyperlinked arguments are the same as described above):
attributelist
colorlist
labellist
network
node
nodelist
position
valuelist


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