Node and edges shapes

[Emanuel]

Hi all,

I’m developing a plugin to extend Cytoscape’s support to SBGN diagrams (CySBGN plug-in).

I’m having problems covering all the nodes and edges shapes of SBGN using the ones available in Cytoscape. In fact, this limits a lot the correct visualisation of the diagrams.

I would like to know if you are considering developing a way to add custom nodes shapes and custom edges target/source shapes? 

This would improve a lot the integration of SBGN as well as other graphical notations into Cytoscape.

For the nodes I'm using the Custom Node Shape feature, though there are some limitations that make it a rather limited solution for this propose (e.g. node image quality, node shape doesn't fit the node image). 

Thank you very much in advance.

Best,

[Scooter Morris]

Hi Emanuel,
��� I'm in the process of implementing custom graphics for Cytoscape 3, so your query is timely.� We're patterning our implementation after the Cytoscape 2 one, so I'm interested in the limitations you see.� I've used the custom graphics API in Cytoscape 2 to very good effect.

-- scooter

On 09/03/2012 05:49 AM, Emanuel wrote:

Hi all,

I�m developing a plugin to extend Cytoscape�s support to SBGN diagrams (CySBGN plug-in).

I�m having problems covering all the nodes and edges shapes of SBGN�using�the ones available in Cytoscape. In fact, this limits a lot the correct�visualisation�of the diagrams.

I would like to know if you are considering developing a way to add custom nodes shapes and custom edges target/source shapes?�

This would improve a lot the integration of SBGN as well as other graphical notations into Cytoscape.

For the nodes I'm using the Custom Node Shape feature, though there are some limitations that make it a rather limited solution for this propose (e.g. node image quality, node shape doesn't fit the node image).�

Thank you very much in advance.

Best,

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[Emanuel]

Hi Scooter,

That's great then.

When you paste an image on a node the shape of the node may not fit exactly the image shape. You can check here an example http://www.ebi.ac.uk/saezrodriguez/cno/cysbgn/images/limitationshape.png 

There's also the loss of quality when you zoom in. The network rendering speed is also affected when there's a high number of custom shape nodes.

Another problem is the limited amount of edges target/source arrows shapes. It would be really useful for me to have a way to add different edges's shapes.

I would also like to know if you are considering to add a way to detect the order of the nodes, i.e. a way to find which nodes are in the front and which ones are in the back when they overlap.

Thank you very much for your reply.

Best,

--

Emanuel Gonçalves

[Scooter Morris]

On 09/04/2012 05:20 AM, Emanuel wrote:
> Hi Scooter,
>
> That's great then.
>
> When you paste an image on a node the shape of the node may not fit
> exactly the image shape. You can check here an example
> http://www.ebi.ac.uk/saezrodriguez/cno/cysbgn/images/limitationshape.png

That's correct, which is why I don't use an image, I use a java Shape.
If you want to play with this a little, install the nodeCharts plugin
and read the documentation on how to use it at:
http://www.rbvi.ucsf.edu/cytoscape/utilities/index.html#nodeCharts.
There is no UI so you'll also want to install the commandTool. What you
should be able to see is that the pie charts are shapes and you can
scale them without any loss of quality.

>
> There's also the loss of quality when you zoom in. The network
> rendering speed is also affected when there's a high number of custom
> shape nodes.
>
> Another problem is the limited amount of edges target/source arrows
> shapes. It would be really useful for me to have a way to add
> different edges's shapes.
>

We have no capability for custom edge graphics at this point and
probably won't be adding them for the 3.0 release. I agree that more
options for number of arrow shapes would be a very good thing. That we
might be able to do...

> I would also like to know if you are considering to add a way to
> detect the order of the nodes, i.e. a way to find which nodes are in
> the front and which ones are in the back when they overlap.

That's a major problem with our underlying renderer. One of the
features in 3.0, and a major motivation behind the design is the ability
to "swap out" the renderer. After the release is out, we'll be working
hard on alternative renderers that provide the same performance with the
added ability to support z-ordering.

>
> Thank you very much for your reply.
>
> Best,
> --

> Emanuel Gon�alves
My pleasure. By the way, the source for nodeCharts is at
http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/nodeCharts/ if
you want to see how it's done....

-- scooter

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[Emanuel]

Hi Scooter,

Many thanks for your reply. 

That will be certainly useful for me. I'll see how can I integrate it with my plug-in.

As for the edges shapes if you could add the following shapes it would already be great. There's a list of the shapes required to represent the SBGN notation: http://www.ebi.ac.uk/saezrodriguez/cno/cysbgn/images/edgesShapes.png 

Many thanks for all the help.

Best,

[Scooter Morris]

Hi Emanuel,
Do you have a set of node shapes also?

-- scooter

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[Emanuel]

Hi Scooter,

If you could add this list: http://www.ebi.ac.uk/saezrodriguez/cno/cysbgn/images/nodesShapes.png

It would be already a great improvement.

Cheers,

[Emanuel]

Hi all,

I would like to use this topic to announce the new version of CySBGN plug-in, v1.2.

I would also like to stress the importance of extending the available node and edge shapes in Cytoscape. This would allow not only to enable full support to SBGN diagrams visualisation but also to extend Cytoscape features to edit SBGN diagrams. 

This would be a great step towards making Cytoscape one of the SBGN compliant tools.

You’re doing a great work with Cytoscape 3.

Best,