(feat): match pbmc3k tutorial to seurat's

[ilan-gold]

TODO:

• Figure out best way for ranking genes so that we recover meaningful results. At the moment, running the method on the full gene list yields a lot of RP genes for the CD4 cluster ,which I would guess is basically noise. But it seems that seurat uses the full list. Separately I can't seem to figure out how to get the scores from seurat - they are claimed to be present but I don't seem them. I don't think they are just lfc.
• Marker gene documentation CD8A and CD8B are not present in the ranked genes either here or in seurat but are noted as marker genes. So I think we should just change that table and note that some genes are not present the ranked genes (maybe explain why? talk to Rahul again?)
• PCA Rahul's PCA is quite similar but not exact. It would be nice maybe for them to have arpack since an R implementation exists: https://search.r-project.org/CRAN/refmans/igraph/html/arpack.html and
• Clustering Same as above, especially since igraph is available in R: https://igraph.org/r/doc/cluster_leiden.html

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[ilan-gold]

@flying-sheep Still very rough, but looking for some feedback given the above "outstanding" issues, especially on framing the reproducibility aspect

[flying-sheep]

Blast from the past: I also use an ARPACKy PCA in destiny, using RSpectra:

• Non-deterministic behaviour with set.seed() theislab/destiny#5
• theislab/destiny@b4e8dad

If nothing changed in the space, that might be their way forward as well, but of course I don’t know if RSpectra’s PCA is 100% identical to ARPACK.

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flying-sheep commented on 2025-05-15T15:26:26Z
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there seems to be no output from print_header

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flying-sheep commented on 2025-05-15T15:26:27Z
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I don’t really get what “up to ties” means

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flying-sheep commented on 2025-05-15T15:26:28Z
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Line #2.    adata_subset_hvg = adata[:, adata.var["highly_variable"]].copy()

hmm, maybe explain that you’re using that subset for a while until you go back to the non-subset one?

I think it’s maybe a bit confusing that there are two adata objects being used interspersedly. I think modifying a notebook like that can easily result in copy-pasting the wrong name.

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flying-sheep commented on 2025-05-15T15:26:28Z
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We should just switch to sc.tl.marker_gene_overlap instead of changing these around everytime this file is touched.