Cytoscape ring network visualization

Question

[Shinster007]

Hello,

I am trying to recapitulate a figure in the following paper; figure 4F (both left and right panels):

https://www.cell.com/cell-reports/pdf/S2211-1247(21)01473-X.pdf

Does anyone know how to do these types of diagrams? I'm assuming they're done in Cytoscape. My data includes TFs in 4 different cell types, as well as the target genes (TFs) of those TFs in all 4 cell types, and then a column designating if that interaction if activating or repressing.

Currently I can create a circle network diagram in Cytoscape, but the TFs aren't organized by cell type other than the node color, so it just looks like one big circle. It also filtered any repeat TFs to just one node, so if I have the same TF in multiple cell types I can't visualize that...

Thank you!

Answer 1

[xanderpico]

Yes. This figure was made using Cytoscape (it is mentioned in the Methods). Here is how I would do it.

Data prep: As you noted, you'll need unique node names for every TF you want represent. This means concatenating gene names with cell types in your case, e.g., Sox9_RPC and Sox9_MG. So, your data would look something like this:

Sox9_RPC | activates | Nfia_MG
Sox9_RPC | represses | Pax6_TT
Nfib_MG | activates | Lhx2_TT

In Cytoscape:

1. You can load these data into Cytoscape using File>Import>Network from file.
2. Next, you want to select the nodes for each of the cell types. Using the search bar, you can use name:*_RPC to select all the nodes with "_RPC", for example.
3. Then run the Circular Layout on selected nodes only". Move that circle off to the side while it is selected. Repeat the selection and layout of each of the cell types.
4. You can use the Style panel to map edge color to the interaction type (a discrete mapping for "activates" or "represses"). You can also use bypass node border color to set the color of nodes per cell type when selected.
5. You can use the Annotation panel to add large font labels like "RPC" and "MG" for your cell types on the network (like in the figure).

These steps should reproduce that figure.

[Shinster007]

Worked like a charm, thank you!