Awkward to pandas

[amoschoomy]

Created functions to_ak, from_ak, from_scirpy, to_scirpy

Functions are mostly adapted from scirpy.io modules

addresses #261

[zktuong]

@grst

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (83bd5fc) 82.84% compared to head (f426e6a) 83.77%.
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #342      +/-   ##
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+ Coverage   82.84%   83.77%   +0.93%     
==========================================
  Files          47       52       +5     
  Lines        8550     9062     +512     
==========================================
+ Hits         7083     7592     +509     
- Misses       1467     1470       +3     

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unittests	83.77% <ø> (+0.93%)	⬆️

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see 16 files with indirect coverage changes

[zktuong]

@amoschoomy, forgot we also need to update the notebooks. Specifically https://github.com/zktuong/dandelion/blob/master/docs/notebooks/1c_dandelion_scirpy.ipynb

[amoschoomy]

@amoschoomy, forgot we also need to update the notebooks. Specifically https://github.com/zktuong/dandelion/blob/master/docs/notebooks/1c_dandelion_scirpy.ipynb

right will do

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[amoschoomy]

@amoschoomy, forgot we also need to update the notebooks. Specifically https://github.com/zktuong/dandelion/blob/master/docs/notebooks/1c_dandelion_scirpy.ipynb

right will do

@zktuong updated notebook, have a look and removed those references to scirpy functions, let me know if anything needs to be changed/improved

[zktuong]

PR is ready to merge pending final tests. Now the default behaviour is to convert to/from dandelion in mudata (with the option to return as anndata), using scirpy's read_airr functions internally.

@grst, should the default obsm key for gene expression be gex or rna? seems like muon is using rna while scirpy is using gex.

[grst]

LGTM

[grst]

@grst, should the default obsm key for gene expression be gex or rna? seems like muon is using rna while scirpy is using gex.

Please go with gex to be consistent with scirpy. I wasn't aware of the muon convention at the time I implemented this.