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migrate to Seurat version 3 #94
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Thanks for migrating the PR!
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This seemed to have done the trick. The workflow went almost completly through, but raised an error in the `plot_violine.R':
Not sure what happened there since I haven't tested your changes yet, do you have a way to test what's going on (it seems the read10x call is the culprit)? |
I ran into the same issue. It seems that Read10X expects either features.tsv (and all files as .gz) or genes.tsv. Be default gene names are expected in column 2 but it is possible to change this. Update: I think it may be easier to keep "genes" instead of "features" rather than compressing output files (as cellranger version 3 does). I have updated to accept "genes.tsv" with one column. |
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scripts/plot_violine.R
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@@ -219,7 +219,7 @@ ggsave(gg, file = snakemake@output$pdf_count_vs_gene, width = 12, height = 7) | |||
# sample1_CAGCCCTCAGTA 264 437 sample1_CAGCCCTCAGTA sample1 CAGCCCTCAGTA 100 100 batch1 sample1 0.0389016 0.07551487 0.1144165 0.0228833 0.5102975 1.655303 | |||
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# saving snakemake meta information into misc slot so all can be exported as one object | |||
seuratobj@misc <- snakemake | |||
Misc(object = pbmc_small, slot = "misc") <- snakemake |
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What does this do?
I changed the snakemake object to a list since that's what the seurat object was asking but I haven't doublechecked how it looked like.
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Seurat version 3 uses “Assay” slots so I think it needs to be specified differently. Their function seems to be recommended for this so they can update it if they change the object in future versions. The test environment on Travis threw an error on this and this fixes it.
Not sure you saw it, but I sent you a PR on your branch. Could you merge it and PR it again? Sorry for the hassle, still struggling to keep PR authors properly in the history when merging. |
This looks nice. |
I've crudely tested it and it seems to work fine, so fine with me to merge it in. |
See #93 for previous discussions