Color scale legend

[cris...@gmail.com]

Hello,
my name is cristina I have generated a network using the ClueGo BP enrichment between genes differentially expressed from two groups / experiments. I want to know how I can add a color scale bar where the minimum value was the number of genes included in group / experiment 1 (yellow color in my network) and the maximum value corresponds to group / experiment 2 (green color in my network). Nodes from my network that appear in yellow color indicate that they involves genes exclusively differentially expressed in experiment 1 and the same for green nodes and experiment 2. The gray color in my network corresponds to nodes with the same number of genes differentially expressed between experiments.
Thank you

[Alex Pico]

Hi Cristina,

I'm not sure if this is a ClueGO feature you are asking about or if it relates to the general visual style capabilities in Cytoscape. I can provide advice on the latter...

You will need to prepare a column in your Node Table that contains the ratio of exp1 gene counts / exp2 gene counts. I would recommed doing this in Excel or your favorite spreadsheet software and then import it into Cytoscape.  Then it's a simple matter of choosing Fill Color in the Style Panel for nodes, selecting the column with your ratio values and choosing "continuous. Some default colors will be chosen for you, but you can double-click on the gradient to edit it and pick yellow, gray and green to your liking.

Hope this helps,

 - Alex

[Bernhard]

Hi Cristina,

you can see the proportion of genes from the two experiments as a color gradient by selecting the visual style "Clusters".

Best,