README Cytoscape plugin menu 1.0x

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A new menu called "iRefScape" will be created when the plugin is activated.

Search tools

This sub menu contain search related operations.

Retrieve interactions for the selected nodes

This option will load interactions involving the selected nodes. Nodes could be selected using the mouse or using an operation such as applying a filter.

Expand one level

This will load interactions involving all the nodes in the current network.

Load interactions between neighbours

Clear load history (Reload everything next time)

Reset node degree

Load user variables

View tools

Toggle selected multi-edges

Zoom to selected

Select last iRefScape selection

Select nodes with different taxid than query node

Select between nodes

Select between nodes with originals

Show spoke-represented complexes

(Currently hidden, used for debuging) Show live details of nodes and edges


Reset Group

Set group=1 for selection

Set group=2 for selection

Create comparison table


Hide selected nodes

Hide nodes (except pseudonodes)

Hide nodes not selected

Hide nodes not selected (except pseudonodes)

Un-hide all

Grouping and adjacency matrix

This feature provides a way to examine the Cytoscape node-link diagram using a adjacency matrix.

Create groups

The first step in using the matrix_view feature is group the nodes in the current network into two groups.The grouping could be achieved as a result of another operation or done manually.

Manual grouping

  1. Select one or more nodes using the mouse (first group)
  2. Select the menu: iRefScape -> Grouping -> set group=1 for selection
  3. Select one or more nodes which were not in the first group* using the mouse (second group)
  4. Select the menu: iRefScape -> Grouping -> set group=2 for selection
  5. Select the menu: iRefScape -> Grouping -> Create comparison table
*If a node is selected both as in group 1 and group 2, this is considered as an especial case. These nodes will appear in both as column headings and as row heading.

Grouping as part of a filter

Interpreting results from a grouping operation