iRefScape plugin menu

==Search tools== .

Retrieve interactions for the selected nodes

To load all protein-protein interactions and complexes involving one or more selected nodes. This action is same as performing a iteration=1 search using iRefScape for the selected nodes.

Expand one level

To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes.

Load interactions between neighbours

To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape the network retuned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is same as performing a iteration=0 search using iRefScape for all the nodes. This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.

Clear load history (Reload everything next time)

This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keep track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice without requesting to make a new view or selecting this menu option the network will not be re-loaded. If the user wishes to reload the network then this option has to be used. When using other methods of expanding network like “Expand one level” iRefScape handles the cache clearing automatically.

Reset node degree

This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters).

=Load user variables

Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;

1. Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).
2. First column should contain the ROGID
3. Second column should contain the user attribute/variable.
4. The file name should have the format _rog_#USER_VARIABLE_NAME.iruv (The text between # and the .iruv will be variable name)

e.g
#rog	USER_VARIABLE
j4H4IZH/ecTvEDjCel+eLTCmFyE9606	1
j4H4IZH/ecTvEDjCel+eLTCmFyE9606	1
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606	2
8sODZSppCsuEgRmhSHp3UjwOf2M9606	3
obze7v7i2yTIIcJjd7laIriNFg89606	4
Ty0OLkmhoUPjUuLQQv5ykN057oM9606	5
4bhW4sEt1YhYwHnHCyDNV3vvThs9606	6
Al8M+JdB4H+QnwITh8KcicdI2x49606	6
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606	6

View tools

Toggle selected multi-edges

iRefScape creates multiple edges between nodes to represent multiple evidences (if the same interaction a between two proteins represented by two nodes appears in MINT and IntAct there will be 2 edges, one for MINT and one for IntAct). Although this provides more information for the user, sometime the user may prefer to collapse this edges to a single edge to ease the observation. When this action is performed on a network all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the once remain has i.flag=0. Therefore, all this process is random by default the user can control which edges to remain and which to hid by using the i.flag edge attribute,

Zoom to selected

This action brings the selected node/nodes to the centre of the screen and make the nodes large as possible given that all selected nodes are visible. This action could also be performed using Cytoscapes zoom option.

Select last iRefScape selection

This action show the last selection operation performed by an iRefScape operation. This features do not record mouse selection of selection by other means than iRefScape selection operations (e.g filters)

Select nodes with different taxid than query node

Some interactions may involve proteins from multiple species. This may be due to that the interaction is really between proteins of two specises (e.g. an interaction between a Human protein and a virus protein), or may be because the proteins selected to demonstrate the interaction exists as from different species in the protein databases.

Select between nodes

This option highlights (selects) nodes interacting with at least two selected nodes by the user.

Show spoke-represented complexes

Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode.

Hide/Un-hide

Hide selected nodes

This action hides the selected nodes. When this action activated the nodes which are selected (manually or by a filter) are hidden from the view. This operation is performed in a independent thread and more efficient than hiding using Cytoscape node hide for large networks.

Hide nodes (except pseudonodes)

This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a hub bi-parse.

Hide nodes not selected

Hides all nodes which are not currently selected

Hide nodes not selected (except pseudonodes)

Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a hub bi-parse.

Un-hide all

Un-hides all nodes which are hidden by the user.

Safe mode

This option is only available when using JAVA 1.5 and will not appear for Java 1.6 or never. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in JAVA 1.5. When this mode is activated not all graphic features will be available.