[REF] Updates get_expression_data() #38
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Rather than needing to separately fetch human microarray expression data prior to wrangling it with `get_expression_data()` the function now automatically fetches it for you. Need to provide a mechanism for users to specify where the data are kept so it doesn't try to download it to the present working directory every time...
Much faster thanks to more effective use of scipy.ndimage functionality. 🤦 for the way it was being used initially, though I guess you have to learn somehow!
Users can now specify directory where AHBA files are to be downloaded (or are kept)
Removes `files` parameter, adds `data_dir` and `donors` kwargs
Changed `labels_of_interest` parameter in utils.get_centroids() to `labels` but didn't change any of the references to it throughout the package
Usage documentation now reflects updated API of `abagen.get_expression_data()`
Codecov Report
@@ Coverage Diff @@
## master #38 +/- ##
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- Coverage 97.09% 96.98% -0.12%
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Files 24 24
Lines 965 961 -4
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- Hits 937 932 -5
- Misses 28 29 +1
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rmarkello
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Closes #35.
Calling
abagen.get_expression_data()no longer requires users to pass afilesobject obtained fromabagen.fetch_microarray_data()-- it just calls it automatically!