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Preliminary remarks

This tutorial has been made using Cytoscape version 2.5.0.
For any questions related to the installation of the plugin and Cytoscape please relate to the project page.
VizMapper is a set of mapping facilities provided by Cytoscape.

--- CLICK ON A PICTURE IF YOU WANT TO SEE IT IN HIGH-RESOLUTION ---

Tutorials

1. Building an ab initio network: steps to build and visualize an ab initio network.
2. Adding correlation edges: selecting thresholds, correlation order before computing correlation edges.
3. Mapping color on edges: for instance coloring in red correlation edges.

Please note that if the label on buttons can't be read, you should maximize the application window.

Building an ab initio network

1. Select "MetaNetter" in the "Plugin" menu.
2. Click the “Mass File” button and select the “SampleMassFile.txt” file.
3. Click the “Transformation File ” button and select the “SampletransformationFile.txt” file.
4. Select the “Transformation edges” checkbox. Click “Ok” to launch the computation.
5. The network is created but to draw it you will have to select the menu Layout->yFiles->Organic.
6. You will get this view of the network.

Adding correlation edges

1. Select the correlation order and the max and min thresholds (you can use default values).
2. Select the “Correlation edges” checkbox.
3. Select again the menu: “Layout->yFiles->Organic” to get this layout.

Mapping colors on edges

1. In the left panel select the VizMapper sub-panel. VizMapper is a Cytoscape facility for the modification of nodes and edges aspects.
2. Select Edge Color in the list. Then, by clicking next to it, select the interaction attribute.
3. Then click on Mapping type, you will obtain a list of all the possible interactions. Look for r0 in that list and select it.
4. Click on the button containing points and choose a color. Then click OK.
5. You will obtain a view where correlation edges are in red and ab initio ones in black.