Coming from Cytoscape: visual styles improvement

Discussion about future features
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Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Coming from Cytoscape: visual styles improvement

Post by Gogolo » 08 Nov 2010 16:06

Hi

Coming from Cytoscape I miss (or do not know?) some basic features concerning linking visual styles to attribute values:

- Transparency for Nodes, Edges and Arrows.
- Color for Arrows
- Arrow Size (although this is missing in Cytoscape too)
- Different Node Shapes inside one Network
- Border color of Nodes
- linebreak / wrap Texts of labels (I have some long label texts)

I think these are rather basic features and should have high priority. (I know you want to have also some coffee rests :-)

As it is now I think Gephi has a extremely high potential, especially with the integration of dynamic change of networks (which should be analyzable). But I cannot leave Cytoscape missing these visual style features.

Thanks for your great work on Gephi. I think, when it grows up it will be THE network tool of the future.
Greetings
Olivier

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mbastian
Gephi Architect
Posts: 728
Joined: 10 Dec 2009 10:11
Location: San Francisco, CA

Re: Coming from Cytoscape

Post by mbastian » 08 Nov 2010 16:44

Yes I also think these features are high priority and mostly fits to the Preview module, where users can customize the output. The Preview unfortunately frozen for now, as we wait to make a complete refactoring, as explained here. We need more manpower on that! However some of the things you want to do can be achieved by opening the SVG output in Inkscape or Illustrator, it's a useful workaround.
The Overview module is also changing with a new visualization engine, which include different shapes for network features in its specifications.
dynamic change of networks (which should be analyzable)
Work is currently done to bring dynamic metrics computing and charts in Gephi, see Dynamic Statistics. This will be available in the 0.8 version of Gephi and are very exciting features!
Thanks for your great work on Gephi. I think, when it grows up it will be THE network tool of the future.
Thanks, please consider joining the consortium to support the project.

Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Re: Coming from Cytoscape

Post by Gogolo » 08 Nov 2010 21:41

Thanks very much for your explanations. Its really exiting to see whats coming up, especially dynamic statistics and bundled edges. (I imagine how bundled edges behave in a dynamic view... :geek: )

These are cool features and I look forward to them. Also going to OpenGL and Shaders will surely offer a lot of powerful options.

I also consider joining the consortium.

Hoping that someone will apply to adding more features of Node, Edge and Arrow customization (unfortuately I cant) I look forward to more "Gephism" around.

Greetings
Olivier

Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Re: Coming from Cytoscape

Post by Gogolo » 10 Nov 2010 21:12

One thing: I think these features should not be associated to the preview module, maybe except transparency. I imagine that nodeborder size, arrow size and color etc. will not affect performance much and help reading and understanding the network when working with it in Overview.

I made a feature request here: https://blueprints.launchpad.net/gephi/ ... ent-ranks/

I'd welcome it if it was set to high priority.

I also see, that when adding nodeborder size and color to the symbols it may get a little confusing. Im posting a mockup of a symbol list containing symbols for size, color, border size, border color, Text Color and Text Size. (Sorry I cant do it better). Personally I like the scale symbol more for size as the diamond. When choosing editing edges the border symbols would disapear. What do you think?
edit: I changed the symbol for border size to a clearer one.
edit2:
Nodes have Symbols for Size, Color, Border Size, Border Color, Label Size, Label Color
Edges have Symbols for Size, Color, Label Size, Label Color
Arrows have Symbols for Size and Color

If Performance allows one more Symbol (e.g. a fading one) would be Transparency for Nodes, Edges and Arrows.
mokup-ranking.png
mokup-ranking.png (11.33 KiB) Viewed 7661 times
Last edited by Gogolo on 11 Nov 2010 09:52, edited 7 times in total.

admin
Gephi Community Manager
Posts: 964
Joined: 09 Dec 2009 14:41

Re: Coming from Cytoscape

Post by admin » 11 Nov 2010 00:01

These are good ideas, and I agree that these features should be also in Overview. I move this topic to the Specification sub-forum so as we can continue to discuss like this.

Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Re: Coming from Cytoscape: visual styles improvement

Post by Gogolo » 11 Nov 2010 21:18

I also suggest taking a look at cytoscape which offers a lot of different visual styles for each element. The question for me is then which Interface should be choosen to offer a complex but simple handling. I fear that the symbols/icons eventually will have limits when a lot more options will be added in the future (like transparency, position, line styles etc.). Then maybe a list will be more convenient. On the other hand I find the list view in cytoscape already cluttered. The list or tree view also uses a lot of space.

I will continue to think of a smart possibility and maybe can contribute a little to the gephi project like this.

Greetings
Olivier

Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Re: Coming from Cytoscape: visual styles improvement

Post by Gogolo » 11 Nov 2010 23:35

I thought about it tonight 8-)

I imagine something like this: Initially only the first row is visible : Nodes Edges Arrows (as it is now (without arrows)). When choosing Nodes a second row appears with options for Nodeelements, after choosing one a third row appears with options for styles. After choosing a style the interface with adjustments appears. Look at the quick and dirty images. I think like this Gephi will be ready to add more and more style options in the future. What do you think?

Selectionpaths for Nodes:
Selecting Nodestyles.png
Selecting Nodestyles.png (5.23 KiB) Viewed 7489 times
Selectionpaths for Edges:
Selecting Edgestyles.png
Selecting Edgestyles.png (3.43 KiB) Viewed 7489 times
Selectionpaths for Arrows:
Selecting Arrowstyles.png
Selecting Arrowstyles.png (3.34 KiB) Viewed 7489 times
Last edited by Gogolo on 19 Nov 2010 18:15, edited 3 times in total.

admin
Gephi Community Manager
Posts: 964
Joined: 09 Dec 2009 14:41

Re: Coming from Cytoscape: visual styles improvement

Post by admin » 12 Nov 2010 01:13

The mockups are interesting, however I still doubt to put all of these options in Overview, as it is designed to remain quite easy and limited. Don't forget that the performances of the current rendering engine are possible because it is not flexible. I don't know how the future engine will work.

But there are ideas for the Preview refactoring, which is designed to tweak totally the output.

Gogolo
Posts: 10
Joined: 08 Nov 2010 15:55

Re: Coming from Cytoscape: visual styles improvement

Post by Gogolo » 12 Nov 2010 08:54

Thanks for your reply. I think the advantage of having a Overview and a Preview can also be problematic. When options will be splitted - which one will be assigned where? The main question is: how can I work fast with a network, visualize and make understandable its properties. From this question maybe a logical way of assigning the options to either overview or preview will be possible. However I think these questions will be of importance sometimes.

Maybe some of these ideas could be implemented in Preview refactoring.

Greetings
Olivier

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