Cytoscape_3/UserManual/Filters

Enhanced Search

Cytoscape includes a search feature, which enables you to quickly find nodes and edges.

Using Search is very simple. For example, type in "YL*" in the search box will find all the nodes/edges with string "YL" as prefix in the attributes. Type in "name:YL*" will restrict the search to attribute 'name' only. You can also use 'and', 'or' to make the complex search. The searching is actually based on Apache Lucene. Please look at this page for more about search syntax.

Filters

Filters allow you to quickly select multiple nodes or edges of interest by comparing node and edge attributes to properties you specify. For example, you can select all the nodes whose name contains a specific pattern, or whose numeric attribute value falls within a certain range. You can also perform complex selection by defining filters and performing the Boolean operation between them.

Since Cytoscape 2.5, the filters are redesigned to provide more user-friendly interfaces. The newly designed filters preserve most of the functionality of the old filters while introducing more, its API can also be used by other plugins. The old filters are still preserved, because there are still a few features are not implemented in new filters, and many users already got used to the old ones.

Using Filters

By default, you should see a filter icon on the toolbar: . If you click on it, the filters tab on the Control Panel will be selected. You can also access the filters by clicking directly on the tab or by using the Select menu pull-down and choose “Use Filters” menu item. The filters panel initially looks like this:

1. Filter Definition

To create a new filter, click the option button and select “Create new filter” from the list provided. Enter a name for the new filter.

Definition of simple filter

When a new filter is created, it is empty initially. It can be defined by choosing attributes (one at a time) in the Attribute/Filter comboBox and clicking the Add button. Note that in the comboBox each attribute has a prefix, either node. or edge., denoting what type of attribute it is. After add button is clicked, a widget, depended on the item selected, will be added to the definition panel. If the attribute type is text-based (or String), the widget will be a indexed-text-box widget, if numeric attribute, the widget will be a range slider; both are shown below.

For each widget, the name of the attribute it represents is on the left. A NOT checkbox gives the option to get the negation of selection for the widget. There is a trash-can icon on the right. Clicking on the trash-can icon will delete the widget. In this way, the filter definition can be modified after it is defined.

Note that if more than one widget is added on the filter definition panel, the relationship between them is “AND” by default. This relationship can be changed to “OR” by selecting the OR relation in Advanced Panel.

The Advanced panel can be opened by clicking on the plus (+) sign.

There are three rows in the advanced panel:

1. The first row, labeled Save. The two checkboxes (Global and Session) will determine where the filter is saved. By default, filters are saved in individual sessions. If the Global checkbox is checked, the filter will be saved in the global properties file. Note also that the prefix of the filter name in the Current Filter dropdown list reflects where it is saved.

2. The second row, Relation, will determine what Boolean operation (AND or OR) will be applied to each individual widget.

3. Negation checkbox. If this checkbox is checked, the result of the filter will be negated.

Definition of complex filter

In the pull-down list of Attribute/Filter comboBox, there are two sections, the top one is the list of attributes, the bottom one is the list of previously defined filter. Those previously dfined filters can also be used as components of other filters. By combinational use of AND, OR, NOT and pre-defined filters, filters with arbitary complexity can be defined.

3. Apply the filter

If a network is small (number of nodes or edges less than 1000), the filter will be applied dynamically when a widget is added or any value is adjusted. If the network is large, then Apply button should be clicked to apply the filter.

The threshold (1000 by default) can be changed by defining a Cytoscape property value dynamicFilterThreshold.

4. Other filters

In the option menu pulldown, there are menu items “Create new topology filter”, “Create new NodeInteraction filter” and “Create new EdgeInteraction filter”.

Topology Filter

Topology filter will select nodes based on the properties of its near-by nodes (neighbors). To create a topology filter, choose the menu item “Create new topology filter” from the option menu. See below,

Interaction filter

Interaction filters are used to select nodes/edges based on the properties of their neighboring edges/nodes. See below for a node interaction filter.

The Select Menu

The Select → Nodes and Select → Edges menus provide several mechanisms for selecting nodes and edges. Most options are fairly straightforward; however, some need extra explanation.

Select → Nodes → From ID List File... selects nodes based on node identifiers found in a specified file. The file format is simply one node id per line:

Node1
Node2
Node3
...