Gökçen Eraslan

> Are you able to make a loom object passing your expression matrix to `loomR::create`? Yes, `loomR::create('filename', obj@data)` works without any errors.

You can also check scanpy dotplot legend here: https://scanpy-tutorials.readthedocs.io/en/latest/plotting/core.html#dotplot and https://scanpy.readthedocs.io/en/stable/_images/scanpy.pl.dotplot.png (two different styles are shown here) and https://scanpy-tutorials.readthedocs.io/en/latest/plotting/core.html#Visualize-marker-genes-using-dotplot Few things related to "what color represents" discussion we had: 1)...

@has2k1 If it's hard to do automatically without a proper layout manager, would it be a good compromise to allow users to specify some multipliers for the panels manually e.g....

Is the layout manager in [matplotlib v2.2](https://github.com/matplotlib/matplotlib/pull/9082) sufficient for proper subplots in plotnine?

Thanks so much for your contribution @dwnorton ! Looks good. Two questions: 1) is there any way to do without densifying the matrix? it's not a big deal though since...

Hi @dwnorton, Sorry for the delay. I can see now that there are a few changes about this on the [UMAP side](https://github.com/lmcinnes/umap/blob/master/umap/spectral.py#L98): Few questions: - Can we improve the sparse...

I also like the `normalization` and `normalization_axis` suggestion, I use z-score also all the time but it's very painful right now. I also agree with Stephen's concerns, minmax is not...

Btw I think the color map contributes to minmax scaling being more misleading in the upper dotplot, i.e. white color gives the impression that the gene is not expressed. So...

@meeseeksdev backport to 1.9.x

(Orthogonal to this suggestion: We can maybe talk to the SCP people and ask how difficult would it be to use h5ad as a native format.)