Bad layout

[GoogleCodeExporter]

attached graphml file (provided by Ozgun) produces a bad layout (extremely long 
edges).

similar problem can be easily reproduced by querying the neighborhood of p53 in 
ChiBE (?)

Original issue reported on code.google.com by [email protected] on 30 May 2012 at 12:59

Attachments:

• badlayout.graphml

[GoogleCodeExporter]

Following is a comment from Huaiyu Mi on ChiBE layout:

... The layout for compartments and complexes is slightly better than some of 
the other software we used before, but the overall layout is still not ideal 
for signaling pathways. ...

...I think if the following 2 changes can be made, the layout may improve quite 
a bit.
1.  Avoid edge from crossing the node.
2.  Keep input, output and process node in a straight line. 
...

Original comment by [email protected] on 6 Jun 2012 at 5:42

[GoogleCodeExporter]

Layout of TP53 neighborhood is not the worst example. Try neighborhood of 
PIK3CA with default query parameters.

Original comment by [email protected] on 23 Jul 2012 at 3:02

[GoogleCodeExporter]

An example of high node overlaps in layout happens in L3 sample graph "PI3K 
Events in ERBB2 Signaling.owl". Open the outermost pathway. Layout in nucleus 
(innermost compartment) is good, but nodes are too close in cytoplasm, and 
overlapping in cytoplasmic membrane.

Original comment by [email protected] on 25 Sep 2012 at 8:35