NAViGaTOR

An Introductory Tutorial

Contents

Section 1: Opening an existing Network
Section 2: Selecting Nodes and Edges
Section 3: Moving Nodes and Edges
Section 4: Nodes
Section 5: Edges
Section 6: Selection and Groups
Section 7: Saving Networks
Section 8: File Formats

Section 1: Opening an existing Network

The following example will walk you through the process of loading a network into NAViGaTOR.

Download one of the sample files from from http://ophid.utoronto.ca/navigator/sample_data
Select File->Open File from the menu.
Select the sample file you've downloaded and click on 'Open'
You should now see a 'Choose Data Source' dialog, asking which gives you the option of only selecting interactions from specific data sources. In this case, click 'Select All' and then 'OK'. In later cases where you may only want to view interactions from limited datasources you may select only the sources you are interested in.

NAViGaTOR supports several network formats aside from it's own internal format. To see what features are supported by each refer to Section 8: File Formats

On loading a file that contains existing node position information you will be asked whether or not you wish to apply the GRIP Layout algorithm. Doing so will change the node positions from those that were saved.

Some files will also display a 'Select Data Columns' dialog, allowing you to load experiment data into NAViGaTOR. This is an advanced feature which will be addressed in its own tutorial.

Section 2: Selecting Nodes and Edges

To select a node, left-click on it once. Double clicking will alternate between fixing and un-fixing the node. Fixed nodes will not have their positions altered by the force-directed algorithm while other nodes continue to find more optimal positions. It is possible to fix any number or nodes or none at all.
To select an edge, left-click on it once. Edges have no 'fix' option; they rely on the fixed settings of their terminal nodes.
Left-clicking on additional nodes or edges will expand your selection to include them.
To deselect a node or an edge, hold down the Ctrl key while right-clicking on the node or edge you wish to deselect.
To select nodes and edges over a rectangular area, hold down the Alt key, left-click, hold down and then drag to cover the area you would like to select. You can also use this tool to deselect nodes by holding down Alt and using a right-click and drag.
To select nodes over an irregular area, hold down Alt+Shift, left-click, hold and outline the area you wish to select. You can also use this tool to deselect nodes by holding down Alt+Shift and using a right-click and outline.

Section 3: Moving Nodes and Edges

To move a single node, left-click and drag it to the desired position. Note that if you have not fixed the node (see Section 2), the force-directed algorithm may move it to another position. To prevent this, fix the node before you remove it.
To move your entire selection, hold down the Ctrl key while left-clicking to drag the nodes to a new position. Fixing all of these nodes can be done more rapidly by using the methods in Section 6 .

Section 4: Nodes

Select a node from the Network and then left-click on the Node panel on the right hand side of the NAViGaTOR window. You should see a panel indicating the different features of that node. Some are editable, while others are dependent on information from the underlying network. Some of the fields you can change:

	Short Name	Sets the label attached to a node on the screen.
	Node Color	Sets the color of a node.
	Automated Coloring Drop-down Menu	Sets the nodes color according to one of the available coloring algorithms.
	Highlight Color	Sets the color of the halo that appears around highlighted nodes
	Highlight Checkbox	Sets the highlighting of a node on/off
	Shape Drop-down Menu	Sets the shape of the node
	Show Label Checkbox	Sets the node to display its label all the time or only when the mouse is over it.
	Blend Slider	Sets the transparency of a node.
	Fixed Checkbox	Sets the node as fixed or unfixed (see Section 2)

Section 5: Edges

Select an edge from the Network and then left-click on the Edge panel on the right hand side of the NAViGaTOR window. You should see a panel indicating the different features of that edge. Some are editable, while others are dependent upon the underlying network. Some of the data you can change:

	Edge Color	Sets the color of a node.
	Automated Coloring Drop-down Menu	Sets the edges color according to one of the available coloring algorithms.
	Blend Slider	Sets the transparency of an edge.
	Show Label Checkbox	Sets the edge to display or hide its label

Section 6: Selection and Groups

Once you've selected a subset of nodes and edges within your network, you can perform changes to the node and edge properties of both that group and the whole network.

Right-clicking anywhere within the network should give you a drop-down menu with 'Node Appearance' and 'Edge Appearance' sub-menus. From these sub menus, you will have several options, each of which will open a dialog containing appearance settings, just like in the Node and Edge side panels.

Current Node/Edge: Applies settings to the last selected node or edge only
Current Group: Applies settings to the entire group
All: Applies settings to the entire network
Inverse: Applies settings to every node/edge that is not selected. This is particularly useful to increase the visibility of the current group by, for example, increasing the transparency of everything outside the selection.

Your current selection can be saved within NAViGaTOR using the 'Groups' sidepanel tab. This is an advanced feature which will be addressed in its own tutorial.

Section 7: Saving Networks

After working on a network, you can save your workspace as it appears by selecting File->Save As->Navigator XML Format (*.xml). Subsequent saves can be performed through File->Save.

Section 8: File Formats

NAViGaTOR supports loading and saving in several formats, though some formats cannot store NAViGaTOR-specific data, such as node color and transparency and NAViGaTOR ignores some format-specific data. The chart below indicates what data is supported by each format.

Format	Node/Edge Appearance	Node Label/Description	GO Annotation for Proteins	Groups	PSI-MI Data
NAViGaTOR XML Format (*.xml)¹	YES	YES	YES	YES	NO
PSI-MI Level 1 Format (*.xml)	NO	YES	NO	NO	YES
Text File (*.txt)	NO	YES	NO	NO	NO

1. The PSI-MI format is a third party format defined by the The HUPO Proteomics Standards Initiative

Navigator

Network Analysis and Graphing Toronto

NAViGaTOR