Update osteo data prep#990
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…we should be using mouse mito
…plained in the notebook
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Woops, forgot to request review here amid all the paper things I've been up to! |
jashapiro
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jashapiro
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Overall this looks good. Sorry that it took a bunch of extra work to make it useable!
My main notes are about updating the renv to include qs and a suggestion about downloading files with snakemake.
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| Turns out there is no overlap, which is not actually unexpected. | ||
| This data is from Visium and has 19465 genes, corresponding to the Mouse Visium v1 probe set which does not have mitochondrial genes. |
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<tapping-head.gif> Can't have low quality spots if you don't look at markers of low quality.
| make_option( | ||
| opt = c("-i", "--input"), | ||
| type = "character", | ||
| help = "Path to the input osteo reference RDS file." |
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| help = "Path to the input osteo reference RDS file." | |
| help = "Path to the input osteo reference qs file." |
| This code requires the `qs` (not `qs2`) package to read in the raw `OsteoCAR` reference. | ||
| As of January 2026, this package is not currently from CRAN (but it may be back one day), so you may need to install with `remotes::install_github("qsbase/qs")`. |
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This should probably be part of the renv. (also why we don't use non-standard formats!)
| # for the deconvolution notebooks | ||
| rule reformat_osteo_ref: | ||
| input: | ||
| osteo_ref = "mm_mets_osteo_ref_raw.qs", # doesn't need temp() |
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inputs are never flagged as temp, but I also wouldn't set this file as temp at all? Is there a reason you would want to not keep the file around?
Alternatively, you can let snakemake handle the download directly, which may be preferable here (see https://snakemake.readthedocs.io/en/v6.1.0/snakefiles/remote_files.html)
You would need to add the following at the top:
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()
Then you can replace this with:
| osteo_ref = "mm_mets_osteo_ref_raw.qs", # doesn't need temp() | |
| osteo_ref = HTTP.remote(config["osteo_ref_url"]) |
and remove the manual download.
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| #!/usr/bin/env Rscript | |||
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| # This script reformats the osteo reference: | |||
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| # This script reformats the osteo reference: | |
| # This script reformats the osteo reference Seurat object |
2 participants
Closes #987
Partly addresses #988
This PR updates the Snakemake workflow that prepares osteo data in several ways:
qssituation - authors fell out of compliance with CRAN so the package got removed, andqs2doesn't work to read in files created withqs. This is a known annoyance for a lot of people! Now we too can be annoyed./shared