perf: avoid dense BasePlot aggregation

[srikarjy]

Summary

• preserve sparse and backed plotting inputs instead of eagerly building a dense cell-level dataframe in BasePlot

• aggregate dotplot sizes/colors and matrixplot values with Scanpy aggregation kernels

• keep obs_tidy lazy for plot types that still require cell-level values

• preserve mean_only_expressed semantics for nonzero expression cutoffs

• Closes Refactor BasePlot not to create a dataframe representation of the data #3718

• Tests included

• Release notes not necessary because: a performance release note is included

Testing

• uv run ruff check on changed Python files
• uv run ruff format --check on changed Python files
• .venv/bin/python -m pytest tests/plotting/legacy/test_plotting.py -k "dotplot or matrixplot or stacked_violin" --disable-pytest-warnings -q (50 passed, 5 skipped, 2 xfailed)
• complete legacy plotting module: 129 passed, 18 skipped, 6 xfailed; three unrelated violin image comparisons exceeded the local pixel tolerance

[codecov]

Codecov Report

❌ Patch coverage is 94.78261% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.88%. Comparing base (7ad567d) to head (12dd884).

Files with missing lines	Patch %	Lines
src/scanpy/plotting/legacy/_baseplot_class.py	94.00%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4399      +/-   ##
==========================================
+ Coverage   83.78%   83.88%   +0.10%     
==========================================
  Files         134      134              
  Lines       12691    12796     +105     
==========================================
+ Hits        10633    10734     +101     
- Misses       2058     2062       +4     

Flag	Coverage Δ
hatch-test.low-vers	80.62% <94.78%> (+0.12%)	⬆️
hatch-test.pre	83.69% <94.78%> (+0.10%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/scanpy/plotting/legacy/_dotplot.py	92.39% <100.00%> (+0.50%)	⬆️
src/scanpy/plotting/legacy/_matrixplot.py	96.59% <100.00%> (ø)
src/scanpy/plotting/legacy/_baseplot_class.py	83.82% <94.00%> (+3.46%)	⬆️

... and 1 file with indirect coverage changes