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CyOog Tutorial

Content

Getting started
Power graph examples
Power graph visualization used by CyOog
         Colors and symbols
         Technical details and limitations
Navigation and keyboard and mouse
         CyOog panel
         Selection
Create your own power graphs - Step-by-step
All features of CyOog
         Power Graph Actions
         Power Graph Layout
         Power Graph Organisation
         Power Graph Editor

First of all you need to run an instance of Cytoscape with CyOog. Read first how to get and run CyOog and what requirements are necessary. Additional information can be found in the paper Unraveling the modular nature of protein interaction networks with power graphs.

Two windows will appear. The Cytoscape window showing the CyOog panel on the left hand side and the 'Power Graph Examples' window of CyOog.

CyOog provides some examples to help the user become familiar with power graphs. The 'Power Graph Examples' window of CyOog appears when Cytoscape starts.

After closing the window you can open it again by clicking the 'Power Graph Examples ...' button in the 'Power Graph Actions' panel. Read more about navigation within the CyOog panel.

Each example is represented by a button with a picture of the network on it on the left hand side and a description of the network on the right hand side. The description provides a link to the related publication.

Click on a button to open the corresponding power graph in Cytoscape.

You can load more than one example and switch between them as usual in Cytoscape. Have a look at the Cytoscape Tutorial to learn how to navigate in Cytoscape but also read below about features of Cytoscape which change when working with CyOog and power graphs.

This sections explains the meaning of colors and 'symbols' used for power graphs in CyOog and how power nodes are technically realized and what limitations this brings about.

The image on the left shows the same graph in Cytoscape with at the top a power graph representation and below a usual graph representation. The power graph shows all 'symbols' used for power graphs in CyOog. The small gray circles are single nodes. The big circles containing other nodes are power nodes. A power node will be displayed green if it is a clique - each pair of nodes inside a green power node is connected. Attention: Nodes are not connected only because they are together in a power node. For instance there is no edge between E and F. A and B are connected since they belong to a clique (green power node). Compare with normal graph visualization below. Gray edges are single edges. Thick, black edges are power edges and can connect a normal node with a power node or a pair of power nodes together. A power edge means that all nodes within a power node on one side are connected to all nodes on the other side of the edge. Examples: The green power node at the top abstracts six edges inside since it contains four nodes and is connected to itself by a power edge symbolized by the green color. The power edge between this power node and the black power node at the bottom abstracts 36 edges because it connects four nodes (A - D) to nine nodes (E - M). The light gray power node which is not part of any power edge and contains the nodes E through J is a grouping bubble which is used to obtain a better layout of the power graph.

Since grouping bubbles are not really part of the graph they can be hidden by disabling the option 'Display grouping bubbles' in the 'Power Graph Layout' panel.

The filling of the power nodes can also be switched off. This option will be useful if you have a graph with a lot of nesting power nodes. Have a look at the technical details below for more information.

Since power nodes are as new as power graphs, Cytoscape does not support them. Our trick is to use normal nodes as power nodes. This technique causes several limitations for cytoscape features when working with CyOog and power graphs.

Layout algorithms provided by cytoscape and other plugins are not working because they can not distinguish normal nodes and power nodes.

Copying a sub-network to a new network is not possible for the same reason.

Alternative for power graphs: By clicking the button 'Clone Power Graph (from selected nodes, all edges)' a network with a power graph cloned from the selected nodes and power nodes is opened. Select the whole power graph to clone it completely.

CyOog may be incompatible with other plugins.

A very important issue is the rendering which does not provide a possibility to influence the drawing order. This means that a big power node may be drawn in front of small nodes. This is mostly resolved through re-implementing the whole mouse-handling for selecting nodes and edges. Furthermore transparency has to be used for power nodes. Attention: Be careful when modifying visual attributes. The modification of node colors and sizes may destroy your power graph. Despite using transparency the filling of power nodes may shroud nodes but the fill colors can be made completely transparent (see at the end of the last section: Colors and symbols).

Saving a power graph in a session is not implemented yet.

There are several mouse-key combinations you should know, for instance how to select a power node without selecting the nodes it contains.

The CyOog panel contains all control items necessary to deal with power graphs. Next to the CyOog logo there is the help button (question mark) linking to a small direct help and to this tutorial. Below are several collapsible panels. Each covers the control items of a certain category like 'Power Graph Actions' or 'Power Graph Layout'. Each collapsible panel can be collapsed or expanded by clicking on its title or its expand/collapse button in its upper left corner. If [Ctrl] is pressed when clicking, all collapsible panels are collapsed or expanded, respectively. By default only the two essential panels 'Power Graph Actions' and 'Power Graph Layout' are shown. But there are more features. At the bottom of the first collapsible panel you can find the option 'show advanced features'. If this option is activated all features are shown in the CyOog panel. The image on the left shows the CyOog panel in advanced mode. The control items in the different categories are mainly explained under Create your own power graphs - Step-by-step and All features of CyOog.

The mouse handling for selecting graph elements had to be re-implemented. Read about the reason in the section about technical details and limitations. Nevertheless, all actions you may be familiar with should work as usual. But there are additional possibilities.

Seleting power nodes: The selection of a power node by just clicking also selects the nodes and power nodes it contains. Is [Crtl] pressed when selecting only the power node is selected and the contained elements are not.

Selecting several power nodes is possible - as usual - with [Shift].

To change the size of a power node you have to select the power node first. If there are no other nodes selected than the power node and its children (they don't have to be selected) you change its size be pressing [Ctrl] and turning the vertical mouse wheel.

Zoom: By default you can zoom by pressing the right mouse button and dragging. With CyOog you can zoom the view of a power graph also with the vertical mouse wheel.

Pan: By default you can pan the view by pressing the middle mouse button and dragging. With CyOog you can pan the view of a power graph also with [Alt], left mouse button, and dragging.

I. Load normal network

Just load a network from a network file. If you are new to Cytoscape: In the Cytoscape menu you can find the way 'File', 'Import', 'Network (various file types) ...'. Click there and choose a network file. The loaded network will appear in Cytoscape.

II. Extract power graph

You can extract a power graph from the current network view in Cytoscape by clicking 'Extract Power Graph ...' in the 'Power Graph Actions' panel. In a small dialog which pops up, you have to choose one power graph extraction algorithm. If you choose the hierarchical based algorithm you can modify two thresholds. Through increasing the minimum similarity or decreasing the maximum iterations the algorithm will finish sooner. We advice you to use the suggested values in the beginning. Additional information to the extraction algorithms can be found in the paper Unraveling the modular nature of protein interaction networks with power graphs. An additional network view is opened in Cytoscape when the extraction is finished.

III. Save power graph

To save your power graph you just have to click on the button 'Save Power Graph ...' in the 'Power Graph Actions' panel. You can save the power graph in '.bbl' format which only covers the power graph and no layout information. To preserve the layout save the power graph in a '.pgf' file.

IV. Load power graph

To load a power graph you have saved just click on the button 'Load Power Graph ...' in the 'Power Graph Actions' panel. You can load power graphs from '.bbl' and '.pgf' files, but also directly from '.edg' and '.sif' files.

This section gives a tutorial to all features of the CyOog. Since the collapsible panels on the CyOog panel are functional groups there will be a subsection to each of this.

The items in this panel are the most important when dealing with power graphs. They are already explained in this tutorial. The button 'Power Graph Examples ...' is explained with the power graph examples. The buttons 'Extract Power Graph ...', 'Load Power Graph ...', and 'Save Power Graph ...' are part of the section 'Create your own power graphs - Step-by-step'. The button 'Clone Power Graph (from selected nodes, all edges)' is described in the section about technical details and limitations. In the section about the navigation in the CyOog panel you find information about the option 'Show advanced features'. You will always find an image of the control item next to its description.

More tutorial goes here ...

More tutorial goes here ...

Every graph has many different power graph representations. With the power graph editor you can modify your power graph. You can also build a power graph directly from a usual network. You can create a bubble (which is a grouping bubble (or clique) in the beginning, but can become an power node through adding a power edge), remove bubbles (which can be grouping bubbles, cliques, or power nodes), merge nodes and bubbles, split a bubble, create power edges, and remove power edges. Which elements are surrounded by the new bubble or connected by the new power edge depends on the current selection. If the choosen action can not be applied for the current selection a message with the reason will be shown.

Adds a bubble containing at least all currently selected nodes and power nodes to the power graph. The new bubble will automatically appear as clique if the nodes which are finally in the bubble are complete connected. Otherwise the new bubble is a grouping bubble until a power edge is added. Case: If there are two nodes selected and only one of these is within a bubble B, the new bubble will contain the whole bubble B since partly intersection of bubbles is not allowed.

Removes all selected bubbles (which can be grouping bubbles, cliques, or power nodes) which are not contained by another selected bubble. You can not remove nodes. Case: If there are a power node A and all the nodes and power nodes it contains selected (normal selection), only the power node A will be removed from the power graph.

This option adds a bubble containing all currently selected nodes and power nodes to the power graph and removes all bubbles which are direct children of the new bubble. In this case all selected nodes and power nodes must have the same parent power node or be contained by an also selected power node. This is more restrictive than when adding just a new bubble. Case: Picking up the case from 'Create bubble': If there are just two nodes selected and only one of these is within a bubble B, the message 'Selected elements can not be merged due to different parents.' will be shown. Nodes and power nodes can only be merged if the sets of nodes and power nodes they are connected with by power edges are equal. The power edges will be merged too.

This option removes the power node which contains all selected nodes and power nodes and creates two new power nodes whereby on of these contains at least all selected elements. The power nodes will only be created if they contain at least two elements. Case: If there is a power node A containing just two power nodes and one of these two is selected, only power node A is removed but new power nodes are not created. Power edges will be splitted too.

Creates a power edge between the two selected elements if they actually are a biclique. Otherwise the completeness of the incomplete biclique is given.

Removes the power edge between the two selected nodes or power nodes.

More tutorial goes here ...