start with this project, ideas

[eparejatobes]

@bio4j/bio-people @pablopareja is starting to work on this, and it'd be good to have some ideas as a starting point. I think that we should start with something based on one of the basic existing D3 layouts; the par-coords plugin is also stable and easy to use.

[pablopareja]

Hello hello! So could you please tell which one of the ideas you mentioned in the last e-mail should I start with? @eparejatobes (is it possible that neither @epareja nor @rtobes can access this repository right now?) :question:

[laughedelic]

Sorry to disturb, but I just wanted to tell that there is no such team: @bio4j/bio-people.

[eparejatobes]

there is!

[eparejatobes]

@pablopareja maybe they're not watching, so I don't know what happens when you mention them through a team that does not have this repo added. I added them anyway. Let's try again @bio4j/bio-people hola hola

[laughedelic]

Ah, ok. I guess I just came from the wrong level of conspiracy.

[marina-manrique]

@rtobes said something like this. For a given set of GO terms and Taxonomy nodes show the proteins linked to their GO term and their Taxon node. I don't know if I'm clear

For this I suggest something simple to start with, something based on this https://github.com/mbostock/d3/wiki/Force-Layout

where the protein nodes have a color, the taxon nodes another color and the go terms another one.

@rtobes WDYT? I think it's a good example to start with

[eparejatobes]

but @laughedelic you can see it now? I mean, it works or something"

[laughedelic]

No, I get 404 when I click on it. And it doesn't get highlighted when I use it. But I guess, it works when you use it.

[pablopareja]

@marina-manrique OK, and any extra details about whether you want to include some kind of simple form holding the data of clicked items or something like that?

[marina-manrique]

Maybe for this time you could display when roll-over the Taxon Name, GO Term name or protein name (depending on the kind of node)

and it'd also be good to highlight the nodes connected directly with a given node and set the others in light grey,

[pablopareja]

The latter also on roll-over?

[marina-manrique]

:+1:

[rtobes]

I am here now. on roll over highlighting the connected nodes and on click I would like to have the names of all the nodes connected to the clicked node.

[eparejatobes]

http://cs.brown.edu/people/jcmace/d3/graph.html?id=small.json

[eparejatobes]

http://cpettitt.github.io/project/dagre-d3/latest/demo/etl-status.html

[pablopareja]

The first one is molto brutto :stuck_out_tongue:

[eparejatobes]

is ugly sure but that's easy to fix. The thing is that you can do a lot in it!

[eparejatobes]

try to zoom-in and right-click on a vertex

[pablopareja]

cool ! It even has options to manipulate it, that's nice :space_invader: So let me know what you want exactly so that I can get to work! :smiley:

[pablopareja]

One question about the dataviz idea that Marina previously described, should all the proteins be linked to both at least one of the GO terms and at least one of the taxonomic units? @marina-manrique @rtobes

[marina-manrique]

I think so

[pablopareja]

OK, and would you also like to have the possibility of getting only the proteins linked to all GO terms specified?

[marina-manrique]

mmm don't know... let's see what @rtobes says

[pablopareja]

Ahh one more thing, could you please detail me the data (I mean the properties) you want to see from the three different entities that would be shown? that's to say:

• GO terms
• Proteins
• NCBI taxonomic units

Since we won't be performing any request to the server at this point of development all the data that would be shown through interaction should already be included in the JSON file generated for the whole visualization.

[eparejatobes]

It'd make me really happy if you could move all this to a different issue, and open a pull request for it.

[eparejatobes]

:smile:

[marina-manrique]

done, we keep on working here #3