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1091 independent coloring of static umaptsnepca plots in view curator - #1346

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adkinsrs merged 3 commits into
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1091-independent-coloring-of-static-umaptsnepca-plots-in-view-curator
Oct 8, 2026
Merged

adkinsrs merged 3 commits into
develfrom
1091-independent-coloring-of-static-umaptsnepca-plots-in-view-curator

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@adkinsrs adkinsrs commented Oct 8, 2026

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This pull request improves the handling and user experience of t-SNE plots when colorizing by continuous (numeric) annotation fields, ensuring these panels use a distinct colormap and are visually and functionally separated from gene expression panels. It also clarifies the UI and code logic around which plot options are available for categorical vs. continuous colorizations.

t-SNE Plot Rendering and Colormap Handling:

  • Continuous colorize_by panels now use a dedicated, colorblind-friendly colormap (viridis or plasma) that is always visually distinct from the gene expression palette, addressing confusion when both were previously similar. This colormap is applied only to the annotation panel, and expression panels retain their own settings. [1] [2] [3] [4]
  • The value range (vmin, vmax, vcenter) for continuous annotation panels is now independent from gene expression panels, preventing unintended scaling or color mapping. [1] [2]

User Interface Improvements:

  • The t-SNE plot configuration UI now explicitly informs users that numeric fields use their own colorscale, and that expression color settings do not apply to them.
  • The "Bring highest and lowest values to front of plot" option is now grouped with other expression-specific settings, clarifying its scope. [1] [2]
  • UI controls for plot grouping, legend orientation, and hiding group nonmembers are now correctly enabled or disabled based on whether the selected colorization is categorical or continuous, improving usability and preventing invalid configurations. [1] [2]

Testing and Documentation:

  • New tests were added to verify the correct assignment of colormaps and value ranges for continuous annotation panels, and to ensure group subplots and legends behave as intended.

Code Maintenance:

  • Minor code cleanups and clarifications, including improved docstrings, argument descriptions, and imports. [1] [2] [3]

These changes collectively make t-SNE plots more interpretable and the UI more intuitive, especially when working with continuous annotation data.

@adkinsrs
adkinsrs merged commit aa261b4 into devel Oct 8, 2026
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Separate expression and continuous annotation colorings in scanpy plots

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