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Revision 11 as of 2012-12-19 18:07:25
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Revision 12 as of 2012-12-20 21:00:48
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Deletions are marked like this. Additions are marked like this.
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 * Dragging Box on Network Overview - You can also pan the image by holding down the left mouse button over the blue box in the Network Overview panel in the lower left hand of the Cytoscape desktop.
 * Control + Arrow keys - You can pan the network by holding down Control key and press arrow keys. For faster movement, press both Shift and Control.
 * Dragging Box on Network Overview - You can also pan the image by holding down the left mouse button over the blue box in the overview panel in the lower part of the Network tab in the Control Panel.
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This menu can change based on the current context. Typically it shows:
 * Visual Mapping Bypass
 * Nested Network
 * Use Web Service
s
 * Link Out
This menu can change based on the current context. For nodes, it typically shows:
 * Edit
 * Select
 * Gro
up
 * Nested Networks
 * Apps
 * External
Links
* Preferences
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Context menu will be used by Plugins, and your version of Cytoscape may have more menu items. For those menues, please read the documentation from the plugin developers. Edges usually have the following menu:
 * Edit
 * External Links

Apps can contribute their own items into node and edge context menus. These additions usually appear in the '''''Apps''''' menu.
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 * Set Nested Network
   Let's the user select any network in Cytoscape as the current nodes nested network. If the current node already has a nested network it will be replaced.
 * Delete Nested Network
   After being selected the current node will no longer have a nested network associated with it. No actual network will be deleted!
!!! menu items changed names
* Add Nested Network
   Lets the user select any network in Cytoscape as the current node's nested network. If the current node already has a nested network it will be replaced.
 * Remove Nested Network
   After being selected the current node will no longer have a nested network associated with it. The associated network is not deleted. Only the association between the node and the network is removed.
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This algorithm produces layouts that emphasize group and tree structures within a network. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. The circles themselves are arranged in a radial tree layout fashion. This algorithm is available by selecting '''Layout → yFiles → Circular'''. This algorithm produces layouts that emphasize group and tree structures within a network. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. The circles themselves are arranged in a radial tree layout fashion. This algorithm is available by selecting '''Layout → yFiles Layouts → Circular'''.
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The hierarchical layout algorithm is good for representing main direction or "flow" within a network. Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings. This algorithm is available by selecting '''Layout → yFiles → Hierarchical'''. The hierarchical layout algorithm is good for representing main direction or "flow" within a network. Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings. This algorithm is available by selecting '''Layout → yFiles Layouts → Hierarchical'''.
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The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph. This algorithm is available by selecting '''Layout → yFiles → Organic'''. The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph. This algorithm is available by selecting '''Layout → yFiles Layouts → Organic'''.
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The grid layout is a simple layout the arranges all of the nodes in a square grid. This is the default layout and is always available as part of the Cytoscape core. It is available by selecting '''Layout → Cytoscape Layouts → Grid Layout'''. A sample screen shot is shown above. The grid layout is a simple layout the arranges all of the nodes in a square grid. This is the default layout and is always available as part of the Cytoscape core. It is available by selecting '''Layout → Grid Layout'''. A sample screen shot is shown above.
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The spring-embedded layout is based on a “force-directed” paradigm as implemented by Kamada and Kawai (1988). Network nodes are treated like physical objects that repel each other, such as electrons. The connections between nodes are treated like metal springs attached to the pair of nodes. These springs repel or attract their end points according to a force function. The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network. This algorithm can be applied to the entire network or a portion of it by selecting the appropriate options from '''Layout → Cytoscape Layouts → Spring Embedded'''. The spring-embedded layout is based on a “force-directed” paradigm as implemented by Kamada and Kawai (1988). Network nodes are treated like physical objects that repel each other, such as electrons. The connections between nodes are treated like metal springs attached to the pair of nodes. These springs repel or attract their end points according to a force function. The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network. This algorithm can be applied to the entire network or a portion of it by selecting the appropriate options from '''Layout → Edge-weighted Spring Embedded'''.
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The attribute circle layout is a quick, useful layout, particularly for small networks, that will locate all of the nodes in the network around a circle. The node order is determined by a user-selected node attribute. The result is that all nodes with the same value for that attribute are located together around the circle. Using '''Layout → Cytoscape Layouts → Attribute Circle Layout →''' '''''attribute''''' to put all nodes around a circle using '''''attribute''''' to position them. The sample screen shot above shows the a subset of the galFiltered network organized by node degree. The attribute circle layout is a quick, useful layout, particularly for small networks, that will locate all of the nodes in the network around a circle. The node order is determined by a user-selected node attribute. The result is that all nodes with the same value for that attribute are located together around the circle. Using '''Layout → Attribute Circle Layout →''' '''''attribute''''' to put all nodes around a circle using '''''attribute''''' to position them. The sample screen shot above shows the a subset of the galFiltered network organized by node degree.
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The group attributes layout is similar to the attribute circle layout described above except that instead of a single circle with all of the nodes, each set of nodes that share the same value for the attribute are laid out in a separate circle. The same network shown above (network generated by PSICQUIC Client) is shown above, using '''Layout → Cytoscape Layouts → Group Attributes Layout → taxtonomy'''.

==== Label Force-Directed Layout ====

The Label Force-Directed Layout is an automatic label repositioning plugin that can be accessed through '''Layout → Cytoscape Layouts → Label Force-Directed Layout'''. The layout is designed to be applied to position labels after another network layout is run to position nodes. It is compatible with any node positioning layout. Specific numerical values that the algorithm makes use of can be set by the user through the '''Layout → Settings...''' menu. Through adjusting these values, you can control how much you want to spread the labels and/or nodes of the network by.

This label layout can be applied to the entire network, or only to those nodes that are selected (through enabling the ''Only layout selected nodes'' option). Upon the application of this plugin, node labels will be repositioned according to the Force-Directed algorithm, using the ''Default Label Spring Coefficient'' and ''Default Label Spring Length'' fields:
 * '''Default Label Spring Coefficient: ''' The strength of the pull between the label of a node and the node itself. The distance between nodes and their labels will be closer to the ''Default Label Spring Length'' if this value is larger.
 * '''Default Label Spring Length: ''' The desired length between the label and the node that the label belongs to.

Users can also choose to move the network nodes. This option can be activated by enabling the ''Allow nodes to move'' option. All network nodes (or just the selected ones) will be moved according to the Force-Directed layout algorithm, while making use of the ''Default Spring Coefficient'', ''Default Spring Length'', and ''Default Percentage (%)'' fields:
 * '''Default Spring Coefficient: ''' The strength of the pull between a network node and its connected neighbours. The larger the value, the closer the distance between the two objects will be to the ''Default Spring Length'' value.
 * '''Default Spring Length: ''' The desired length of an edge that is connecting two network nodes together.
 * '''Default Percentage (%): ''' The percentage of the total ''Number of Iterations'' in which you would like the algorithm to move the network nodes as well, in addition to strictly moving the labels.
  For example: Number of Iterations = 200; Default Percentage (%) = 80. Then the network nodes will be moved for (80% / 100) * 200 = 160 of the 200 iterations.

Other algorithm settings include:
 * '''Default Node Mass: ''' The mass that a default network node should take on. Nodes with a greater node mass require more strength to move.
 * '''Number of Iterations: ''' The total number of times to run the algorithm for each execution of this label layout.
 * '''Reset the label position of all nodes: ''' Reposition the label of each node to their default position.

'''''Note: ''''' In order to yield the best layout for the labels, this plugin may need to be executed more than once.

Before
 {{attachment:LabelForceDirectedLayout_Before.png}}
After
 {{attachment:LabelForceDirectedLayout_After.png}}
The group attributes layout is similar to the attribute circle layout described above except that instead of a single circle with all of the nodes, each set of nodes that share the same value for the attribute are laid out in a separate circle. The same network shown above (network generated by PSICQUIC Client) is shown above, using '''Layout → Group Attributes Layout → taxonomy'''.
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The force-directed layout is a layout based on the "force-directed" paradigm. This layout is based on the algorithm implemented as part of the excellent [[http://www.prefuse.org/|prefuse toolkit]] provided by Jeff Heer. The algorithm is very fast and with the right parameters can provide a very pleasing layout. The '''Force Directed Layout''' will also accept a numeric edge attribute to use as a weight for the length of the spring, although this will often require more use of the '''Settings...''' dialog to achieve the best layout. This algorithm is available by selecting '''Layout → Cytoscape Layouts → Force-Directed Layout → (unweighted)''' or the edge attribute you want to use as a weight. A sample screen shot showing a portion of the galFiltered network provided in sample data is provided above. The force-directed layout is a layout based on the "force-directed" paradigm. This layout is based on the algorithm implemented as part of the excellent [[http://www.prefuse.org/|prefuse toolkit]] provided by Jeff Heer. The algorithm is very fast and with the right parameters can provide a very pleasing layout. The '''Force Directed Layout''' will also accept a numeric edge attribute to use as a weight for the length of the spring, although this will often require more use of the '''Settings...''' dialog to achieve the best layout. This algorithm is available by selecting '''Layout → Force-Directed Layout → (unweighted)''' or the edge attribute you want to use as a weight. A sample screen shot showing a portion of the galFiltered network provided in sample data is provided above.
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Many layouts have adjustable parameters that are exposed through the Layouts → Settings... menu option. This will pop up the following dialog, which allows you to choose which layout algorithm settings to adjust. The settings presented vary by algorithm and only those algorithms that allow access to their parameters will appear in the drop-down menu at the top of the dialog. Once you've modified a parameter, clicking the "Execute Layout" button will apply the layout. This be repeated until a useful layout is achieved.  Settings can be saved using the "Save Settings" button. Many layouts have adjustable parameters that are exposed through the Layouts → Settings... menu option. This will pop up the following dialog, which allows you to choose which layout algorithm settings to adjust. The settings presented vary by algorithm and only those algorithms that allow access to their parameters will appear in the drop-down menu at the top of the dialog. Once you've modified a parameter, clicking the "Execute Layout" button will apply the layout. This be repeated until a useful layout is achieved.
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Selecting the Layout → Rotate option will open the Rotate window in !CytoPanel 5. This function will either rotate the entire network or a selected portion of the network. The image below shows a network with selected nodes rotated. Selecting the Layout → Rotate option will show the Rotate window in the Tool Panel. This function will either rotate the entire network or a selected portion of the network. The image below shows a network with selected nodes rotated.
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Selecting the Layout → Scale option will open the Scale window in !CytoPanel 5. This function will scale the position of the entire network or of the selected portion of the network. Note that only the position of the nodes will be scaled, not the node sizes. Node size can be adjusted using the !VizMapper. The image below shows selected nodes scaled. Selecting the Layout → Scale option will open the Scale window in the Tool Panel. This function will scale the position of the entire network or of the selected portion of the network. Note that only the position of the nodes will be scaled, not the node sizes. Node size can be adjusted using the !VizMapper. The image below shows selected nodes scaled.
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Selecting the Layout → Align/Distribute option will open the Align/Distribute/Stack window in !CytoPanel 5. The Align buttons provide different options for either vertically or horizontally aligning selected nodes against a line. The differences are in what part of the node gets aligned, e.g. the center of the node, the top of the node, the left side of the node. The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis. The differences are again a function what part of the node is used as a reference point for the distribution. And the Stack buttons vertically or horizontally stack selected nodes with the full complement of alignment options. The table below provides a decription of what each button does. Selecting the Layout → Align/Distribute option will open the Align/Distribute/Stack window in the Tool Panel. The Align buttons provide different options for either vertically or horizontally aligning selected nodes against a line. The differences are in what part of the node gets aligned, e.g. the center of the node, the top of the node, the left side of the node. The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis. The differences are again a function what part of the node is used as a reference point for the distribution. And the Stack buttons vertically or horizontally stack selected nodes with the full complement of alignment options. The table below provides a decription of what each button does.
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Mouse movement has also been enhanced. If the Shift key is held down while dragging a node, the node will only move horizontally, vertically, or along a 45 degree diagonal.

Basic Network Navigation

Cytoscape uses a Zoomable User Interface for navigating and viewing networks. ZUIs use two mechanisms for navigation: zooming and panning. Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see. Panning allows users to move the focus of a screen to different parts of a view.

Zoom

Cytoscape provides two mechanisms for zooming: either using mouse gestures or buttons on the toolbar. Use the zooming buttons located on the toolbar to zoom in and out of the interaction network shown in the current network display. Zoom icons are detailed below:

[ATTACH]

From Left to Right:

  • Zoom In
  • Zoom Out
  • Zoom Out to Display all of Current Network
  • Zoom Selected Region

You can also zoom in/out by holding down the right mouse button and moving the mouse to the right (zoom in) or left (zoom out).

Pan

There are several ways to pan the network:

  • Middle Click and Drag - You can pan the network image by holding down the middle mouse button and moving the mouse.
  • Command Key + Drag (Mac only) - If you use Mac without middle button, you can pan the view by holding down Command key and then drag.
  • Dragging Box on Network Overview - You can also pan the image by holding down the left mouse button over the blue box in the overview panel in the lower part of the Network tab in the Control Panel.

Other Mouse Behaviors

Select

Click the left mouse button on a node or edge to select that object. You can hold down the Shift key to select more than one node/edge or you can hold down the left mouse button and drag the mouse to select groups of nodes/edges.

Context

Click the right mouse button on a node/edge to launch a context-sensitive menu with additional information about the node/edge.

Node Context Menu

This menu can change based on the current context. For nodes, it typically shows:

  • Edit
  • Select
  • Group
  • Nested Networks
  • Apps
  • External Links
  • Preferences

Edges usually have the following menu:

  • Edit
  • External Links

Apps can contribute their own items into node and edge context menus. These additions usually appear in the Apps menu.

Nested Network Node Context Submenu

!!! menu items changed names

  • Add Nested Network
    • Lets the user select any network in Cytoscape as the current node's nested network. If the current node already has a nested network it will be replaced.
  • Remove Nested Network
    • After being selected the current node will no longer have a nested network associated with it. The associated network is not deleted. Only the association between the node and the network is removed.
  • Go to Nested Network
    • After selecting this the network view of the current node's nested network will be the current network view and have the focus. Should a network view for the nested network not exist, it will be created.

Automatic Layout Algorithms

The Layout menu has an array of features for organizing the network visually according to one of several algorithms, aligning and rotating groups of nodes, and adjusting the size of the network. Cytoscape layouts have three different sources, which are reflected in the Layout menu.

yFiles Layouts

yFiles layouts are a set of commercial layouts which are provided courtesy of yWorks. Due to license restrictions, the detailed parameters for these layouts are not available (there are no yFiles entries in the Settings... dialog). The main layout algorithms provided by yFiles are:

yFiles Circular Layout

  • yCircular.png

This algorithm produces layouts that emphasize group and tree structures within a network. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. The circles themselves are arranged in a radial tree layout fashion. This algorithm is available by selecting Layout → yFiles Layouts → Circular.

yFiles Hierarchical Layout

  • yHir.png

The hierarchical layout algorithm is good for representing main direction or "flow" within a network. Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings. This algorithm is available by selecting Layout → yFiles Layouts → Hierarchical.

yFiles Organic Layout

  • yOrganic.png

The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph. This algorithm is available by selecting Layout → yFiles Layouts → Organic.

Cytoscape Layouts

Cytoscape Layouts are those layouts that have been written or integrated by Cytoscape developers. These layouts are fully integrated with Cytoscape. All Cytoscape Layouts have the option to operate on only the selected nodes, and all provide a Settings... panel to change the parameters of the algorithm. Most of the Cytoscape layouts also partition the graph before performing the layout. In addition, many of these layouts include the option to take either node or edge attributes into account. Some of these layouts are:

Grid Layout

  • grid_layout.png

The grid layout is a simple layout the arranges all of the nodes in a square grid. This is the default layout and is always available as part of the Cytoscape core. It is available by selecting Layout → Grid Layout. A sample screen shot is shown above.

Spring-Embedded Layout

  • spring.png

The spring-embedded layout is based on a “force-directed” paradigm as implemented by Kamada and Kawai (1988). Network nodes are treated like physical objects that repel each other, such as electrons. The connections between nodes are treated like metal springs attached to the pair of nodes. These springs repel or attract their end points according to a force function. The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network. This algorithm can be applied to the entire network or a portion of it by selecting the appropriate options from Layout → Edge-weighted Spring Embedded.

Attribute Circle Layout

  • attribute_circle_layout.png

The attribute circle layout is a quick, useful layout, particularly for small networks, that will locate all of the nodes in the network around a circle. The node order is determined by a user-selected node attribute. The result is that all nodes with the same value for that attribute are located together around the circle. Using Layout → Attribute Circle Layout → attribute to put all nodes around a circle using attribute to position them. The sample screen shot above shows the a subset of the galFiltered network organized by node degree.

Group Attributes Layout

  • group_by_attributes_layout.png

The group attributes layout is similar to the attribute circle layout described above except that instead of a single circle with all of the nodes, each set of nodes that share the same value for the attribute are laid out in a separate circle. The same network shown above (network generated by PSICQUIC Client) is shown above, using Layout → Group Attributes Layout → taxonomy.

Prefuse Layouts

Force Directed Layout

  • force_layout.png

The force-directed layout is a layout based on the "force-directed" paradigm. This layout is based on the algorithm implemented as part of the excellent prefuse toolkit provided by Jeff Heer. The algorithm is very fast and with the right parameters can provide a very pleasing layout. The Force Directed Layout will also accept a numeric edge attribute to use as a weight for the length of the spring, although this will often require more use of the Settings... dialog to achieve the best layout. This algorithm is available by selecting Layout → Force-Directed Layout → (unweighted) or the edge attribute you want to use as a weight. A sample screen shot showing a portion of the galFiltered network provided in sample data is provided above.

Layout Parameters

Many layouts have adjustable parameters that are exposed through the Layouts → Settings... menu option. This will pop up the following dialog, which allows you to choose which layout algorithm settings to adjust. The settings presented vary by algorithm and only those algorithms that allow access to their parameters will appear in the drop-down menu at the top of the dialog. Once you've modified a parameter, clicking the "Execute Layout" button will apply the layout. This be repeated until a useful layout is achieved.

layout_settings_dialog.png

Edge Bundling

bundle1.png

From Cytoscape 3.0, Edge Bend is regular Visual Property and can be used as a part of Visual Style.

bundle2.png

Manual Layout

The simplest method to manually organize a network is to click on a node and drag it. If you select multiple nodes, all of the selected nodes will be moved together.

Rotate

  • rotate_dialog.png

Selecting the Layout → Rotate option will show the Rotate window in the Tool Panel. This function will either rotate the entire network or a selected portion of the network. The image below shows a network with selected nodes rotated.

Before

  • rotate_networkA.png

After

  • rotate_networkB.png

Scale

  • scale_dialog.png

Selecting the Layout → Scale option will open the Scale window in the Tool Panel. This function will scale the position of the entire network or of the selected portion of the network. Note that only the position of the nodes will be scaled, not the node sizes. Node size can be adjusted using the VizMapper. The image below shows selected nodes scaled.

Before

  • scale_networkA.png

After

  • scale_networkB.png

Align/Distribute/Stack

  • align_distribute_dialog.png

Selecting the Layout → Align/Distribute option will open the Align/Distribute/Stack window in the Tool Panel. The Align buttons provide different options for either vertically or horizontally aligning selected nodes against a line. The differences are in what part of the node gets aligned, e.g. the center of the node, the top of the node, the left side of the node. The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis. The differences are again a function what part of the node is used as a reference point for the distribution. And the Stack buttons vertically or horizontally stack selected nodes with the full complement of alignment options. The table below provides a decription of what each button does.

Button

Before

After

Description of Align Options

V_ALIGN_TOP.gif

small.align_begin.png

small.align_vertical_top.png

Vertical Align Top - The tops of the selected nodes are aligned with the top-most node.

V_ALIGN_CENTER.gif

small.align_begin.png

small.align_vertical_center.png

Vertical Align Center - The centers of the selected nodes are aligned along a line defined by the midpoint between the top and bottom-most nodes.

V_ALIGN_BOTTOM.gif

small.align_begin.png

small.align_vertical_bottom.png

Vertical Align Bottom - The bottoms of the selected nodes are aligned with the bottom-most node.

H_ALIGN_LEFT.gif

small.align_begin.png

small.align_horizontal_left.png

Horizontal Align Left - The left hand sides of the selected nodes are aligned with the left-most node.

H_ALIGN_CENTER.gif

small.align_begin.png

small.align_horizontal_center.png

Horizontal Align Center - The centers of the selected nodes are aligned along a line defined by the midpoint between the left and right-most nodes.

H_ALIGN_RIGHT.gif

small.align_begin.png

small.align_horizontal_right.png

Horizontal Align Right - The right hand sides of the selected nodes are aligned with the right-most node.

Button

Before

After

Description of Distribute Options

V_DIST_TOP.gif

small.distribute_begin_vertical.png

small.distribute_vertical_top.png

Vertical Distribute Top - The tops of the selected nodes are distributed evenly between the top-most and bottom-most nodes, which should stay stationary.

V_DIST_CENTER.gif

small.distribute_begin_vertical.png

small.distribute_vertical_center.png

Vertical Distribute Center - The centers of the selected nodes are distributed evenly between the top-most and bottom-most nodes, which should stay stationary.

V_DIST_BOTTOM.gif

small.distribute_begin_vertical.png

small.distribute_vertical_bottom.png

Vertical Distribute Bottom - The bottoms of the selected nodes are distributed evenly between the top-most and bottom-most nodes, which should stay stationary.

H_DIST_LEFT.gif

small.distribute_begin_horizontal.png

small.distribute_horizontal_left.png

Horizontal Distribute Left - The left hand sides of the selected nodes are distributed evenly between the left-most and right-most nodes, which should stay stationary.

H_DIST_CENTER.gif

small.distribute_begin_horizontal.png

small.distribute_horizontal_center.png

Horizontal Distribute Center - The centers of the selected nodes are distributed evenly between the left-most and right-most nodes, which should stay stationary.

H_DIST_RIGHT.gif

small.distribute_begin_horizontal.png

small.distribute_horizontal_right.png

Horizontal Distribute Right - The right hand sides of the selected nodes are distributed evenly between the left-most and right-most nodes, which should stay stationary.

Button

Before

After

Description of Stack Options

V_STACK_LEFT.gif

small.stack_vertical_begin.png

small.stack_vertical_left.png

Vertical Stack Left - Vertically stacked below top-most node with the left-hand sides of the selected nodes aligned.

V_STACK_CENTER.gif

small.stack_vertical_begin.png

small.stack_vertical_center.png

Vertical Stack Center - Vertically stacked below top-most node with the centers of selected nodes aligned.

V_STACK_RIGHT.gif

small.stack_vertical_begin.png

small.stack_vertical_right.png

Vertical Stack Right - Vertically stacked below top-most node with the right-hand sides of the selected nodes aligned.

H_STACK_TOP.gif

small.stack_horizontal_begin.png

small.stack_horizontal_top.png

Horizontal Stack Top - Horizontally stacked to the right of the left-most node with the tops of the selected nodes aligned.

H_STACK_CENTER.gif

small.stack_horizontal_begin.png

small.stack_horizontal_center.png

Horizontal Stack Center - Horizontally stacked to the right of the left-most node with the centers of selected nodes aligned.

H_STACK_BOTTOM.gif

small.stack_horizontal_begin.png

small.stack_horizontal_bottom.png

Horizontal Stack Bottom - Horizontal Stack Center - Horizontally stacked to the right of the left-most node with the bottoms of the selected nodes aligned.

Node Movement and Placement

In addition to the ability to click on a node and drag it to a new position, Cytoscape now has the ability to move nodes using the arrow keys on the keyboard. By selecting one or more nodes using the mouse and clicking one of the arrow keys (←, →, ↑, ↓) the selected nodes will move one pixel in the chosen direction. If an arrow key is pressed while holding the Shift key down, the selected nodes will 15 pixels in the chosen direction.

Cytoscape_3/UserManual/Navigation_Layout (last edited 2016-04-26 22:17:44 by server2)

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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