NAViGaTOR Workshop

http://ophid.utoronto.ca/navigator/



Contents


Introduction


Section 1: Creating and Editing a Basic Network


Section 2: Opening an Existing Network and Applying Basic Layout and Visualization


Section 3: Opening and Manipulating an Existing Network with Features


Introduction


Network Analysis, Visualization, & Graphing TORonto (NAViGaTOR) is a software package for visualizing and analyzing protein-protein interaction networks. It's open framework is designed to allow the user to freely define the data associated with their network. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D and 3D visualization system for multiple hardware platforms. NAViGaTOR also provides analytical capabilities provides connectivity to online databases such as I2D and cPath. It also supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI) XML format.

The Application

The NAViGaTOR main window is broken into several sections which will be referenced frequently in this text. The figure below illustrates these sections:


NAViGaTOR components

Menu
This is a standard GUI menu system, through which most global NAViGaTOR functions can be accessed.

Toolbar
There are several tools that can be used within the Network Panel which can be selected using the toolbar, as well as some quick-reference items for layout and zoom.

Network Panel
This is the main workspace in which networks will be displayed and edited. You can have multiple network panels open at the same time, which can be selected using the tabs located on the top left of each panel.

Popup Menu
This menu is available from within the Network Panel through a right-click on your mouse. It makes many NAViGaTOR tools and actions accessible without leaving the Network Panel, allowing for faster network editing and manipulation.

Search Panel
This panel allows searches of the network currently displayed. It will change format depending on the features contained in the current network.

Network Object Tabs
This series of tabs allows closer inspections of network, node, edge and subset features. The presently selected object will have all of it's viewable and editable features displayed here.

Console
For some analysis methods and plugins, data is output to the console, annotated with timestamps and network source.


Section 1: Creating and Editing a Basic Network

1.1 Creating new network


1.2 Using the Tool Menu

  • Most user actions within the Network Panel are governed by the current tool. The default tool, referred to as the Select Tool is represented by this button in the Toolbar:
  • This will be the tool most used in this workshop.
1.3.1 Creating a new node

  1. Right click in the Network Panel and from the Popup Menu select Node → New
  2. Give the node a unique ID by filling in the Node ID text box. For this node, use the ID 'A'.
  3. (Optional) Give the node a name by filling in the Node Label text box. When you put your mouse over this node in the Network Panel, this is the text that will appear to identify it, so an adequately descriptive name such as 'Node A' is recommended.
  4. Click Add. You should now see a single node in the Network Panel.

1.3.2 Creating more nodes

Repeat the procedure from 1.3.1 to add two more nodes with the IDs 'B' and 'C'.

1.4.1 Selecting nodes


1.4.2 Modifying your node selection


1.5 Moving your selection


1.6.1 Creating a new edge

  1. Select only nodes 'A' and 'B'
  2. Right-click in the Network Panel and in the Popup Menu, select Edge → New. You should now see an edge drawn between nodes 'A' and 'B'.

1.6.2 Creating more edges

  1. Select all the nodes in the network.
  2. Right-click in the Network Panel and in the Popup Menu select Edge → New.
  3. You will be informed that the edge between nodes 'A' and 'B' already exists. Creating edges will generate all possible edges between the selected nodes. You can choose any action at this point, but note that if you choose to overwrite the existing edge, any data or visualization information connected to that edge will be lost, and the new edge will have no data and default visualization qualities.

1.7.1 Selecting edges


1.7.2 Modifying your edge selection


1.8.1 Deleting nodes

  1. Select only node 'C'.
  2. Right-click in the Network Panel and select Edit → Delete Nodes. Note that this also deletes all the edges that were incident upon node 'C'.

1.8.2 Deleting edges

  1. Select the edge connecting nodes 'A' and 'B'.
  2. Right-click in the network panel and select Edit → Delete Edges. Note that this deletes the edge between nodes 'A' and 'B' but does not delete either node.

1.9 Closing your file 

Close your network by clicking on the 'X' in the left-hand corner of your network tab or going to the Menu and selecting File → Close Tab.


Section 2: Opening an Existing Network and Applying Basic Layout and Visualization

2.1.1 Opening a tab-delimited file in NAViGaTOR

  1. Optional: Open the file section_2.txt in notepad or Excel to see what the file looks like.
  2. From the File Menu select File→Open... You can also use the Welcome screen button labeled Browse.
  3. IMPORTANT: Set the Files of Type drop down box to (.txt) Tab-Delimited Data.
  4. Open the file section_2.txt.

2.1.2 Setting Header Information

  1. After selecting your file, you should be presented with a dialog and page like the one below:
  2. Adjust the Header Size (rows) spinner to ignore the first six header lines. Click Next

2.1.3 Setting Node ID Columns
  1. After setting the the desired Header information, you should be presented with the Set Node ID Columns Page, as shown below.
  2. The columns in the tab-delimited file are arranged as follows:
    • Column 1: Edge Label
    • Column 2: Node A ID
    • Column 3: Node B ID
  3. Use the drop-down menu above each column to select the correct columns corresponding to the two Node ID's. In this case, these should be the second and third columns.
  4. Once you are done selecting the Node ID Columns, left-click on Next

2.1.4 Setting Feature Import Columns

  1. After setting the desired Node ID information, you should be presented with the 'Set Feature Import Columns' Page, as shown below
  2. As noted in 2.1.3, the first column represents the Edge Label
  3. Set the Feature Object of the first column to Edge by first selecting Edge from the Feature Object drop-down box.
  4. The Feature Type should already be set to Edge Label by default. If this is not the case, set it now using the Feature Type drop-down box.
  5. Once the fist column is correctly identified, left-click on Done. A new tab should open with a graph that looks similar to the one below:

2.2 Changing node/edge appearance

  1. Select a group of nodes or edges using the methods discussed in Section 1.
  2. Right-click in the Network Panel and select Node → Appearance (Selection) or Edge → Appearance (Selection) .
  3. Depending on your previous action you will be presented with a dialog that looks like one of the following:

Experiment with both Node and Edge appearances. Try changing the following settings:

Node Edge
Color
Highlight
Highlight Color
Highlight Size
Shape
Height & Width
Blending
Show Label
Label appearance options
Color
Width
Spring Resting Length
Spring Constant
Blend

Once you have experimented with these, try using the other options under the Node Appearance and Edge Appearance Popup Menu items, such as Selection, Inverse and All. These will allow to change the visual appearance of single nodes/edges, unselected nodes/edges (Inverse), or all nodes/edges (All).

2.3 Fixing nodes in position

  • Double-click on your selection or
  • Using the Node Appearance panel, check mark the Fixed Position box.

2.4 Pausing/Unpausing the network

  • Click the Pause button in the Network Tab located in the Sidebar, or double-click on any whitespace area in your graph.

2.5 Arranging nodes in a straight line

  1. Select the nodes you want to arrange on the line.
  2. (Optional, but recommended) Either fix the nodes or pause the network.
  3. Go to the Toolbar and click on one of the Linear Layout buttons

Linear Layout Buttons



Linear Layout
2.6 Arranging nodes in a circle

  1. Select the nodes you want to arrange in a circle.
  2. (Optional, but recommended) Either fix the nodes or pause the network.
  3. Go to the Toolbar and click on the Circle Layout button

Circular Layout Button
Circular Layout

2.7.1 Scaling the selection

  1. Select the nodes that you want to scale.
  2. (Optional) Either fix the nodes or pause the network.
  3. Hold down the Shift key and the left mouse button while in the network panel. Drag the mouse to scale the selected nodes.
  4. You can also use the scale tool exclusively by selecting it's icon in the Toolbar

2.7.2 Rotating the selection

  1. Select the nodes that you want to rotate.
  2. (Optional) Either fix the nodes or pause the network.
  3. Hold down the Alt and key and the left mouse button while in the network panel. Drag the mouse to rotate the selected nodes.
  4. You can also use the rotate tool exclusively by selecting it's icon in the Toolbar

2.8 Saving network data

  1. Go to File → Save As.
  2. Set Files of Type to the format you want to save the network in. (.xml) NAViGaTOR 2.0 XML is NAViGaTOR's internal XML format and will save every detail about your current NAViGaTOR session. (.txt) NAViGaTOR 2.0 Text is for exporting data to tab-delimited format. Other formats are also available. Choose whatever best fits your needs.
  3. Browse to the folder where you want to save your file. Give the file a name and click Save.

2.9 Saving the network as an image

  1. Go to the Export menu and select an image format to export to. For the best results, use JPG or SVG formats. In this case, use SVG.
  2. Using the file selection dialog choose where you would like to export the file, and click on Save.
  3. You can open the file to view the image using Internet Explorer.

2.10 Closing your file

Close your network by clicking on the 'X' in the left-hand corner of your network tab or going to the Menu and selecting File → Close Tab.


Section 3: Opening and Manipulating an Existing Network with Features

3.1 Opening a Tab-delimited File with additional data

  1. Optional: Open the file section_3.txt in notepad or Excel to see what the file looks like.
  2. From the Menu, select File → Open...
  3. Set 'Files of Type' drop down box to (.txt) Tab-Delimited Data.
  4. Open the file section_3.txt. You should be presented with a dialog like the one below:
  5. IMPORTANT: Remember to adjust the Header Size (rows) to encompass the first three header lines.
  6. The columns are arranged as follows:
    • Column 1: Node A ID
    • Column 2: Node A Label
    • Column 3: Node B ID
    • Column 4: Node B Label
    • Column 5: Edge Label
    • Column 6: Node A Description (String)
    • Column 7: Node B Description (String)
    • Column 8: Edge Confidence (Double Number)
  7. Use the header above each column to match it's description above. Each column should specify a Network Object (Node A, Node B or Edge) a data type (ID, Label, GO Info, String, Double Number, etc) and in some cases a unique identifier is required for the ID of a feature that is to be created (in this case, 'Description' and 'Confidence').
  8. Once you are done describing the columns you wish to load, click on 'Open'. You should see a file similar to the one you loaded in Section 2, except this file now contains more information to describe the network.

3.2 Exploring Node and Edge Features 

Within the loaded network, try selecting different nodes and edges. You should be able to see the information you loaded in the Node and Edge tabs in the Sidebar, similar to the tabs shown below:

Each feature has its own header tab, which can be collapsed and expanded using the triangular icon in it's left hand corner.

3.3.1 Finding Nodes through Searching

  1. (Optional) Go to the Selection menu and click on 'Deselect all Nodes and Edges'.
  2. In the sidebar, select Search Nodes.
  3. Make sure that 'ID/Label Search' is selected for the search type, and then enter the ID 'P51948'.
  4. Click on the 'Search' button. The node labeled MNAT1 should have been added to your selection.

3.3.2 Finding Nodes through Searching 2

  1. Optional: Open the file 'Desktop\NAViGaTOR Workshop\section_3_list.txt' in notepad or Excel to see what the file looks like.
  2. In the sidebar, select Search Nodes
  3. Make sure that 'ID/Label Search' is selected for the search type, and then click on the 'Load from File' button.
  4. A file selection dialog should appear. Select the file 'Desktop\NAViGaTOR Workshop\section_3_list.txt' and click on open. You should now see a list of ID's in the search panel.
  5. Select the ID Match option. This constrains the search to only node ID's which makes the search faster on larger networks.
  6. Click on the 'Search' button. The series of ID's you entered should now be selected.

3.3.3 Finding Edges through Searching

  1. In the sidebar, select Search Edges
  2. Make sure that 'Confidence' is selected for the search type.
  3. Where you are prompted for From and To search values, select any values from 0.0 to 1.0 (These are the minimum and maximum values in this network; other files will have other ranges both positive and negative)
  4. Click on the 'Search' button. You should now see all the edges that matched your search added to your selection.

3.4 Adding Features to nodes/edges

  1. Right-click on a node/edge and select New → Node Feature(s)... or New → Edge Feature(s).
  2. Give the feature a name by filling in the Feature Name text box.
  3. Select the type of data to store in this feature using the Feature Type drop down box.
  4. Click Current Node to add the feature only to the node that was right-clicked on, Current Selection to add the feature for all selected nodes, All to add the feature for all nodes and Inverse to add the feature for all unselected nodes. Similar instructions apply for edge features.
  5. In the pop-up text box enter a new value for the feature. All features added to the nodes/edges will have this value stored in it.
  6. Click Done.