HoloViews dotplot and umap elements

[droumis]

HoloViz-ifying the scanpy clustering tutorial and making:

WIP POC:

• HoloViews anndata Interface
• HoloViews DotPlot Element
• HoloViews/Panel Dim Reduction (PCA, UMAP) App

UPDATE:

• started a new hv-anndata repo

[droumis]

Violin

[droumis]

Scatter

[droumis]

Variance ratio

[droumis]

PCA

[droumis]

UMAP

[droumis]

UMAP Leiden graph-clustering

[droumis]

UMAP QC metrics

[droumis]

UMAP cell-type classification labels

[jbednar]

Nice! The results seem quite different in this case between Matplotlib and Bokeh:

[droumis]

Nice! The results seem quite different in this case between Matplotlib and Bokeh:

Yea, honestly, I don't know what's going on with the coloring. I'm not sure this particular plot is improved with rasterization.. it is suboptimal to have to play with spreading.

[jbednar]

Yea, honestly, I don't know what's going on with the coloring. I'm not sure this particular plot is improved with rasterization.. it is suboptimal to have to play with spreading.

If that coloring difference isn't deliberate, it seems like a bug that should be addressed. I'd be happy to have hvplot respect the size argument (translating it to a spread value) so that people wouldn't have to play around with spreading.

[droumis]

Highly variable genes

[droumis]

If that coloring difference isn't deliberate, it seems like a bug that should be addressed.

fixed the coloring issue.. it wasn't using the first two colors of the cmap for the two categories so I just limit the cmap to the first two colors and that resolves it.

[jbednar]

fixed the coloring issue.. it wasn't using the first two colors of the cmap for the two categories so I just limit the cmap to the first two colors and that resolves it.

That sounds like a workaround, with a bug that still needs fixing. What it sounds like is that it is treating the list of colors as a colormap (which is sampled at equal intervals due to its continuous nature) rather than as a color key or color cycle (which are taken in order due to their discrete nature). Definitely should not be confusing those usages! So unless I'm confused, you shouldn't be using cmap, you should be using a color key or color cycle.