cytomining / cytomining/CytoTable
Update `identifying_cols` to use `ObjectNumber` reference within presets
- Dominant language
- Python
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- Avg merge
- 2d 3h
- Merged PRs (30d)
- 6
Description
> Thank you so much for your help, @d33bs! I would like to share that I was able to use Cytotable on another dataset using the following [script](https://gist.github.com/Zitong-Chen-16/8a48675a784d372ec05ddd9b69a9d248) though not without changes to the parameters that were passed in. Ane downstream analysis confirmed that the files were merged successfully.
>
> For my specific dataset, I had to change the `identifying_cols ` and `join_command ` in order for it to work with the `cell-health-cellprofiler-to-cytominer-database` preset. Specifically, I changed `identifying_cols ` to include `ObjectNumber ` and removed `Cells_ObjectNumber` and `Nuclei_ObjectNumber`, and was wondering if that would actually make more sense in a general setting since IIUC ObjectNumber is a shared metadata column across the tables. For the `join_command` I changed the `Image_Metadata_Well` and `Image_Metadata_Plate` [here](https://github.com/cytomining/CytoTable/blob/d64f954edce640d2559defc49be3a099b07bb4e5/cytotable/presets.py#L193C10-L193C10) to `Metadata_Well` and Metadata_Plate`, but not quite sure if that is dataset specific.
_Originally mentioned by @Zitong-Chen-16 in https://github.com/cytomining/CytoTable/issues/105#issuecomment-1738081608_
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