- Download and install latest version of Cytoscape: http://cytoscape.org/download.php
- Get familiar with main Cytoscape file formats (->)
- Load a "cytoscape sesion" (.cys) file (network plus nodes' and edges' associated data): File > Open > galFiltered.cys (directory: sampleData)
- Cytoscape panels (network panel, table panel, control panel)
- Navigate (zoom in/out, scale, move, ...)
- Try a couple of different layouts.
- Select/unselect a node. Inspect its properties on the "Data Panel". Linkout.
- Select nodes by their names in the "search bar".
- Sort "Data Panel" (e.g. by "degree") and select nodes there.
- Move a node; select the first neighbors of a node and move them together; ...
- Select a bunch of nodes/edges. Move them together, and inspect their properties on the "Data Panel"
- Style tab: Try a couple of different styles for visualizing the network.
- Style: Play with the "Default" parameters for the representation ("Style > Def"): e.g. node shape, node border width and color, edge width, ...
- Change repersentation for subset of selected nodes ("Style > Byp")
- Associate graphical elements to network parameters ("mapping") ("Style > Map."):
- Node size proportional to Degree. Node color representing "betweennessCentrality" in a color scale.
- Edge width proportional to "edge betweenness". Add edge arrow for protein-DNA interactions ("pd", interactions representing transcriptional control).
- Select a bunch of nodes. "Propagate" them by heat diffusion: Tools > Diffuse > Selected nodes with options
- Color nodes by propagated heat.
- Save session / Export image, ...
- Import this network from a external text file: test_net.tsv (File > Import > Network from file).
And this file with attributes for the nodes: test_net_attr.tsv (File > Import > Table from file).
- Take a look at APPs.
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Additional resources
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