Diff for "Cytoscape_3/UserManual/Styles"

What is a Visual Style?

One of Cytoscape's strengths in network visualization is the ability to allow users to encode any table data (name, type, degree, weight, expression data, etc.) as a Visual Property (such as color, size of node, transparency, or font type). A set of these encoded or mapped table data sets is called a Visual Style and can be created or edited using the Cytoscape VizMapper. With the VizMapper, the visual appearance of your network is easily customized. For example, you can:

• Specify a default color and shape for all nodes.

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• Set node sizes based on the degree of connectivity of the nodes. You can visually see the hub of a network...

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• ...or, set the font size of the node labels instead.

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• Visualize gene expression data along a color gradient.

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• Encode specific physical entities as different node shapes.

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• Use specific line types to indicate different types of interactions.

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• Control edge transparency (opacity) using edge weights.

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• Control multiple edge visual properties using edge score.

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• Browse extremely-dense networks by controlling the opacity of nodes.

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• Show highly-connected region by edge bundling and opacity.

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• Add photo/image/graphics on top of nodes.

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Cytoscape 3 has several sample Visual Styles. You can try those to examine how Visual Styles change the appearence of a network. The following is a list of network views based upon sample styles applied to the galFiltered.sif network :

VizMapper is located in a tab on the Control Panel at the left-hand side of the screen.

Introduction to the VizMapper User Interface

There are two main control panels in the VizMapper:

1. Main Panel

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This panel allows you to create/delete/view/switch between different visual styles using the Current Visual Style options. The panel displays the mapping details for a given visual style and is used to edit these details as well.

Introduction to Visual Styles

The Cytoscape distribution includes several predefined visual styles to get you started. To examine these styles, try out the following example:

Step 1. Load some sample data

• Load a sample session file: From the main menu, select File → Open, and select the file sampleData/galFiltered.cys.

• The session file includes a network, some annotations, and sample visual styles. By default, the Sample for galFiltered style is selected. Gene expression values for each node are colored along a color gradient between red and green (where red represents a low expression ratio and green represents a high expression ratio, using thresholds set for the gal4RGexp experiment bundled with Cytoscape in the sampleData/galExpData.csv file). Also, node size is mapped to the degree of the node (number of edges connected to the node) and you can see the hubs of the network as larger nodes. See the sample screenshot below:

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Step 2. Switch between different Visual Styles

You can change visual styles by making a selection from the Current Visual Style dropdown list (found at the top of the VizMapper Main Panel).

For example, if you select Sample1, a new visual style will be applied to your network, and you will see a white background and round blue nodes. If you zoom in closer, you can see that protein-DNA interactions (specified with the label "pd") are drawn with dashed edges, whereas protein-protein interactions (specified with the label "pp") are drawn with solid edges (see sample screenshot below).

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Finally, if you select Solid, you can see the graphics below:

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This Visual Style does not have mappings except node/edge labels, but you can modify the network graphics by editing the Default Value for any visual property.

Additional sample styles are available in the sampleStyles.xml file in the sampleData directory. You can import the sample file from File → Import → Vizmap File...

Visual Attributes, Graph Attributes and Visual Mappers

The Cytoscape VizMapper uses three core concepts:

• A visual attribute is any visual setting that can be applied to your network. For example, you can change all nodes from circles to squares by changing the node shape visual attribute.

• A network attribute is any data attribute associated with a node or an edge. For example, each edge in a network may be associated with a label, such as “pd” (protein-DNA interactions), or “pp” (protein-protein interactions).

• A visual mapper maps network attributes to visual attributes. For example, a visual mapper can map all protein-DNA interactions to the color blue, and all protein-protein interactions to the color red.

Cytoscape allows a wide variety of visual attributes to be controlled. These are summarized in the tables below.

For each visual attribute, you can specify a default value or define a dynamic visual mapping. Cytoscape currently supports three different types of visual mappers:

1. Passthrough Mapper

   • The values of network attributes are passed directly through to visual attributes. A passthrough mapper is typically used to specify node/edge labels. For example, a passthrough mapper can label all nodes with their common gene names.

2. Discrete Mapper

   • Discrete data attributes are mapped to discrete visual attributes. For example, a discrete mapper can map different types of molecules to different node shapes, such as rectangles for gene products and ellipses for metabolites

3. Continuous Mapper

   • Continuous data are mapped to visual attributes. Depending on the visual attribute, there are three kinds of continuous mappers:

     1. Continuous-to-Continuous Mapper: for example, you can map a continuous numerical value to a node size.

     2. Color Gradient Mapper: This is a special case of continuous-to-continuous mapping. Continuous numerical values are mapped to a color gradient.

     3. Continuous-to-Discrete Mapper: for example, all values below 0 are mapped to square nodes, and all values above 0 are mapped to circular nodes.

   • However, note that there is no way to smoothly morph between circular nodes and square nodes.

The table below shows visual mapper support for each visual property.

Legend

Node Visual Mappings

Edge Visual Mappings

Text Passthrough Mapper (New feature for version 2.8)

In Cytoscape 2.8.0 and later versions, the Passthrough Mapper can recognize some text representations of values. This means, if you have an integer attribute named Node Size Values, you can directly map those values as the Node Size by setting Node Size Values as controlling attribute name for Node Size Passthrough mapping. The following value types are supported:

• Color: Standard color names supported by all browsers or RGB representation in hex

• Numerical Values: Automatically mapped to the specified Visual Property.
• Custom Graphics: URL String. If the URL is valid and an actual image data exists there, Cytoscape automatically downloads the image and maps it to the node.

Examples

1. Color Passthrough Mapping

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2. Node Size Passthrough Mapping

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3. Custom Graphics Passthrough Mapping

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Custom Graphics Manager

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For Cytoscape 2.8.0 and later versions, Cytoscape supports Custom Graphics for nodes. You can add all kinds of bitmap images, such as jpg, png, or gif, on the top of network nodes. From the user's point of view, this is simply an addition to the Visual Properties, and you can use same VizMap user interface to map Custom Graphics to nodes. However, before mapping images, you need to prepare Custom Graphics in the Custom Graphics Manager. It is a simple GUI component to add/remove images to or from a Cytoscape session.

Taxonomy Icon set used in this section is created by Database Center for Life Science (DBCLS) and is distributed under Creative Commons License (CC BY 2.1.)

Adding New Images to Cytoscape

The Custom Graphics Manager supports drag and drop for image files and URLs. If you want to add images from a web browser or local file system, you can drag images from them and drop those images onto the list of images on the left.

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If you want to add all images in a folder, press the + button on the bottom of the Custom Graphics Manager window.

Note: When you drag and drop images from web browser, make sure that you are actually dragging the URL for the image. In some cases, images are linked to an HTML page or scripts, and in such cases, this drag and drop feature may not work.

Removing Images

To remove images from the current session's Custom Graphics library, simply select graphics from the list and press the - button.

Resizing Images

You can resize images by typing width/height in the text box. If Keep Aspect Ratio box is checked, the width-height ratio is always synchronized. You can resize the image to the original size by pressing Original button.

Using Custom Graphics in the VizMapper

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Custom Graphics is a new type of Visual Property and you can use them from the standard VizMapper user interface. There are nine Custom Graphics Visual Properties (Node Custom Paint 1 - 9) and they will be displayed in the standard VizMapper Default View Editor or Mapping Editors.

Custom Graphics Positions

Each Custom Graphics Visual Property is associated with a position. You can edit their positions by using same UI as Label Position.

Z-Ordering

This number that appears with the Custom Graphics Visual Property represents an ordering of layers. Basic node color and shape are always rendered first, then Node Custom Graphics 1, 2, ..., through 9.

Synchronize Custom Graphics to Node Size

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By default, Custom Graphics objects are automatically resized to be consistent with the Node Size Visual Property. To control Custom Graphics size separately, uncheck the Fit Custom Graphics to node dependency. You can find this check box in the Default Editor's Dependencies panel.

Custom Graphics Selector

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To select a Custom Graphics, just click one of them and press Apply. To remove a value from mappings/defaults, select the Remove Graphics option from the Custom Graphics list.

Saving and Loading Custom Graphics

In general, saving and loading Custom Graphics is automatic. When you quit Cytoscape, all of the Custom Graphics in the manager will be saved automatically. There are two types of saving:

1. To session file

   • When you save the current session to a file, the Custom Graphics used in Visual Styles will be saved to that file. For example, if you have a Visual Style with a discrete mapping for Custom Graphics, all Custom Graphics used in the style will be saved to the session file. Other graphics will not be saved in your session file. This is because your image library can be huge when you add thousands of images to the Custom Graphics Manager and it takes very long time to save and load the session file.

2. Automatic saving to CytoscapeConfiguration/images3 directory

   • When you select File → Quit, all of Custom Graphics in the Manager will be saved automatically to your Cytoscape setting directory. Usually, it's YOUR_HOME_DIRECTORY/CytoscapeConfiguration/images3.

In any case, Custom Graphics will be saved automatically to your system or session and will be restored when you restart Cytoscape or load a session.

Visual Styles Tutorials

The following tutorials demonstrate some of the basic VizMapper features. Each tutorial is independent of the others.

Tutorial 1: Create a Basic Visual Style and Set Default Values

The goal of this tutorial is to learn how to create a new Visual Style and set some default values.

Step 1. Load a sample network. From the main menu, select File → Import → Network → File..., and select sampleData/galFiltered.sif.

Step 2. Create some node/edge statistics by Network Analyzer. Network Analyzer calculates some basic statistics for nodes and edges. From the main menu, select Tools → Network Analyzer → Network Analysis → Analyze Network, and click OK. Once the result is displayed, simply close the window. All statistics are stored as a regular table data.

Step 3. Open the VizMapper. Select the VizMapper tab in the Control Panel at the left of the screen. You will now see the VizMapper main panel, as shown below.

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Step 4. Create a new visual style. Click the Options button, and select Create New Visual Style. Then enter a name for your new visual style when prompted. You will see an empty visual style in the VizMapper Main Panel, as shown below.

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Since no mappings are set up yet, all visual attributes are listed in the Unused Properties category. From this panel, you can create node/edge mappings for all visual properties.

Step 5. Edit default values. Open the Default Appearance Editor by clicking on the Defaults graphics window (shown below) in the VizMapper Main Panel.

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Step 6. Change the default node color and shape. To set the default node shape to triangles, click Node Shape in the Default Visual Properties list. A list of available node shapes will be shown. Click on the Triangle icon and then click the Apply button. The Default Appearance Editor will be automatically updated. You can edit other default values by clicking on visual attribute names on the list. In the example shown below, the node shape is set to Round Rectangle, while the Node Fill Color is set to white.

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Step 7. Apply your settings. When you finish editing, click the Apply button at the bottom of the editor. Your new Visual Style will be applied to the current network, as shown below.

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Tutorial 2: Creating a New Visual Style with a Discrete Mapper

Now you have a network with new Visual Style. The following section demonstrates how to create a new visual style using a discrete mapper. The goal is to draw protein-DNA interactions as dashed lines, and protein-protein interactions as solid lines.

Step 1. Choose a visual attribute. Double click the Edge Stroke Color (Unselected) entry listed in Unused Properties. It will now appear at the top of the list, under the Edge Visual Property category (as shown below).

Step 2. Choose an edge column. Click on the cell to the right of the Edge Stroke Color entry and select "interaction" from the dropdown list that appears.

Step 3. Choose a mapping type. Set the "Discrete Mapping" option as the Mapping Type. All available attribute values for "interaction" will be displayed, as shown below.

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Step 4. Set the mapping relationship. Click the empty cell next to "pd" (protein-DNA interactions). On the right side of the cell, ... and X buttons will appear. Click on the ... button. A popup window will appear; select green or similar, and the change will immediately appear on the network window.

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Repeat step 4 for "pp" (protein-protein interactions), but select a darker color as edge stroke color. Then repeat steps 3 through 4 for the Edge Line Type attribute. You can select the correct line style ("Dash" or "Solid") from the list.

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Now your network should show "pd" interactions as dashed green lines and "pp" interactions as solid lines. A sample screenshot is provided below.

Tutorial 3: Creating a New Visual Style with a Continuous Mapper

At this point, you have a network with some edge visual mappings. Next, let's create mappings for nodes. The following section demonstrates how to create a new visual style using a continuous mapper. The goal is to superimpose node statistics (in this example, node degree) onto a network and display it along a color gradient.

Step 1. Choose a visual attribute. Double click the 'Node Fill Color' entry listed in Unused Properties. Node Fill Color will now appear at the top of the list, under the Node Visual Property category.

Step 2. Choose a node table column. Click on the cell to the right of the Node Fill Color entry and select "Degree" from the dropdown list that appears.

Step 3. Choose a mapping type. Set the "Continuous Mapping" option as the Mapping Type. This automatically creates a default mapping

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Step 4. Define the points where colors will change. Double-click on the black-and-white gradient rectangle next to Graphical View to open the Color Gradient Mapper. Click and drag one to left, and move the second point to right.

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Step 5. Define the colors between points. Double-click on the leftmost triangle (facing left) and a color palette will appear. Choose a shade of yellow and click OK. Double-click on the triangle at left and set the color white. For the triangle at the right, set its color to green.

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The color gradients will immediately appear in the network window. All nodes with degree 1 will be set to white, and all values between 1 and 18 will be painted with a white/green color gradient. A sample screenshot is below.

Step 6. Repeat for other Visual Properties. You can create some more mappings for other numeric table data. For example, edge data table column "EdgeBetweenness" is a number, so you can use it for continuous mapping. The following is an example visualization by mapping Edge Width to "EdgeBetweenness".

Tutorial 4: How to Use Utilities for Discrete Mappers

The following tutorial demonstrates utilities for editing discrete mappings. The goal of this section is learning how to set and adjust values for discrete mappings automatically.

1. Switch the Visual Style to Minimal. Now your network looks like the following:

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3. Cretate a Discrete Node Color Mapping. Select "AverageShortestPathLength" (generated by Network Analyzer) as controlling attribute.

4. Click the Node Fill Color cell, then right-click it to show the popup menu. Select Mapping Value Generators → Rainbow. It generates different colors for different table values as shown below:

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6. Create a Discrete Node Label Font Size Mapping. Select "AverageShortestPathLength" as controlling attribute.

7. Click the Node Label Font Size cell, then right-click it to show the popup menu. Select Mapping Value Generators → Number Series. Type 3 for the first value and click OK. Enter 3 for increment.

8. Apply Layout → yFiles Layouts → Organic. The final view is shown below:

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This mapping generator utility is useful for categorical data. The following example is created by adding node color discrete mapping from species column to color.

Tutorial 5: Using Custom Graphics in Visual Styles

This tutorial is a quick introduction to Custom Graphics feature. You can assign up to nine images per node as a part of Visual Style.

1. Prepare images. These can be any type of bitmap graphics. In this tutorial, we are going to use the Crystal Project's PNG icons. You can download it from here.

2. Start Cytoscape and select View → Open Custom Graphics Manager. Cytoscape 3 has some preset images and in this example, we use these presets. You can close the Custom Graphics Manager window for now.

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3. Load a network and run the Network Analyzer (Tools → Network Analyzer → Network Analysis → Analyze Network). This creates several new table columns (statistics for nodes and edges).

4. Click the VizMapper tab in the Control Panel, and select the Solid style.

5. Click the Defaults section to open the Default Appearance Editor.

6. Click Node Custom Graphics 1 and select any of the custom graphics from the list. Click Node Transparency and set the value to zero.

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7. Press Apply. Now your network looks like the following:

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8. Open the Custom Graphics Manager again. Drag and Drop this icon to the image list. It automatically adds it to the manager.

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1. Create a Continuous Mapping for Node Custom Graphics 2. Select "BetweennessCentrality" as controlling column and move the handle to 0.2. Double click the region over 0.2 and set the new icon you have just added in the last step.

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1. Press Apply and now open the Default Appearance Editor again. Click Node Custom Graphics Position 2 and move the position of the graphics to upper left.

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1. Press Apply. Now the important nodes in the network (nodes with high betweenness centrality) is annotated with the icon.

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Advanced Topics

Editing Discrete Mappings

Several utility functions are available for Discrete Mappings. You can use those functions by right clicking anywhere on the Visual Mapping Browser (shown below.)

Automatic Value Generators

• Mapping Value Generators - Functions in this menu category are value generators for discrete mappings. Users can set values for discrete mappings automatically by these functions.

  • Rainbow and Rainbow OSC - These functions try to assign as diverse a set of colors as possible for each data value.

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  • Random Numbers and Random Colors - Randomize numbers and colors. If you use this function for numerical values (node size, opacity, etc.) you need to specify a range. For example, if you want to set values from 1 to 100, you need to type 1-100 in the dialog.

  • Number Series - Set a series of numbers to the specified mapping.

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  • Fit label width - This function is only for node width and height. When the node size is unlocked AND Node Width/Height discrete mappings are available, you can fit the size of each node to its label automatically by selecting this function. See the example below:

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Edit Selected Values at Once

You can set multiple values at once. First, you need to select rows in which you want to change values then select Edit all selected rows... under Edit right-click menu. A dialog pops up and you can enter the new value for the selected rows.

Visual Property Dependencies

The fourth tab in the Default Editor is the list of available Visual Property Dependencies. A Visual Property Dependency can be established between different visual properties. Currently there are three dependencies: Lock Node with and height, Edge color to arrows, and Fit Custom Graphics to node.

• Lock Node with and height - If this menu item is checked, Node Width and Node Height mappings are ignored and Node Size overrides them. If you want to use Fit node size to label function, you need to unlock this.

• Edge color to arrows - If this menu item is checked then Edge Source Arrow Color and Edge Target Arrow Color are overridden and Edge Color is used in both cases.

• Fit Custom Graphics to node - If a Custom Graphics is assigned to a node and this option is enabled, Custom Graphics will be resized to fit in the node.

Working with Continuous Mapping Editors

There are three kinds of Continuous Mapping Editors. Each of them are associated with a specific visual attributes:

Range Setting Panel

Each editor has a common section named Range Setting.

1. Handle Value Box - This box displays the current value for the selected slider handle. Also you can directly type the value in this box to move the slider to an exact location.

2. Min/Max Button - Set the overall range of this editor. First time you open the editor, the Min and Max values are set by the range of attribute you selected, i.e., minimum and maximum value of the attribute will be set to the range of this editor. You can change this range anytime you want by pressing this button.

3. Add Handle Button - Add a new handle to the editor.

4. Delete Handle Button - Delete the selected handle from the slider widget.

5. Handle Value Editor Button - Edit value assigned to the selected handle.

Gradient Editor

The Gradient Editor is an editor for creating continuous mappings for colors. To change the color of each region, just double click the handles (small triangles on the top). A Color gradient will be created only when the editor has two or more handles (see the example below).

Continuous-Continuous Editor

The Continuous-Continuous Editor is for creating mappings between numerical attributes and numerical visual properties (size/opacity). To change the value assigned on Y-axis (the visual property shown in the example above is node size), drag the red squares or double click on the squares to directly type an exact value.

Continuous-Discrete Editor

The Continuous-Discrete Editor is used to create mappings from numerical attribute values to discrete visual properties, such as font, shape, or line style. To edit a value for a specific region, double click on the icon on the track.

Managing Visual Styles

All Cytoscape Visual Style settings are initially loaded from a default file that cannot be altered by users. When users make changes to the visual properties, a session_vizmap.xml file is saved in the session file. This means that if you save your session, you will not lose your visual properties. No other vizmap files are saved during normal operation.

Saving Visual Styles

Visual styles are automatically saved with the session they were created in. Before Cytoscape exits, you will be prompted to make sure you save the session before quitting. It is also possible to save your visual styles in a file separate from the session file. To do this, navigate to the File → Export → Vizmap... menu option and save the properties as an XML file. This feature can be used to share visual styles with other users.

Importing Visual Styles

To import existing visual styles, navigate to the File → Import → Vizmap File... menu option and select a vizmap.props (Cytoscape 2 format) or vizmap.xml (Cytoscape 3 format) file. Imported properties will supplement existing properties or override existing properties if the properties have the same name. You can also specify a visual properties file using the -V command line option (cytoscape.sh -V myVizmap.props). Visual properties loaded from the command line will override any default properties.

Bypassing Visual Styles

Cytoscape has a feature that allows users to override visualizations created by the VizMapper for individual nodes and edges. This feature is available by right-clicking on a node or edge and then clicking on Edit → Bypass Visual Style.

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Each visual property of the node or edge is displayed. When a property is overridden, a lock icon appears next to the property and Clear / Edit Bypass menu options appear. By clicking the Clear option, the bypass will be removed and the attribute will be displayed as defined by the VizMapper. At the bottom of the menu a Reset All option appears. When clicked, this will remove all bypasses for the specified node or edge. In the example above, you can see the selected node size, color, and shape have been overridden. This is apparent in the appearance of the node itself and by the check marks in the popup menu.

It is important to realize that the Visual Mapping Bypass only works for individual nodes and edges and not for all nodes or edges of a specific type. Using the bypass function is not particularly resource intensive, you can use it as much as you like. However, if you find yourself repeating the same bypasses, then you should consider using the VizMapper instead.

The bypass values will persist between sessions only as long as you save your session. If you don't save your session, you will lose whatever bypass values you set.

Visual Property Dependencies

In some cases, you want to use the same value for multiple Visual Properties. For example, if you want to use the same value for Node Width and Node Height, you have to use the Visual Property Dependency feature in VizMapper. Currently, Cytoscape supports the following Visual Property Dependencies:

• Edge color to arrows - Assign same color for edge and arrows.

• Fit Custom Graphics to node - Adjust the size of Custom Graphics based on Node Size.

• Lock node width and height - Assign the same value to node width and height.

Example: Unlocked

Example: Locked