mu.pl.embedding layers substitues the content of `mudata.X`

[dawe]

Describe the bug
After struggling a lot because of reproducibility issue, I've noticed that specifying a layer when plotting with mu.pl.embedding , the MuData object is changed. In particular, the values in mdata['mod'].X of displayed features are substituted with the corresponding content of `mdata['mod'].layers['displayed_layer']

To Reproduce

Bug Report.html

I've attached a notebook containing the bug. In any case, it is sufficient to plot specifying a layer

System

• OS: Linux 5.14.0-503.14.1.el9_5.x86_64
• Python version: 3.12.9
• Versions of libraries involved: muon 0.1.7, mdata 0.3.1

[ilia-kats]

I believe this should be fixex in #167, can you try that branch?