[ENH,REF] Adds new region_agg parameter
#131
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Now users can specify whether to aggregate samples belonging to the same region in `atlas` across donors or samples.
donor_norm --> gene_norm, and batch no longer accepted in normalize_expression
Codecov Report
@@ Coverage Diff @@
## master #131 +/- ##
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- Coverage 90.14% 89.95% -0.19%
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Files 32 32
Lines 1959 1962 +3
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- Hits 1766 1765 -1
- Misses 193 197 +4
Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## master #131 +/- ##
==========================================
+ Coverage 90.14% 90.23% +0.08%
==========================================
Files 32 32
Lines 1959 1996 +37
==========================================
+ Hits 1766 1801 +35
- Misses 193 195 +2
Continue to review full report at Codecov.
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Handling of annotation files wasn't being done correctly after I removed `samples.update_samples` and merged the functionality into `allen.get_expression_data()`
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Related to #125 (insomuch as it temporarily removes
batchnormalization as an option)This adds the
region_aggparameter (and renamesmetrictoagg_metric) in theabagen.get_expression_data()function. This parameter controls how samples belonging to the same region are combined (i.e., [1] aggregated separately for each donor and then combined across donors or [2] aggregated across all donors simultaneously).Also some minor updates to various typos and doc-strings throughout the package.
To Do:
sample_normvsdonor_normdifferencesregion_aggandagg_metricoptionsabagen.get_expression_data()andabagenCLI is up-to-dateabagen.samplesabagen.get_expression_dataandabagenCLI