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[r] Add Seurat -> SOMA Ingestor#1146

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Merged

mojaveazure merged 52 commits intomainsingle-cell-data/TileDB-SOMA:mainfrom ph/feat/from-seuratsingle-cell-data/TileDB-SOMA:ph/feat/from-seuratCopy head branch name to clipboardApr 20, 2023

+1,847-5

Commits

Commits on Apr 18, 2023

• Implement write_soma

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• Add roxygen template

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• Reorganize the code

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• Add docs for write_soma

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• Improved type testing and warnings in write_soma.data.frame

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• Index SOMADataFrames by soma_joinid

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• Add tests for R-object methods for write_soma()

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• Matrix is annoying

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• Hide info messages

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• Adjustments to write_soma.Graph

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• Add tests for writing Seurat subobjects

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• Add tests for writing Seurat objects

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• Add logging

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• Improve pad_matrix for scale.data slot

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• Remove unnecessary code

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• Replace lambdas with functions

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• Update apis/r/R/write_soma.R

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• Update apis/r/R/write_soma.R

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• Update apis/r/R/write_soma.R

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• Update docs from GH changes

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• Update docs for write_soma.data.frame

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• Change to in

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• Rename test file with -

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• Change soma param to soma_parent

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• Update tests with new parameter names

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• Simplify user_dir()

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• Always write reductions as sparse arrays

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• Don't automatically overwrite soma_joinid in write_soma.data.frame()

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• Error out when trying to write out data frames with non-atomic columns

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• Update docs to reflect always writing sparsely

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• Remove automatic URI creation for Seurat objects

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• Remove unused function

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• Spell out 'layer' for clarity

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• Change default SOMADataFrame index to obs_id or var_id

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• More informative variable names

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• Update tests for obs_id

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• Update apis/r/R/write_seurat.R

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• Update apis/r/R/write_seurat.R

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• Update apis/r/R/write_soma.R

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• Update apis/r/R/write_soma.R

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• Fix typo

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• Remove overwrite

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• Replace overwrite with absolute

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• Error when trying to write a sparse matrix densely

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• Add logging when padding matrix

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• Proper spdl formatting

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• Better variable names

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• Remove unused code

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• Let SOMADataFrame validate soma_joinid

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• Allow the user to set their own index when writing data frames

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Commits on Apr 20, 2023

• Update variable name

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• Update changelog

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