Added by Laura Pace, last edited by Laura Pace on Jan 13, 2016  (view change)

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Network analysis utilizing Cytoscape 3.2.1

Cytoscape is an open source software platform for visualization and annotation of networks. Cytoscape is available for download from; http://www.cytoscape.org. The instructions below assume that you have installed Cytoscape 3.2.X and have downloaded your completed workflow from GNPS. There are additional instructions and documentation available from the creators of Cytoscape at http://www.cytoscape.org/documentation_users.html.

Importing your network

When Cytoscape first opens a Welcome to Cytoscape dialog box appears which can be closed without further action.

From the Toolbar go to File ? Import ? Network ? File and then select the file from your networkedges folder or networkedges_selfloop folder. 

Folder Name Description
networkedges Network Topology File, describing similarity (edges) between spectra (nodes)
- Each node has at least one neighbor connected by an edge
networkedges_selfloop
Network Topology File, describing similarity (edges) between spectra (nodes)
- Allows individual nodes without neighbors to be viewed
clusterinfosummarygroup_attributes
Node metadata file. Describes the spectra
- Used with data that did not include library search
clusterinfosummarygroup_attributes_withIDs Node metadata file. Describes the spectra
- Used with data that included a library search
clusterinfosummarygroup_attributes_withIDs_arbitraryattribute
Node metadata file. Describes the spectra
- Used with data that included a library search and attribute mapping

Once a file has been imported another Import Network From Table dialog box will open. Within the Advanced section of this dialog box, check the box Show Text File Import Options

Within the Advanced section make certain to check the box next to Tab within the Delimiter section and Transfer first line as column names within the Column Names section.  

  • For Source Interaction select Column 1. The appropriate column will then turn purple
  • For Interaction Type select Default Interaction
  • For Target Interaction select Column 2. The appropriate column will then turn orange
  • Select the columns for DeltaMZ and Cosine. The appropriate columns will then turn blue and will be loaded as Edge Attributes. 
  • Once your selections are complete, press OK

Applying Layout

Prior to applying a layout your network will appear very disorganized. 

From the Toolbar go to Layout ? Apply Preferred Layout. You can explore other Layouts but the preferred Layout will get you started. 

Importing Attribute Data

This section only applies to users who used Attribute and Group mapping when running their GNPS workflow.

From the Toolbar go to File ? Import ? Table ? File and then select the file from your clusterinfosummarygroup_attributes_withIDs_arbitraryattribute folder. 

A dialog box will appear with a table of attributes that can be imported into Cytoscape. A column that has a ? next to the Column name will be imported, a column with a × next to the Column name will not be imported. Clicking by the Column name will allow you to select and deselect each column. 

At the minimum select the following columns for import:

  • Cluster index
  • Parent mass or Precursor mass
  • ProteoSAFeClusterLink
  • RTMean
  • All Files

Click OK to begin the import process. 

Note: All columns that are to be imported will need to be imported as a String rather than as an Integer or Floating point. The user can change these properties by right clicking the Column name and modifying the Column Type in the Set Column Name and Type dialog box that appears. Click OK to apply these changes. 

Node Annotation

From the Control Panel select the Style Tab and from the Properties menu you will be able to change the appearance of the Nodes, Edges and Network. Within the Node menu, you will be able to apply a label to each of your nodes, you may select the Attribute from the drop down menu to use as a label and then select Passthrough Mapping as the Mapping Type. Typically Parent mass or Precursor mass is selected for node labels of networks generated using GNPS. From this menu you may also modify the appearance of your node, including Border color, Width, Shape, Label color, Font size. All these modifications can be made through the associated drop down menus. 

Edge Annotation

To aid in the visualization of individual node relatedness within a cluster, the cosine score is used. This value will determine the thickness of the edge between related nodes. The thicker the edge, the higher the cosine score and therefore the more related the two individual nodes are to each other. 

Again working within the Style Tab, select the Edge menu. From the Width drop down menu, select Cosine for the Column and Continuous Mapping for the Mapping Type.

Double click on the Continuous Mapping area of the menu to adjust the thickness of the edge. Click OK to apply the setting changes. 

Below is a zoomed in portion of a network demonstrating the use of Cosine score for edge width determination. 

Visualization using Group Mapping

Again working within the Style Tab, select the Node menu. From the Fill Color drop down menu, select the Spectrum Files group (i.e. G1, G2, etc.) or the Attribute and Group mapping feature that you would like to distinguish with a unique color within the Column. Select Discrete Mapping for the Mapping type.

In the example below Source was selected as the Attribute to map. Within the Attribute.group file that was run during the generation of this network within GNPS, Source included the following Groups: HUMAN, STOOL, CONTROL, therefore for this network these particular groups can be designated by unique colors. The colors are chosen by clicking the column adjacent to the Group.

The image below shows a cluster with Node color applied based on Group designation.  

Basics of Visualizing your Annotated Network

Highlighting and zooming an area of interest within your network

Adjacent to an area of interest within your visualized network, click and drag the cursor creating a box that surrounds the area of interest.

From the Toolbar within Cytoscape select the icon of the magnifying glass with the box overlaying it  . This will zoom the chosen area within your network. 

From the Toolbar within Cytoscape select the icon of the magnifying glass with the 1:1 overlaying it  . This will return the network to the original size. 

Exploring nodes of interest within your network

Highlight the node of interest, which will then display the associated Attributes for this node. For example clicking on the ProteoSAFeClusterLink will allow the user to view the related spectra in GNPS. 

Saving a new sub-network

Adjacent to an area of interest within your visualized network, click and drag the cursor creating a box that surrounds the area of interest.

From the Toolbar ? New ? Network ? From selected nodes, all edges. This will save the selected portion of the original network as a sub-network.