Difference between revisions of "README Cytoscape plugin menu 1.0x"
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Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]] | Content of this page will be transferred to :[[README_Cytoscape_plugin_1.0x]] | ||
| + | |||
| + | =iRefScape= | ||
| + | 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=== | ||
| + | |||
| + | ==Grouping== | ||
| + | ===Reset Group=== | ||
| + | ===Set group=1 for selection=== | ||
| + | ===Set group=2 for selection=== | ||
| + | ===Create comparison table=== | ||
| + | |||
| + | ==Hide/Un-hide== | ||
| + | ===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=== | ||
| + | #Select one or more nodes using the mouse (first group) | ||
| + | #Select the menu: iRefScape -> Grouping -> set group=1 for selection | ||
| + | #Select one or more nodes which were not in the first group* using the mouse (second group) | ||
| + | #Select the menu: iRefScape -> Grouping -> set group=2 for selection | ||
| + | #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 === | ||
Latest revision as of 15:01, 28 June 2011
Content of this page will be transferred to :README_Cytoscape_plugin_1.0x
Contents
- 1 iRefScape
- 1.1 Search tools
- 1.2 View tools
- 1.2.1 Toggle selected multi-edges
- 1.2.2 Zoom to selected
- 1.2.3 Select last iRefScape selection
- 1.2.4 Select nodes with different taxid than query node
- 1.2.5 Select between nodes
- 1.2.6 Select between nodes with originals
- 1.2.7 Show spoke-represented complexes
- 1.2.8 (Currently hidden, used for debuging) Show live details of nodes and edges
- 1.3 Grouping
- 1.4 Hide/Un-hide
- 2 Grouping and adjacency matrix
iRefScape
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
Grouping
Reset Group
Set group=1 for selection
Set group=2 for selection
Create comparison table
Hide/Un-hide
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
- Select one or more nodes using the mouse (first group)
- Select the menu: iRefScape -> Grouping -> set group=1 for selection
- Select one or more nodes which were not in the first group* using the mouse (second group)
- Select the menu: iRefScape -> Grouping -> set group=2 for selection
- 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.
