Minor updates - Githubissues

waldronlab / SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets

https://bioconductor.org/packages/SingleCellMultiModal

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Minor updates #31

Closed cvanderaa closed 3 years ago

cvanderaa commented 3 years ago

Hi Marcel @LiNk-NY ,

This is a very small PR to change 2 things:

The assays in the macrophage_differentiation project (SCoPE2) were called macrophage_protein and macrophage_rna. Laurent pointed out to me that this can be confusing because monocyte data are also present in the assays. I renamed the assays using the project abbreviation macroph_diff_protein and macroph_diff_rna.
I adapted the vignette with the new assay names and fixed some typos.

LiNk-NY commented 3 years ago

Thanks for the PR Chris, note that our new function SingleCellMultiModal will return an assay with a name like macrophage_differentiation_macroph_diff_protein, for example.

cvanderaa commented 3 years ago

Oh sorry, I didn't see the new function. It's a great feature you implemented there!

So, I could simply name the assays rna and protein, and once called from SingleCellMultiModal(...), those will become macrophage_differentiation_rna and macrophage_differentiation_protein?

Should I also document this new way of retrieving multiple datasets in the SCoPE2.Rmd vignette?

LiNk-NY commented 3 years ago

Hi Chris, @cvanderaa

So, I could simply name the assays rna and protein, and once called from SingleCellMultiModal(...), those will become macrophage_differentiation_rna and macrophage_differentiation_protein?

Yes, those would be the names you get with the new function. I had to append the DataType to differentiate the different technologies in the assays. I should add a note about that in the documentation.

Should I also document this new way of retrieving multiple datasets in the SCoPE2.Rmd vignette?

You could but you don't have to. The function is complementary to the existing ones.

cvanderaa commented 3 years ago

Hi Marcel @LiNk-NY ,

Thanks for the info! So, this PR simply renames the assays to rna and protein (= names of the modalities on ExperimentHub) and makes some slight improvements to the SCoPE2 vignette.

cvanderaa commented 3 years ago

Oops, sorry about that! I have removed it!