Network visualization: A short introduction to the core concepts of network layout and clustering

[@alibishani9230]

Thank you for clear and useful presentation.

[@larsjuhljensen]

Glad it was useful to you!

[@metteebowz]

This was super useful, thank you!

[@larsjuhljensen]

Glad it was helpful!

[@vicjndarigfan]

Hello, I have been struggling to get positional information or subcellular localization of proteins as demonstrated in 4:44 using Cytoscape String. Can you please provide links/explanations for this?

[@larsjuhljensen]

Which organism are you working on? We only have subcellular localization information for a subset of the organisms in STRING.

[@scottporter4524]

I love that red chair!!

[@larsjuhljensen]

Thanks - it is the Variér Peel chair.

[@scottporter4524]

@@larsjuhljensen Awesome, I was wondering what it was, thanks for sharing! I would absolutely put that in my house, it looks so cool.

[@Saadiahasan]

How do you make the circular layout with the edges curved as seen at 1:33?

[@larsjuhljensen]

I first ran a clustering (MCL) so that each node got a new attribute in the node table, namely the cluster number. I then use this attribute to do an Attribute Circle Layout, thus placing all the nodes on a circle with the nodes from the same cluster being placed next to each other. Finally, I use the Bundle Edges functionality in the Layout menu to curve the edges.