Fix more pandas warnings

[flying-sheep]

• Closes Scanpy uses deprecated Pandas APIs #2788
• Tests included

• Release notes not necessary because:

[codecov]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (8663d33) 72.84% compared to head (6968c26) 72.84%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2789   +/-   ##
=======================================
  Coverage   72.84%   72.84%           
=======================================
  Files         111      111           
  Lines       12382    12382           
=======================================
  Hits         9020     9020           
  Misses       3362     3362           

Files	Coverage Δ
scanpy/external/pl.py	50.36% <100.00%> (ø)
scanpy/external/pp/_scanorama_integrate.py	88.88% <100.00%> (ø)
scanpy/get/get.py	92.59% <ø> (ø)
scanpy/plotting/_anndata.py	84.97% <100.00%> (ø)
scanpy/plotting/_dotplot.py	91.25% <100.00%> (ø)
scanpy/plotting/_matrixplot.py	96.70% <100.00%> (ø)
scanpy/plotting/_stacked_violin.py	83.67% <100.00%> (ø)
scanpy/plotting/_tools/scatterplots.py	86.16% <100.00%> (-0.04%)	⬇️
scanpy/plotting/_utils.py	56.33% <ø> (ø)
scanpy/preprocessing/_combat.py	90.83% <100.00%> (ø)
... and 4 more