Cytoscape: Prevent Edges from Crossing Over Nodes
2
0
Entering edit mode
6.1 years ago
thorerges ▴ 70

I have been utilizing Cytoscape for a few days and find it very powerful. However, some its functionalities I am still trying to unlock. Here is a network I have graphed , but because of how dense it is - the edges are crossing over nodes they aren't connected to.

Is there any way this can be prevented? Here is an illustration of the problem I speak of.

image

Networks Cytoscape • 5.3k views
ADD COMMENT
2
Entering edit mode
6.1 years ago

Choose a different layout guaranteed to have no such overlaps, such as Attribute Circle, or tweak the force-directed layout parameters to make the gravitation parameter negative (to increase repulsion between nodes), and re-render.

ADD COMMENT
0
Entering edit mode

I guess that is the only method then. Thank you. 

ADD REPLY
0
Entering edit mode

Another method is to use hive plots, as Mikhail suggests.

As an example, I used them here to show qualitative, at-a-glance differences between classes of links separated by cell-specificity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679407/figure/F2/

Drawing points on a circle is probably the "optimal" solution for keeping links in a network from overlapping, but even with a circular representation, I don't think there's an easy way to get around hairballs when you're dealing with large datasets, sorry.

Though I will note that a large set of networks can be compared at a glance, so that's a nice feature. Depends on what you're trying to communicate, I guess. 

ADD REPLY
1
Entering edit mode
6.1 years ago

You may also be interested in Hive plots, those are far more flexible than circular layout.

ADD COMMENT
0
Entering edit mode

Looks cool, but these Open Source platforms are difficult to learn, not really looking forward to learning something else of this kind. 

ADD REPLY
0
Entering edit mode

Another nice link is Mike Bostock's d3.js experiments with Krzywinski’s hive plot technique: http://bost.ocks.org/mike/hive/

He includes a nice web demo that shows the effect of bundling links in categories, with adjustable parameters: http://mbostock.github.io/d3/talk/20111116/bundle.html

ADD REPLY

Login before adding your answer.

Traffic: 2432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6