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NAViGaTOR

An Introductory Tutorial

Contents

Section 1: Opening an existing Network

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

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

Section 3: Moving Nodes and Edges

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 NameSets the label attached to a node on the screen.
Node ColorSets the color of a node.
Automated Coloring Drop-down MenuSets the nodes color according to one of the available coloring algorithms.
Highlight ColorSets the color of the halo that appears around highlighted nodes
Highlight CheckboxSets the highlighting of a node on/off
Shape Drop-down MenuSets the shape of the node
Show Label CheckboxSets the node to display its label all the time or only when the mouse is over it.
Blend SliderSets the transparency of a node.
Fixed CheckboxSets 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 ColorSets the color of a node.
Automated Coloring Drop-down MenuSets the edges color according to one of the available coloring algorithms.
Blend SliderSets the transparency of an edge.
Show Label CheckboxSets 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