These are chat archives for nextflow-io/nextflow

8th
May 2016
mariach
@mariach
May 08 2016 09:27
Paolo, how about instead of only outputting the DAG representation, outputting a json file that can be loaded to any visualization library ???
Paolo Di Tommaso
@pditommaso
May 08 2016 09:28
it already produces the graph by using graphiz DOT format
mariach
@mariach
May 08 2016 09:34
and I guess one can use this rhalff/dot-object to then convert them in json! If any one has better suggestions on how to convert DOT notation to JSON please share :)
Paolo Di Tommaso
@pditommaso
May 08 2016 09:45
json would have sense implementing a JavaScript/Html render based on the D3 library
mariach
@mariach
May 08 2016 09:45
yup that's the goal!
Paolo Di Tommaso
@pditommaso
May 08 2016 09:46
that would allow the graph to be interactive, for example to expand/collapse nodes
I will accept pull request for that :smile:
mariach
@mariach
May 08 2016 09:46
which would make so mush sense with huge NF pipelines like the companion one
*Sanger Companion
Paolo Di Tommaso
@pditommaso
May 08 2016 09:47
I agree
Michael L Heuer
@heuermh
May 08 2016 18:56
You may want to consider Cytoscape or cytoscape.js. They can render from many different input formats and have built-in visual mapping and graph layout features.
Paolo Di Tommaso
@pditommaso
May 08 2016 18:57
Cool
mariach
@mariach
May 08 2016 18:58
are there cytoscape DAGs that collapse?
Paolo Di Tommaso
@pditommaso
May 08 2016 18:59
It looks a very advanced framework
Michael L Heuer
@heuermh
May 08 2016 18:59
by collapse, do you mean nested graphs?
mariach
@mariach
May 08 2016 18:59
i mean sth like this:
tap on the nodes :P
Michael L Heuer
@heuermh
May 08 2016 19:01
ah ok, so selectively show/hide parts of the same graph, yes
mariach
@mariach
May 08 2016 19:01
can you send as an example, if you know?
Paolo Di Tommaso
@pditommaso
May 08 2016 19:01
If I'm not wrong @mes5k worked in this project.
Michael L Heuer
@heuermh
May 08 2016 19:02
I'm more familiar with Cytoscape the thick java app than cytoscape.js but I assume similar functionality exists
Paolo Di Tommaso
@pditommaso
May 08 2016 19:02
So I guess he would be very happy to help with this :)
Michael L Heuer
@heuermh
May 08 2016 19:02
if it is the same Mike Smoot, then yes, we submitted a poster to NetBio SIG together :)
Paolo Di Tommaso
@pditommaso
May 08 2016 19:03
Great, actually all this madness started from a suggestion from him a few days ago
Now I understand why he was so interested in this feature :)
Michael L Heuer
@heuermh
May 08 2016 19:09
@mariach with cytoscape.js, you listen for node selection events, toggle the visibility of its outgoing edges, and then force an update of the layout. I don't see an demo that does this though, unfortunately
Mike Smoot
@mes5k
May 08 2016 20:29
It's the same Mike. I'm happy to volunteer to get this into JSON and output for the web. I'll try Cytoscape.js (which, ironically, I have no experience with) and Dagre/D3. Depending on when in the execution of the pipeline the DAG is created it might be possible to dynamically update the DAG with process state, etc..
Michael L Heuer
@heuermh
May 08 2016 20:31
Sweet! Nice seeing you again, Mike!
Paolo Di Tommaso
@pditommaso
May 08 2016 20:32
It sounds great
Tomorrow I will polish the implementation a bit, merge in the master and prepare a snapshot
so you will be able to play with it if you want
The dynamic update it's a bit tricky
Now it is produced and the completion of the execution
Mike Smoot
@mes5k
May 08 2016 21:17
Likewise Michael! Paolo, makes sense that it's created at completion. I'll pull your branch tomorrow and see what I can do.