Discrete Node attributes and multiple edge types

[Karen Dowell]

Hi, I have two questions I'm hoping someone can help me with.  I'm using Cytoscape 2.8.2 and want to import a file with color attributes for nodes.  What are acceptable formats for color palettes for node classes?  I tried loading hex codes, but that doesn't work.  

My next question is a little more complicated.  I have four networks that I want to merge into one to show relationships and strength of correlation (edges) among features and functions (nodes) for different subject classes. Is there a way to assign multiple edges (one for each subject class) between nodes?   Or should I append the feature names with an id to indicate subject class.  Right now, I'm using one network to show relationships among different types of feature nodes (colored by type) and use a color gradient and edge width to indicate strength and significance of correlation.  But this scheme doesn't allow for folding in another layer of visual cues for different subject classes

Any suggestions would be greatly appreciated!

Thanks in advance,

Karen

[piet molenaar]

Hi Karen,

First of all I'd advice you to use the 3.x series of Cytoscape, development of 2.x is discontinued

If you have to use 2.8 for coloring you can use the hexadecimal color codes and map the node color to the column were these are assigned as a passthroughmapping

For assigning multiple edges you'd have to create separate interaction types for each; see below

Hope this helps,

Piet

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Piet Molenaar
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Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
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[Karen Dowell]

Thanks, Piet.  I upgraded to 3.2 yesterday and like the new interface a lot.  It will help with my node coloring problem.  Thanks for the tip on using interaction type for my multiple edge problem.  I'm excited to try that!   

One last question:  is there a way to lock selected hub nodes to specific coordinate locations then use the force directed algorithm?  I want to hold a small (6) set of nodes constant across a series of related networks to make it easy to view differences in relationships.

[piet molenaar]

Upgrading is a good idea! Most plugins have been ported as apps for 3.x by now...

If you invert the selection you can do a layout on selected nodes only.

Hope this helps,

Piet

On Thu, Oct 22, 2015 at 9:42 PM, Karen Dowell <kdowe...@gmail.com> wrote:

Thanks, Piet.  I upgraded to 3.2 yesterday and like the new interface a lot.  It will help with my node coloring problem.  Thanks for the tip on using interaction type for my multiple edge problem.  I'm excited to try that!   

One last question:  is there a way to lock selected hub nodes to specific coordinate locations then use the force directed algorithm?  I want to hold a small (6) set of nodes constant across a series of related networks to make it easy to view differences in relationships.

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[Karen Dowell]

Many thanks!  I'm making huge progress getting these networks to do what I want now.  Appreciate your spurring me to upgrade from my older version.  Cytoscape has come a long way since 2011!