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This page has been deprecated and is no longer updated. The current version of the Cytoscape manual can be found at http://manual.cytoscape.org/

You can search for nodes and edges by column value directly through Cytoscape's tool bar. For example, to select nodes or edges with a column value that starts with "STE", type ste* in the search bar. The search is case-insensitive. The * is a wildcard character that matches zero or more characters, while "?" matches exactly one character. So ste? would match "STE2" but would not match "STE12". Searching for ste* would match both.

searchbar2.png

To search a specific column, you can prefix your search term with the column name followed by a :. For example, to select nodes and edges that have a "COMMON" column value that starts with "STE", use common:ste*. If you don't specify a particular column, all columns will be searched.

Columns with names that contain spaces, quotes, or characters other than letters and numbers currently do not work when searching a specific column. This will be fixed in a future release.

To search for column values that contain special characters you need to escape those characters using a "\". For example, to search for "GO:1232", use the query GO\:1232. The complete list of special characters is:

+ - & | ! ( ) { } [ ] ^ " ~ * ? : \

Note: Escaping characters only works when searching all columns. It currently does not work for column-specific searching. This will be fixed in a future release.

Filters

Cytoscape 3 provides a new user interface for filtering nodes and edges. These tools can be found in the Select panel:

select-panel.png

There are two types of filters. On the Filter tab are narrowing filters, which can be combined into a tree. On the Chain tab are chainable filters, which can be combined in a linear chain.

Narrowing Filters

Narrowing filters are applied to the entire network, and are used to select a subset of nodes or edges in a network based on user-specified constraints. For example, you can find edges with a weight between 0 and 5.5, or nodes with degree less than 3. A filter can contain an arbitrary number of sub-filters.

To add a filter click on the "+" button. To delete a filter (and all its sub-filters) click the "x" button. To move a filter grab the handle filterhandle.png with the mouse and drag and drop the filter on its intended destination. Dropping a filter on top of another filter will group the filters into a composite filter.

Interactive Filter Application Mode

Due to the nature of narrowing filters, Cytoscape can apply them to a network efficiently and interactively. Some filters even provide slider controls to quickly explore different thresholds. This is the default behavior on smaller networks. For larger networks, Cytoscape automatically disables this interactivity. You can override this by manually checking the Apply Automatically box above the Apply button:

apply-automatically.png

Cytoscape comes packaged with the following narrowing filters:

Column Filter

This filter will match nodes or edges that have particular column values. For numeric columns sliders are provided to set minimum and maximum values, or the values may be entered manually.

From string columns, a variety of matching options are provided:

string-column.png

For example, column values can be checked to see if they contain or match exactly the text entered in the text box. More complex matching criteria can be specified by using a Java-style regular expression.

By default string matching is case insensitive. Case sensitive matching requires the use of a regular expression that starts with "(?-i)". For example to match the text "ABC" in a case sensitive way use the following regular expression: "(?-i)ABC".

Cytoscape uses Java regular expression syntax.

Degree Filter

The degree filter matches nodes with a degree that falls within the given minimum and maximum values, inclusive. You can choose whether the filter operates on the in-degree, out-degree or overall (in + out) degree.

Topology Filter

The topology filter matches nodes having a certain number of neighbors which are within a fixed distance away, and which match a sub-filter. The thresholds for the neighborhood size and distance can be set independently, and the sub-filter is applied to each such neighbor node.

The topology filter will successfully match a node if the sub-filter matches against the required number of neighbor nodes.

Grouping and Organizing Filters

By default, nodes and edges need to satisfy the constraints of all your filters. You can change this so that instead, only the constraints of at least one filter needs to be met in order to match a node or edge. This behavior is controlled by the Match all/any drop-down box. This appears once your filter has more than one sub-filter. For example, suppose you wanted to match nodes with column COMMON containing ste or cdc, but you only want nodes with degree 5 or more, you'd first construct a filter that looks like this:

sample-group2.png

This filter will match nodes where COMMON contains ste and cdc. To change this to a logical or operation, drag either of the column filters by its handle filterhandle.png onto the other column filter to create a new group. Now change the group's matching behavior to Match any:

sample-group1.png

You can also reorder filters by dropping them in-between existing filters.

Chainable Filters

Chainable filters are combined in an ordered list. The nodes and edges in the output of a filter become the input of the next filter in the chain. The first filter in the chain gets its input from the current selection or from a filter on the Filter tab. The output of the last filter becomes the new selection.

You can specify the input to the first filter in the chain by selecting a Start with, where Current selection refers to the nodes and edges currently selected. You can also choose a narrowing filter, which produces a different set of selected nodes and edges.

ChainFilter1.png

Chainable filters can be reordered by dragging one by the handle and dropping it between existing filters.

Cytoscape currently bundles the following chainable filters:

Edge Interaction Transformer

This transformer will go through all the input edges and selectively add their source nodes, target nodes, or both, to the output. This is useful for adding nodes that are connected to edges that match a particular filter.

Output options:

A sub-filter may be added as well. When a sub-filter is present the source/target nodes must match the filter to be included in the output.

Node Adjacency Transformer

This transformer is used to add nodes and edges that are adjacent to the input nodes. A sub-filter may be specified as well.

Note that pressing the Apply button repeatedly may cause the selection to continuously expand. This allows adjacent nodes that are at greater distances to be added.

Output options:

Select options:

Edge direction options. (Hidden by default, click the small arrow icon to reveal.):

Sub-filter options. (Available when a sub-filter has been added.):

Working with Narrowing and Chainable Filters

The name of active filter appears in the drop-down box at the top of Select panel. Beside this is the options button which will allow you to rename, remove or export the active filter. It also lets you create a new filter, or import filters.

select-panel-options.png

At the bottom of the Select panel, there is an Apply button that will re-apply the active filter. On the opposite side of the progress bar is the cancel button, which will let you interrupt a long-running 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
...

Cytoscape_3/UserManual/Filters (last edited 2016-04-26 22:17:33 by TimHull)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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