7 Cytoscape

download all materials

The following example will detail how to use the exported `DAVe` analysis results to create a publicastion quality network using Cytoscape.

Import

Use the data module to save and export the selected network `nodes` and `edges`.

Use Cytoscape to create a publication quality network from the exported `node` and `edge` data.

Import the `edge` data.

Specify the `source` and `target` nodes as the `from` and `to` columns in the `edges` data.

After selecting `OK` you should see the resulting network.

Next load the `node` data.

The `node` data should be set as the `id`. Some of the variables like `name` may conflict with `cytoscape` select these and rename them (e.g. rename `name` to `label`).

After selecting `OK` you should now be able to view the imported `node` data (right bottom panel `tab panel`, `node table`).

Style network

This will style the network as shown below.

Next map the `edge` data to network `edge` aesthetics. The settings below display how to map edge color and transparency based on the network `type`.

These mappings will style the network as shown below.

Map the node attributes to change the network node asthetics. The following shows how to map the model importance to border width and the direction and significance of fold change to the node color.

The following shows how to specify the node label text and font size.

The following shows how to alter node size based on the magnitude of the fold change.

After the node mapping is completed the mapped networked should be styled as the image shown below.

Fine-tune network

Next use the node layout tools to optimize the network layout.

Select the `node layout tools`.

Scale and rotate the network as needed. Note you can click and drag to select specific nodes to alter.

Next use the legend creator plugin to generate the network legend.

After some fine-tuning the final network is shown below.

Now the network is ready for export.

Export

Export the network as an `.svg` and use a vector graphics editor like Inkscape to further fine-tune the network legend. A publication quality network might look like the one shown below.

The following example will detail how to use the exported DAVe analysis results to create a publicastion quality network using Cytoscape.

Import

Use the data module to save and export the selected network nodes and edges.

Use Cytoscape to create a publication quality network from the exported node and edge data.

Import the edge data.

Specify the source and target nodes as the from and to columns in the edges data.

After selecting OK you should see the resulting network.

Next load the node data.

The node data should be set as the id. Some of the variables like name may conflict with cytoscape select these and rename them (e.g. rename name to label).

After selecting OK you should now be able to view the imported node data (right bottom panel tab panel, node table).

Style network

Modify the global network setting by selecting a template in the style menu.

This will style the network as shown below.

Next map the edge data to network edge aesthetics. The settings below display how to map edge color and transparency based on the network type.

These mappings will style the network as shown below.

Map the node attributes to change the network node asthetics. The following shows how to map the model importance to border width and the direction and significance of fold change to the node color.

The following shows how to specify the node label text and font size.

The following shows how to alter node size based on the magnitude of the fold change.

After the node mapping is completed the mapped networked should be styled as the image shown below.

Fine-tune network

Next use the node layout tools to optimize the network layout.

Select the node layout tools.

Scale and rotate the network as needed. Note you can click and drag to select specific nodes to alter.

Next use the legend creator plugin to generate the network legend.

After some fine-tuning the final network is shown below.

Now the network is ready for export.

Export

Export the network as an .svg and use a vector graphics editor like Inkscape to further fine-tune the network legend. A publication quality network might look like the one shown below.

The following example will detail how to use the exported `DAVe` analysis results to create a publicastion quality network using Cytoscape.

Use the data module to save and export the selected network `nodes` and `edges`.

Use Cytoscape to create a publication quality network from the exported `node` and `edge` data.

Import the `edge` data.

Specify the `source` and `target` nodes as the `from` and `to` columns in the `edges` data.

After selecting `OK` you should see the resulting network.

Next load the `node` data.

The `node` data should be set as the `id`. Some of the variables like `name` may conflict with `cytoscape` select these and rename them (e.g. rename `name` to `label`).

After selecting `OK` you should now be able to view the imported `node` data (right bottom panel `tab panel`, `node table`).

Modify the global network setting by selecting a template in the `style` menu.

Next map the `edge` data to network `edge` aesthetics. The settings below display how to map edge color and transparency based on the network `type`.

Select the `node layout tools`.

Export the network as an `.svg` and use a vector graphics editor like Inkscape to further fine-tune the network legend. A publication quality network might look like the one shown below.