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romanhaa / Cerebro

Visualization of scRNA-seq data.
MIT License
93 stars 19 forks source link

White screen not going away #14

Open astrovsky01 opened 5 years ago

astrovsky01 commented 5 years ago

Even when reloading, the white screen is remaining, and i can't access the app past it. My hardware isn't particularly slow, so I don't know why.

romanhaa commented 5 years ago

Hi Alex. Sorry for the late reply. Remotely it's a bit hard to say what's going wrong on your end but this might be valuable feedback since I can't test Cerebro on all possible hardware setups.

Are you using macOS or Windows? If you are on macOS, there should be a log file in ~/Library/Logs/Cerebro/. On Windows it should be in C:\Users\<user>\AppData\Roaming\Cerebro.

Best, Roman

astrovsky01 commented 5 years ago

No problem Roman. I'm working on integrating Cerebro as an interactive environment into Galaxy (https://usegalaxy.org/), so let me know whatever feedback you need.

I'm running on macOS Mojave 10.14.5, but while I was exploring code, I found that it runs on port 8080, which I was using for Galaxy at the same time. Loading it after exiting Galaxy, everything runs fine.

While I have your attention, I wanted to let you know that I'm making a conda package for your CerebroPrepare tool.

Thanks, Alex

romanhaa commented 5 years ago

Good to hear you were able to solve it! And also interesting plan to integrate Cerebro into Galaxy. I'm curious to see how the performance will be but this could be very useful for a lot of people! 👌

Let me know if you need any help somewhere/somehow.

Best, Roman

astrovsky01 commented 5 years ago

Where is biocmanager pulling the prepare tool from? Most of the tools which use it are through bioconductor, but cerebro doesn't have a page for it.

romanhaa commented 5 years ago

cerebroPrepare is installed from its respective GitHub repo: romanhaa/cerebroPrepare. The BiocManager::install() function automatically installs from GitHub if the package name contains a /. Is that what you mean?

astrovsky01 commented 5 years ago

Roman, that was what I meant, yes. Thanks!

astrovsky01 commented 5 years ago

The initial screen for the app requests specifically an rds file, but doesn't mention a crb file, by the way.

romanhaa commented 5 years ago

Good catch :) I already included it in the new changes that will come. Not sure when I have the time to finalize it, but it seems to be working well. Brief overview:

astrovsky01 commented 5 years ago

Oh cool! I'm just finishing writing a workflow for cerebroPrepare from tsv to crb for a plug-and-play in galaxy, so once the new version is out, I'll add in the new functionality.

astrovsky01 commented 5 years ago

Do you want to be a maintainer on the conda package? It's ready to upload to bioconda. Also, in the main Cerebro app, is there a way to make the 3d axis labels stay parallel to the axes they label? Currently, when rotating, they can overlap and obstruct the numbers and data.

romanhaa commented 5 years ago

Could you take a screenshot of that? I don't quite understand what you mean. I'm guessing that the same issues happens in the example page of plotly (which is the framework I use in Cerebro)? You can find the example here: https://plot.ly/r/3d-scatter-plots/

astrovsky01 commented 5 years ago

labels_cover_scale labels_cover_scale2

From what I can tell from plotly, it's because the axis labels perpendicular to the axes themselves

romanhaa commented 5 years ago

Oh, I see. That's indeed not ideal. I'll have a look at it.

romanhaa commented 5 years ago

I think this might be something changed in a recent plotly update since I haven't made any changes to the code and now it looks like this: newplot