Feature/transparency

[songgo1]

Description

Added a transparent_below parameter to embed_bivariate_genes and embed_geneset functions that allows users to hide cells below a specified percentile threshold based on expression values.

Motivation

The Contours function allows users to define anatomical landmarks, but embed_bivariate_genes and embed_geneset cannot overlay onto these plots because low-expressing cells obscure the background. The transparent_below parameter hides cells below a specified percentile, enabling contour overlays and clearer visualization of spatial expression patterns.

Changes

• Added transparent_below parameter to embed_bivariate_genes()
• Added transparent_below parameter to embed_geneset()
• Updated docstrings with parameter documentation
• Updated quickstart notebook with examples of transparency thresholds.

Usage

Example

# Hide the lowest 25% of cells by combined expression
uf.pl.embed_bivariate_genes(adata, genes1=['GeneA'], genes2=['GeneB'], transparent_below=25)

Notes

• Backward compatible: defaults to None (existing behavior unchanged)
• Also, get_version(package_name) is causing installation errors for me. Commenting out version=get_version('stuf') resolves installation issues.