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cs190c:cytoscape_tutorial [2008/03/25 01:36]
jvalko
cs190c:cytoscape_tutorial [2008/03/26 03:40] (current)
jvalko
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-====== Brief Cytoscape Tutorial on Visualizing Graphs ======+======= Brief Cytoscape Tutorial on Visualizing Graphs ​=======
  
 Before using Cytoscape, download it from http://​www.cytoscape.org/​download.php?​file=cyto2_5_2 and install it.  ​ Before using Cytoscape, download it from http://​www.cytoscape.org/​download.php?​file=cyto2_5_2 and install it.  ​
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 Save it in a text file named fig1.txt (make sure there are no empty lines after the last line). ​ Save it in a text file named fig1.txt (make sure there are no empty lines after the last line). ​
 +
 +===== Viewing a Graph =====
  
 Open Cytoscape. In the File menu, find File->​Import->​Network from Table. You will be presented Open Cytoscape. In the File menu, find File->​Import->​Network from Table. You will be presented
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 It is also possible to save the result as an image. To do so, see File→Export→Network view as Graphics. Here you will be given the option to choose among a number of image formats. It is also possible to save the result as an image. To do so, see File→Export→Network view as Graphics. Here you will be given the option to choose among a number of image formats.
 +
 +===== Adding node attributes =====
 +
 +in the project it is important to note which nodes belong to which clusters. ​ Conveniently,​ the MCL algorithm gives identical results to the Scc
 +calculation for our example graph
 +(however in general this is not the case). Node attributes can be dumped to a file by using the write_node_attributes function
 +from provided_code.py.
 +
 +To import this file into Cytoscape, use File->​Import->​Node attributes. After this, in the VizMapper tab find the "Node Color" item and expand it
 +by clicking the +. On the right, choose clusterId. For Mapping Type choose Discrete Mapper. Next, right click on Node Color and select
 +Generate Discrete Values->​Rainbow 1 (or one of the other schemes). ​ If you've done this correctly you should see something like:
 +
 +{{cs190c:​cytoscape5.png?​637|}}
 +
 +Notice that in this part of the project we are working with an undirected graph, so if you are following along after the previous section you
 +will need to go back and disable the arrows.
 
cs190c/cytoscape_tutorial.txt · Last modified: 2008/03/26 03:40 by jvalko
 
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