pstjohn / d3flux Goto Github PK

Hey again,
I must say, d3flux works like a charm. But when the number of nodes is large, the representation that it returns is very "tangled" and messy, the user needs to manually arrange the nodes so that the network makes sense. So, is there any way we can solve this problem?

I should add the code for one of the more complicated maps to show off some of the less documented features. Background guides, cofactors, label alignment, etc.

like glc <-- , bounds (-1000, 0). Currently arrowheads run in wrong direction, will need a new flag in map_info.

Hi, I want to plot a pathway on the Python Dash, but I'm not proficient in HTML or js. Can you give me some suggestions?

I was trying to add the fluxes to the reactions by adding the "solution" dictionary to the "flux_dict" parameter. I did get the weighted links, but lost all the reversible links (with arrows on both sides). The cobrapy model and the .json file for the representation still have the "reversibility" property as "true", though. So, is there any workaround?

I have repeatedly failed to run the "test_flux_map.py" both in the Python Shell and in the Anacoda/Jupiter. I run the script exactly as it is but I do not get anything. And when I am trying to call the "test_flux_map" function I get errors. Am I missing something? I have downloaded all the necessary packeges.

Hi Peter,

We love using d3flux, but it only works in jupyter notebook, not jupyter lab. Is there any debug info I can provide to help you figure out what the issue is?

Sincerely,

Jeremy

Hi, first off wanted to say how cool this tool is. I can visualise sub-sections of models no problem, but when I try to visualise an entire model (say 1,700 reactions), I have 3 issues that don't allow proper vis:

1. The spread does not take up the full canvas size. So if I do 1000 x 1000, only the center of the image will be filled out, leaving the sides bare. Is there a way to modify layout behaviour?
2. This also generates massive lag within Jupyter notebook, which means I can't really properly visualise it, or move nodes etc. This also impacts my ability to:
3. SVG or JSON save. Is there a way to programmatically save, without clicking the widget? My current thought process is to direct output as object then save object as svg/json?

Thanks

Hey,
Is it possible to show the names/ids of the reactions??

After this command present in example:
flux_map(model, display_name_format=lambda x: str(x.id), figsize=(300,250))

an ipython html object is created. How to visualise it? I am using ubuntu-14 and executing program through terminal.

Having multiple models plotted in the same notebook can give weird errors

Hi Peter,

I love using d3flux, but I encountered an issue compared to 0.2.6. In the past, I sometimes had reactions overlap and co-factors on top of each other. In 0.2.7 it seems that every time I save a model as json, the overlapping reaction is moved to a free space.
Is there an option to disable this behavior? I am trying to show that the (cofactor) product of one reaction is the cofactor input of another reaction.
I appended a section of a map made with 0.2.6. Unfortunately, I can't replicate it due to the issue with jupyter notebook and 0.2.6.

Sincerely,

Tim

Hi Peter,

I am a big fan of d3flux and am currently writing part of my thesis with it.
I encountered an issue today. All the flux_map commands don't show any network anymore.

Everything worked fine last week but now I am not able to see anything. I tried different browser, reinstalled and don't know what to do. I don't get any error messages. Everything executes fine.

Thanks,
Tim