Tutorial: Introduction to Cytoscape 3. Open. Tutorials. From Open.
Tutorials. Slideshow. Introduction to Cytoscape 3. Networks, Data, Styles, Layouts and App Manager. Handout. Introduction to Cytoscape 3. Networks, Data, Styles, Layouts and App Manager.
Cytoscape is a project dedicated to building open-source network visualization and analysis software. A software 'Core' provides basic functionality to layout and query the network and to visually integrate the network with. Submit a 2.x Plugin; Guide to 3.0 App Development; Sign In; All Apps. (8) annotation (8) Network structure (7). CyNDEx allows users to seamlessly transfer networks between NDEx and Cytoscape and. Cytoscape_User_Manual. RecentChanges; FindPage; HelpContents; Cytoscape_User_Manual; Immutable Page; Comments; Info; Attachments. As of Cytoscape 2.8, attribute values may be formulas. A typical example is =ABS. Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics.
Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks. This tutorial covers network loading, importing data, visualizing data using Styles, network layout and App manager. Loading a Simple Network Go to File → Import → Network → File.. You should see a file chooser dialog. In the Cytoscape 3 directory, open the sample. Data folder and select gal. Filtered. sif and then click on Open.
Tutorial:Introduction to Cytoscape 3.1. The App Manager allows users to quickly and conveniently add extra features to Cytoscape directly from within Cytoscape, eliminating the need for manual searches. Cytoscape 2.
The first time you import a network, it will automatically create a new network collection. If you import an additional network during the same session, you should see the following dialog. In the dialog, you can select to create a new network collection or add the new network to an existing network collection in the drop- down. You can also select which column should be used for mapping between networks.
Manipulating Your Network Now that you have a network loaded, you can interact with it in a number of ways. While useful, hand selecting nodes in dense networks can be error- prone and difficult.
Cytoscape is a Java application verified to run on the Linux, Windows, and Mac OS X platforms. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 8 or later is. Cytoscape 2.8: new features for data integration and network visualization. NCBI Help Manual; NCBI Handbook; Training & Tutorials; Resources Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes.
However, you can specifically search for a node by name or data value. In the Search input field on the toolbar, type in ynr. This will select that node.
The search interface will also allow you to select nodes by other columns, but first, we need to import more data columns.. Visualizing Data on Networks Cytoscape provides a number of features to load arbitrary data and visualize that data by mapping the column values to styles.
Note that this tutorial focuses on importing data from a file to a network that is already loaded in Cytoscape, in this case the gal. Filtered network. The data mapping requires that an attribute in the existing network match a column in the data file to be imported. Importing and Exploring Your Data Cytoscape can read file structures that are delimited Text or Excel files. Go to File → Import → Table → File.. You will see a file chooser dialog.
Select the gal. Exp. Data. csv from the sample. Data folder and then click on Open.
You should see the following dialog. Note that the Key Column for Network represents the attribute in the already loaded network (in this case gal. Filtered) that will be used for mapping.
In the data file, this matches the column shown in blue in the preview. The data column to use can be changed under Show Mapping Options. In the Select a Network Collection section, choose the network to import the data columns to, and the column used as key to map to. Next, under Import Data As, select Node Table Columns. Click OK to import. NOTE: If the data preview shows data from all columns as one field, you need to change which delimiter is used.
Click the Advanced Options.. In the Delimiter field, deselect Tab and instead select Comma. Select Use first line as column names Viewing Data Columns Now explore the Table Panel to confirm the mapping of the data to the network. You now have access to your networked data and can begin playing with visualization.
Go to Layout → Prefuse Force Directed Layout. Go to the Style tab in the Control Panel and select Sample. Current Style drop- down.
Style lists a set of default styles. In the next section you will customize a style to highlight your data values. Details on editing and creating Styles here. Editing Data Columns So far, we have selected a couple of columns to display in the Table Panel.
Next, we will explore columns and the Table Panel in more depth. Visualizing Data with Styles Go to File → Open.. If you already have a network loaded you will get a message warning you that any current session will be lost, click ‘Yes’ to continue. You should see the Session file to load dialog. Open the sample. Data folder and select gal. Filtered. cys and then click on Open.
Modifying the Style Customizing the way you visualize and manipulate networks is a key function of Cytoscape. This is achieved through the use of Styles. The Style interface exists as a tab in the Control Panel and is divided into 3 tabs, for Node, Edge and Network properties. For each property, there are 3 columns describing the current Default (meaning the default value for the current mapping), Mapping and any Bypass. A pre- defined set of properties is displayed by default. Additional properties for display can be selected by clicking the Properties drop- down at the top of the list of properties.
The Styles interface also lists any pre- defined styles in the drop- down at the top of the interface. The below figures shows the default style for the gal. Filtered session file. Try changing the style for one of the properties, for example Label Color for nodes. Click on the default column for Label Color in the Node tab, and select green in the color chart. Notice that the Node Label Color changes in the network. You can also try changing other properties, like setting the Edge Line Type to dashed.
Creating a Style This creates a pseudo- exponential gradient mapping. Notice the change in the view of the network! You can reuse the mappings across multiple data sets. Now is a good time to save your Cytoscape session, to save the style you’ve created. Laying Out Your Network A network layout is a process that positions the nodes and edges for the network.
There are a large variety of layouts in Cytoscape and plugins might add new layouts. All of the layouts will appear under the Layouts menu. In this section, we will explore some of the layouts which are the core layouts supported by the Cytoscape team. Most layouts support the ability to only layout a portion of the network, and most expose parameters that can be used to tune the layout algorithm.
Simple Layouts Grid Layout The simplest layout that Cytoscape provides is the Grid Layout, which simply places all of the nodes in a grid arrangement. Using the network you loaded before, select Layout → Grid Layout. You should see the image below. Now, select Edit → Undo: Grid Layout and notice how your network reverts to the previous condition. Many (but not all) of Cytoscape's actions may be undone. Select a group of nodes in your network and again select Layout → Grid Layout.
Notice that this now has a sub- menu with two options: All Nodes and Selected Nodes Only. Choose Selected Nodes Only. Note that only the nodes you selected are changed. Circular Layout Grid is very fast, but it's of limited usefulness. Alternatives. Circular Layout places all of the nodes in a circular arrangement. Partitions the network into disconnected parts and independently lays out those parts. Hierarchical Layout Hierarchical Layout forces the nodes into a tree structure.
Works best when the network is naturally tree- structured. Also works reasonably well when the network is mostly hierarchical. Data- Driven Simple Layouts Often what is desired is to organize the nodes in space to reflect some data property of the nodes themselves. We'll look at three of the simple ones.
Degree Sorted Circle: Orders the node around a circle based on node degree (number of edges). Attribute Circle Layout: Orders the node around a circle based on the value of a selected column.
Group Attributes Layout: Groups the nodes based on the value of a selected column. Degree Sorted Circle Layout For example, assume you are interested in hubs (nodes with high degree). Select Layout → Degree Sorted Circle Layout. Note the highest degree nodes are in the same region of the circle and the degree decreases as you proceed counter- clockwise around the circle. Also note that this layout supports partitioning of the network into disconnected components. This layout algorithm adds the column degree to every node, which is very useful for coloring nodes.
Attribute Circle Layout Now try Layout → Attribute Circle Layout → Degree. This should give you a very similar layout to the Degree sorted circle layout. You should also try using other columns to layout. Group Attributes Layout Finally, select Layout → Group Attributes Layout → Degree. Note that this layout organizes all of the nodes with the same degree into a circle and then positions the circles into a grid.
Partitions the graph before layouts. These layouts are useful to represent data columns associated with the nodes of a network, however, they don't provide much information about the network structure itself. For that, using more complicated layouts are required. Force- Directed Layouts The force- directed methods for laying out graphs all use some kind of physical simulation that models the nodes as physical objects and the edges as springs connecting those objects together. Cytoscape provides 3 force- directed layouts.
Edge- weighted Force directed (Bio. Layout). Edge- weighted Spring Embedded. Prefuse Force Directed. In this exercise, we'll use the Prefuse Force- Directed Layout (see prefuse.
Force- Directed Layout We'll do all of our work from the Layout settings dialog, so bring up the dialog by Layout → Settings.. In the Layout Settings dialog. Select Prefuse Force Directed Layout under Layout Algorithm. Lets start by creating a layout using the default parameters.
Select Execute Layout. Note how this exposes more of the structure of the network than any of the previous layouts. Now, let's see what the parameters do. Start by changing the Default Spring Length to 2. Execute Layout. The default spring length is the length of a spring (edge) with no forces exerted upon it. Essentially, it's the length of an edge connecting two nodes with no other connections.
Note how the layout has changed. The resulting network tends to be more closely packed in the denser regions. Finally, lets change Default Spring Length back to 5. Default Spring Coefficient to 1. E- 3. The spring coefficient is a measure of the strength of the spring. Now click Execute Layout. Note that the network remains pretty compact, even though we've reset the default spring length back to 5.