An Introductory Tutorial
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.
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)|
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|
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.
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.
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.
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|