Merged dim spatial

[ying39purdue]

This PR includes the combined dimensionality and spatial plots into one function which calls Visualize_2D_scatter. Additionally, it includes Liza's code for pin colors. Additionally, there is testing of the new function in test_embedded_scatter, and a single unit test added to visualize_2D_scatter for the pinned colors.

[Copilot]

Pull Request Overview

This PR enhances the existing 2D scatter function with a user-defined color_map, and introduces a new embedded_scatter_plot to unify PCA/t-SNE/UMAP/spatial visualizations with annotation/feature coloring. It also adds a unit test verifying the custom color mapping in visualize_2D_scatter.

• Added color_map parameter to visualize_2D_scatter and applied it in categorical plotting
• Implemented embedded_scatter_plot for multiple embedding methods with extensive validation
• Added test_color_map to ensure custom color mappings are correctly applied in 2D scatter

Reviewed Changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 3 comments.

File	Description
src/spac/visualization.py	Added color_map, updated cluster color logic, and introduced embedded_scatter_plot
tests/test_visualization/test_visualize_2D_scatter.py	Added test_color_map to verify custom color mappings in the scatter

Details

src/spac/visualization.py:220

[nitpick] The color_map parameter here expects a key name, while in visualize_2D_scatter it expects a dict of label→color mappings; consider renaming one (e.g., to color_map_key) to avoid confusion.
color_map=None,

Elaboration:
The color_map parameter in function embedded_scatter_plot is documented and used as a string (a key to look up colors in adata.uns). (note: get_defined_color_map returns a dictionary mapping). However, the function it calls, visualize_2D_scatter, expects color_map to be a dictionary that maps labels directly to color values.

Why it's a Problem: This creates a confusing and inconsistent API for your library. A user will not intuitively know that the same parameter name means two different things in two different functions. The current code handles this internally by creating a new variable (color_mapping), but the public-facing function signature remains confusing.

How to Fix: Rename the parameter in embedded_scatter_plot function to be more descriptive and avoid the name collision. A better name would be color_map_key or defined_color_map.