Add metric flowsom mapping similarity

[LuLeom]

Describe your changes

Implemented metrics/flowsom_mapping_similarity.
It is an horizontal metric to compare flowsom trees between paired replicate samples.

As this implementation involves quite a bit of switch between python and R and I/O operations I think a careful review of this PR is needed.

NOTE: As the common helper functions implemented in src/utils/ are in python, here I am calling an additional helper script preprocess_with_utils.py from R with system(). Temporary h5ad files are stored in a folder tmp/ and loaded in R.

NOTE 2: Apparently, I cannot store FlowSOM objects in adata$uns. A summary of the results (including the FlowSOM objects) is stored in the variable fs_mapping_similarity_allres. We might want to leverage information stored in this variable for figures/tables on a later stage.

NOTE 3: The parametrization for FlowSOM is dataset specific. As for now the implementation uses a FlowSOM parametrization tailored to the spleen dataset. An issue will be open to fix this behaviour.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!

[rcannood]

LGTM!

[rcannood]

Merged it so we can already run it -- @SofieVG @ghar1821 please review this PR for feedback on the actual content