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omnideconv / spacedeconv

A unified interface to spatial transcriptomics deconvolution tools
https://omnideconv.org/spacedeconv/
GNU General Public License v3.0
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HVG is depreciated in Giotto #140

Closed RolantusdataExp closed 6 months ago

RolantusdataExp commented 6 months ago

Dear developers,

Thanks for a great tool

I think I have encountered a depreciated function in your code

when running: signature <- spacedeconv::build_model( sc_se, cell_type_col = "HEPs_subcluster", method = "spatialdwls", assay_sc="counts", )

I receive the following error: Error: 'calculateHVG' is not an exported object from 'namespace:Giotto'

I suspect this is due to the fact that DriesLab changed the function from calculateHVG to calculateHVF a while back.

When using pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE) You automatically install the newest version of Giotto (4.0.5), and I guess you need to force an older version for instance (1.1.2).

Best regards, Peter

Versions

other attached packages: [1] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-3 Giotto_4.0.5 GiottoClass_0.2.3

czackl commented 6 months ago

Hey, thanks for the feedback!

I am working on this in PR #143. I plan to do some further improvements the next days, but this version should already run now, so feel free to checkout the PR.

Greetings, Constantin

czackl commented 6 months ago

Merged