Color histogram with floats

[zoccoler]

This adds the possibility to assign an array with floats (like representing some feature) as an overlay to the histogram and to the scatter plot.

• update documentation
• check if more tests are needed
• fix log scale problem for histogram

[codecov]

Codecov Report

Attention: Patch coverage is 94.32177% with 18 lines in your changes missing coverage. Please review.

Project coverage is 92.19%. Comparing base (d1ebeb4) to head (0153257).
Report is 5 commits behind head on main.

Files	Patch %	Lines
src/biaplotter/artists.py	93.83%	14 Missing ⚠️
src/biaplotter/colormap.py	78.94%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #18      +/-   ##
==========================================
+ Coverage   90.66%   92.19%   +1.53%     
==========================================
  Files           7        8       +1     
  Lines         621      897     +276     
==========================================
+ Hits          563      827     +264     
- Misses         58       70      +12     

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[zoccoler]

Hi @jo-mueller ,

I am adding here the possibility to display the scatter colors or an histogram overlay based o another features column (not just a categorical array with integers, but rather any float array with a continuous colormap - I renamed categorical_colormap to overlay_colormap).

You can get a feeling of the changes by running the Artists notebook again, which I updated.

Of course a histogram overlay completely hides the original histogram, but it may be useful if the user hide and show it quickly or change its opacity for example.

When you get some time, could you please give it a try to check if we can merge this?

[jo-mueller]

Hi @zoccoler ,

sorry for the late reply. I am a bit undecided on this implementation: On the one hand I like the simplicity of this: Simply change the colormap to something continuous, pass a float to the color indices and have your plot colored. On the other hand, it loads the same property (color) with potentially multiple meanings.

In the context of the clusters plotter, it would be hard to use colored scatter points in conjunction with the clustering. As an alternative suggestion: Would you think that it could make sense to forward the coloring done with color_indeces to the marker edge color? The coloring of the points according to a given feature could then still be done with the facecolor and the two colorings wouldn't superseed each other.

Let me know what you think!

[zoccoler]

Hi @jo-mueller ,

I think we both agree that displaying a feature with different colors is a good enhancement (it also fits the goal of this PR).

Using the edge colors for categories can indeed be a solution, we just have to test if it doesn't look confusing. This wouldn't work for the histogram though.
I was hoping to have some hide/show overlay option, similarly to one showing a labels layer on top of an image layer in napari. That would work for both the histogram and the scatter artists.

I will try to generate some examples for these ideas here, then we can decide.