V2.1 #105
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V2.1 #105
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Removed all files that have not been refactored with SpatialData
Added a modified SpatialData query script that works around their intrinsic_axes issue.
Added a formatting function that reads a Spatial Data object to: sjoin points to shapes, sjoin shapes to shapes, and changes shape object indices to strings. Sjoin functions changed in geometry.
Refactor of _shape_features to read and save to SpatialData.
Refactor point features to read and save to SpatialData.
Refactoring lp function and implementing lp_diff for discrete phenotypes
Implemented lp_diff_continuous, caught phenotype error in lp_diff_discrete, and clipped infinite values to max for -log10p and -log10padj.
Added _neighborhoods.py with no changes
- RNAflux uses incrementalPCA to improve memory usage - pretty logging bc why not - fe handles unweighted enrichment
unit tests and plotting bugs
add rich and bump version
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #105 +/- ##
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- Coverage 71.84% 70.60% -1.25%
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Files 35 36 +1
Lines 2252 2330 +78
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+ Hits 1618 1645 +27
- Misses 634 685 +51 ☔ View full report in Codecov by Sentry. |
Added sync_points function to sync points dask dataframe to groud truth sdata.table anndata + minor fixes
Refactored flux and fluxmap functions to SpatialData. Minor changes to format data and sindex_points.
Removed dask functionality since there is no speed up in the point computations. Changed geometry functions and edited how they were used in io, shape features, point features, and flux.
Refactored _flux_enrichment.py and removed register_points functionality since we are placing cell_raster in a points element that is dynamic instead of leaving it in unstructured.
Refactored colocation.py which relies on _decomposition.py being refactored. Current _composition.py comp_diff function does not work correctly. Refactored to the point where we run across the same error.
Refactoring plotting script and all of its depending scripts: colors, layers, utils
Refactoring plotting scripts for localization patterns
#104 (comment) - defer to native SpatialData API for query - change bento.geo.get_points astype parameter options to lowercase - change bento.geo.sindex_points unindexed points from "None" to empty string - in bento.tl.lp pull out gene expression array into variable so it is not queried twice - cleanup unused @ track, batch, copy - in bento.tl.fe make getting sparse matrix in csr format more readable
Changed all additions to points and shape elements to use Model.parse. Validates added element and maintains transformation metadata.
Changed all additions to shape elements to use Model.parse for _shape_features.py. Validates added element and maintains transformation metadata.
Revamp tutorials with spatialdata overhauled api
- move setters and getters to util - move sjoins to index - fix flux metadata indexing - keep unfiltered genes for sample merfish data
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Major Goals
SpatialDataintegration replacing original modifiedAnnDatadata structure [BPT-155] Spatial Data Refactor #104