Question: Coloring nodes according to attribute value in Cytoscape 3
0
gravatar for orzech_mag
4.4 years ago by
orzech_mag200
Poland/Łódź
orzech_mag200 wrote:

Hallo,

my question is about Cytoscape 3. I would like to color my nodes according to the attribute value which is FDR. I was looking for some method to do it, but I found only manuals for VizMapper. However, I did not find VizMapper for Cytoscape 3, for later versions either. And I did not find any other method for such visualization too. So please, give me any advice or suggestions.

Thanks in advance and best regards!

cytoscape • 3.7k views
ADD COMMENTlink modified 4.4 years ago by russhh4.6k • written 4.4 years ago by orzech_mag200
0
gravatar for russhh
4.4 years ago by
russhh4.6k
UK, U. Glasgow
russhh4.6k wrote:

you should find VizMapper as the second entry in the Control Panel

ADD COMMENTlink written 4.4 years ago by russhh4.6k

I know, but there is not ;/ My Cytoscape version - 3.2.0

ADD REPLYlink written 4.4 years ago by orzech_mag200

Problem solved. Thanks anyway!

ADD REPLYlink written 4.4 years ago by orzech_mag200

Perhaps you should have mentioned CSC3.2 rather than CSC3, and maybe your OS

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by russhh4.6k

hi i have the same issue. How did you solve the problem?

ADD REPLYlink written 2.5 years ago by Bioinformatician_in_trouble10

In newer versions of Cytoscape this option is a bit hidden. You import your data first using option "import network from file". You need to pick that FDR or whatever you want as node attribute. Then: 1. choose Layout -> Degree Sorted Circle Layout 2. in control panel you move to "Style" 3. at the bottom you pick "lock node width and height". Node size and filling color have been unlocked. 4. if you want to change color of the node dependently on FDR value you choose in control panel "fill" (small black triangle at right). Then you change column to FDR (or whatever) and mapping type to discrete mapping. You can pick automatic colors or choose your own. The same thing you do with size, if you want to have node size dependent on FDR. 6. then you can use "apply preferred layout" to make it more clear.

Anyway, you can use anything instead of FDR. If you want to change colors or size dependently on number of edges assigned to one node you do the same procedure, but instead of FDR column you choose "degree.layout".

Best wishes!

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by orzech_mag200

Sorry for late reply.Thank you so much.

ADD REPLYlink written 2.5 years ago by Bioinformatician_in_trouble10

You welcome. I hope it was helpful :-) Best regards!

ADD REPLYlink written 2.5 years ago by orzech_mag200
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