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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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bugs report #270

Closed JLiLab closed 1 year ago

JLiLab commented 2 years ago

Thank you for creating such a promising tool!

I noticed a bug in the new Giotto suite: pDataDT() seems to stop working, creating problems for other functions depending on the cell_metatdata, such as addStatistics() and runGiottoHarmony().

addStatistics(giottoObject) produced the following error message: "Error in data.table::merge.data.table(cell_metadata, by.x = "cell_ID", : Elements listed in by.x must be valid column names in x."

runGiottoHarmony(giottoObject) produced the following error message: "Error in harmony::HarmonyMatrix(data_mat = matrix_to_use, meta_data = metadata, : meta_data must be either a data.frame or a vector with batch values for each cell"

It may have something to do with how giottoObject is created with createGiottoObject function.

RubD commented 1 year ago

If you still see this issue could you please provide a minimal reproducible example? See also https://giottosuite.readthedocs.io/en/latest/github_issues.html

We have not been able to reproduce this error. I'd advise to use the latest Giotto Suite version (suit branch > 3.0).