[WIP] External plotting tools

[ivirshup]

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
• Possibly add section on lasso selection of cells (need to check how many points that can scale to)

[falexwolf]

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... ;)

[ivirshup]

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:

---

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.

[flying-sheep]

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…)

[ivirshup]

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.

[flying-sheep]

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

[giovp]

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

[flying-sheep]

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

[ivirshup]

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

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB