Add pciseq #7
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Add pciseq #7
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LouisK92
reviewed
Nov 22, 2024
| @@ -61,7 +73,7 @@ | |||
| }, | |||
| tables={ | |||
| "table": ad.AnnData( | |||
| obs=sdata.tables["table"].obs[["cell_id", "region"]], | |||
| obs=pd.DataFrame(cell_id_col), # have to make the series a dataframe for some reason | |||
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adata.obs must be a data frame, can kick out the comment
| 'coordinate_system': 'global', | ||
| 'output': '../pciSeq_assigned_transcripts.zarr', | ||
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| 'input_scrnaseq': '../brain_scrnaseq_subsample_WMB-10X.h5ad', |
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Did you test with task_ist_preprocessing/resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad ?
good to stick with the given resources in the VIASH START END section
| } | ||
| ## VIASH END | ||
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| # # Set coordinate system to default if not given |
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can kick out unnecessary comments
| # Assign cell ids to transcripts | ||
| print('Assigning transcripts to cell ids', flush=True) | ||
| y_coords = transcripts.y.compute().to_numpy(dtype=np.int64) | ||
| x_coords = transcripts.x.compute().to_numpy(dtype=np.int64) |
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does pciseq require integer positions?
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use floats if fine for pciseq
| # - segmentation 3D, transcripts 2D | ||
| # - segmentation 2D, transcripts 3D | ||
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| # Subset sdata to transcripts with cell ids |
| shutil.rmtree(par["output"]) | ||
| sdata_transcripts_only.write(par['output']) | ||
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| # TODO: is this a problem? |
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Am also confused why this is always printed, it's not a problem. When writing the object (as done here) and loading again, everything is fine.
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Describe your changes
Added the pciSeq method to assignment methods
Modified the basic assignment method to create new cell_id index only from segmentation image, not prior AnnData
Checklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!