Add DotPlot Element

[droumis]

What I'm referring to as a DotPlot here is like a heatmap with an added dimension encoded by indicator (dot) sizing.

DotPlots are used commonly in genomics visualization, showing both expression magnitude for various genes and percentage of expressing cells, samples, or clusters. While it's mostly possible to create these using scatter/points plots in HoloViews, having a dedicated DotPlot element would make it a lot easier to create these and provide useful defaults.

Is your feature request related to a problem? Please describe.

The key problems this would solve is the manual data preparation to get things in a reasonable state of performance and applying many settings to recreate DotPlot convention default styling/behavior

Describe the solution you'd like

Add a dedicated DotPlot element to HoloViews with the following:

• Support for sparse matrix inputs from AnnData objects
• Dot size scaling that:
  • Maintains data space proportional size during zooming
  • Normalize max dot size to avoid dot-neighbor overlap. Dots should stay within their heatmap-square.
  • Supports different scaling methods (linear, log, sqrt)
• Color scaling based on normalized mean expression
• (maybe) Expression percentages above cutoff
• (maybe) Default reds colormap for expression levels
• Dot Size legend showing e.g. percentage of expressing cells
  • Needs Allow size to vary in legend glyphs bokeh/bokeh#2603
• Color bar showing mean expression levels
• Default inverted y-axis for consistency with existing convention

Describe alternatives you've considered

1. Using existing Scatter or Points element to approximate a DotPlot, but with a lot of manual data preparation and .opts
2. Creating this as a separate package. I received feedback from @philippjfr that this would likely make sense in HoloViews core, but I'm open to it loving elsewhere if it's getting too domain specific.

Additional context

• Popular Python implementation in ScanPy using MPL. We should try to approximate a drop in optional replacement as much as possible for ScanPy users.
• Popular R Implementation in Seurat

I have a working implementation in a separate repository that demonstrates partial functionality:

• https://github.com/holoviz-topics/cancer/blob/main/hv_cancer_modules/hvdotplot.py
• This repo includes a demo notebook, which uses a WIP HoloViews Data Interface for AnnData objects. I'm in the process to moving the data interface to its own repo here.
  

[droumis]

update: Simon is working on this and will likely first go into holoviz-topics/hv-anndata instead of HoloViews to constrain the input data scope to anndata

[jbednar]

Sounds good! I do think it should be in HoloViews eventually.