edges style and outline color

[Steven Blanchard]

Hello,

I create a metabolic network with networkx and then the results are exported in gml format to be visualized in CytoScape.

The arguments outline for nodes and style for edges do not seem to be taken into account by cytoscape.

Are these arguments not used by cytoscape for the gml format or should I give them otherwise?

gml documentation : https://docs.yworks.com/yfiles/doc/developers-guide/gml.html

My gml files :

graph [
  directed 1
  node [
    id 0
    label "CPD-12118"
    graphics [
      fill "blue"
      type "rectangle"
      x 2720.1
      y 18.0
    ]
    common_name "demethylmenaquinol-9"
  ]
  node [
    id 1
    label "RXN-9204_L2R"
    graphics [
      fill "purple"
      type "octagon"
      outline "black"
      x 2720.1
      y 90.0
    ]
    name "RXN-9204"
    common_name "RXN-9204_L2R"
  ]
  edge [
    source 0
    target 1
    graphics [
      fill "green"
      targetArrow "standard"
      style "dotted"
    ]
  ]
]

Thanks,

Regards,

Steven

[Alex Pico]

Hi Steven,

I pasted you gml into a file and imported it into Cytoscape and got a styled network. It appears to match the code (at first glance). Are you seeing the same thing? Is there a specific attribute that is not working?

 - Alex

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[Alex Pico]

Ah, you mentioned “outline” for nodes and “style” for edges. I had to reread that sentence a few times to understand it :)

Let me dig further...

 - Alex

On Jun 6, 2022, at 1:57 PM, Alex Pico <alex...@gladstone.ucsf.edu> wrote:

Hi Steven,

I pasted you gml into a file and imported it into Cytoscape and got a styled network. It appears to match the code (at first glance). Are you seeing the same thing? Is there a specific attribute that is not working?

 - Alex

<Screen Shot 2022-06-06 at 1.54.21 PM.png>

[Alex Pico]

Ok. In order for the node border (or outline) to show, you also have to specify a width, e.g.:

      outline "black"

      width 5.0

I tried a few things to get edge “style” to work, but nothing worked. You can control thickness with “width” and color (as you’ve done) with “fill”, but that’s it.

 - Alex

[Alex Pico]

And if you’re working with networkx in Python, then I’d recommend our https://pypi.org/project/py4cytoscape/ package, which lets you control all aspects of Cytoscape (including all style options) from your Python script.

My typical workflow is thus to convert from networkx (or graphNEL or igraph, etc) to Cytoscape with only the nodes, edges and attributes. And then I do all the layout and styling in Cytoscape. This works in Python or R (using https://bioconductor.org/packages/release/bioc/html/RCy3.html). 

 - Alex

On Jun 6, 2022, at 2:10 PM, Alex Pico <alex...@gladstone.ucsf.edu> wrote:

Ok. In order for the node border (or outline) to show, you also have to specify a width, e.g.:

      outline "black"

      width 5.0

I tried a few things to get edge “style” to work, but nothing worked. You can control thickness with “width” and color (as you’ve done) with “fill”, but that’s it.

 - Alex

<Screen Shot 2022-06-06 at 2.08.41 PM.png>

[Steven Blanchard]

Thanks you for all your reply.

I will try our advices.

Steven