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[WIP] External plotting tools

Open ivirshup opened this issue 6 years ago • 9 comments

Here's my first draft of using some external plotting tools, including interactive ones.

@falexwolf is this what you were thinking of (mentioned in #460)? Or did you want specifically just interactive plots?

Before this gets merged, I want to:

  • [ ] Go over writing
  • [ ] Add something with faceting
  • [x] Possibly add section on lasso selection of cells (need to check how many points that can scale to)

ivirshup avatar Mar 24 '19 05:03 ivirshup

Looks good! Thanks for starting to work on this and excited to see it evolve.

Very modest request: could you rename to external-plotting-tools.ipnyb. It gives a nicer URL, where underscores look ugly... ;)

falexwolf avatar Mar 24 '19 21:03 falexwolf

How should I include static images in these notebooks? I've got some gifs (500 and 200 kb) I'd like to include to show interactivity:

selection

selection_usage

Right now I've got them placed in a directory called img, but maybe that should go under static? Might also be nice to leave them out of the git history due to size.

ivirshup avatar May 08 '19 05:05 ivirshup

I’m personally a fan of altair

It’s based on the vegalite JSON format that is rendered natively by jupyterlab. Therefore it’s much more efficient than any HTML-based solution.

You have a comparison between holoviews and altair here.

(sadly it doesn’t render on GitHub, but neither does holoviews…)

flying-sheep avatar May 08 '19 08:05 flying-sheep

I like altair a bunch too, finally a python plotting package with a consistent and nice api! One major downside is that it doesn't do many points well, so I can't use it for everything. I also don't think it can talk back to the python process, which is what I want to show with this particular example.

I don't really use holoviews to much, I haven't been able to totally wrap my head around their API/ data model. hvplot on the other hand gives me very easy access to datashader and hover over.

ivirshup avatar May 08 '19 08:05 ivirshup

Sorry, I thought it could do that! But it’s not there yet: altair-viz/altair#1153

flying-sheep avatar May 08 '19 09:05 flying-sheep

Just saw this, really cool! Especially for spatial plots this is very useful. Seurat already supports a basic functionality like the one you show https://satijalab.org/seurat/v3.1/spatial_vignette.html

giovp avatar Feb 03 '20 16:02 giovp

Yeah, this got lost somehow! What’s missing from merging this?

flying-sheep avatar Feb 03 '20 18:02 flying-sheep

Haha, I had totally forgotten about this. I think it was just the static images thing?

ivirshup avatar Feb 06 '20 04:02 ivirshup

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