XeniumIO

[LiNk-NY]

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[bioc-issue-bot]

Hi @LiNk-NY

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: XeniumIO
Type: Package
Title: Import and represent Xenium data from the 10X Xenium Analyzer
Version: 0.99.0
Authors@R: c(
    person("Marcel", "Ramos", , "[email protected]", c("aut", "cre"),
        c(ORCID = "0000-0002-3242-0582")
    ),
    person("Dario", "Righelli", role = "ctb"),
    person("Estella", "Dong", role = "ctb")
    )
Description: The package allows users to readily import spatial data
    obtain from the 10X Xenium Analyzer pipeline. Supported formats include
    'parquet', 'h5', and 'mtx' files. The package mainly represents data
    as SpatialExperiment objects.
License: Artistic-2.0
Depends: TENxIO
Imports:
    BiocBaseUtils,
    BiocGenerics,
    BiocIO,
    jsonlite,
    methods,
    S4Vectors,
    SingleCellExperiment,
    SpatialExperiment,
    SummarizedExperiment,
    VisiumIO
Suggests:
    arrow,
    BiocStyle,
    knitr,
    rmarkdown,
    tinytest
biocViews: Software, Infrastructure, DataImport, SingleCell, Spatial
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
BugReports: https://github.com/waldronlab/XeniumIO/issues
URL: https://github.com/waldronlab/XeniumIO
Collate: 
    'XeniumFile.R'
    'TENxXenium-class.R'
    'XeniumIO-package.R'
    'utilities.R'
Date: 2024-10-23

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[HelenaLC]

Hi Marcel! Cool stuff, thanks. Everything's nicely coded of course, so not much to review, but here are my two cents:

• In the DESCRIPTION Description: line 13: "obtain" should be "obtained"

• Currently, nothing is being run in the vignette (file sizes)? 10x has recently made available an artifical lightweight dataset (12MB) here; just wondering whether it'd be worth to include at least this as a runnable example? Maybe also useful for unit testing?

• While being a SpatialExperiment co-developer, I wonder whether it'd be preferred to give users the option to get the data as a SingleCellExperiment instead, and only Suggest:ing SpatialExperiment in the DESCRIPTION. Because (i) this adds magick to the dependency stack, and (ii) being there are no images, an SCE will do just fine for many users/downstream tasks. Just a suggestion...

• Somewhat related, TENxXenium() currently defaults to realizing data from .parquet into memory. Per my understanding, one of the perks of using arrow is not do this, but instead work with a Table that allows dplyr-style ops. E.g., one could filter for a subset of genes (.parquet = molecules) or cell types (.parquet = boundaries) before realizing. Any way to expose an argument that would let the user control this? I usually don't realize these, just stash the pointer, and realize what I need when I need it.

[LiNk-NY]

Hi Helena, @HelenaLC

• In the DESCRIPTION Description: line 13: "obtain" should be "obtained"

Done.

• Currently, nothing is being run in the vignette (file sizes)? 10x has recently made available an artifical lightweight dataset (12MB) here; just wondering whether it'd be worth to include at least this as a runnable example? Maybe also useful for unit testing?

I'm still trying to figure out where to host this data. For now, I made the examples runnable in the vignette and function examples by downloading directly from 10X. Vince suggested hosting on OSN and downloading from there as an option that I will look into. I am not aware of any experiment data packages that provide this example data from 10X. There are some that have Xenium data but their data was pre-processed.

• While being a SpatialExperiment co-developer, I wonder whether it'd be preferred to give users the option to get the data as a SingleCellExperiment instead, and only Suggest:ing SpatialExperiment in the DESCRIPTION. Because (i) this adds magick to the dependency stack, and (ii) being there are no images, an SCE will do just fine for many users/downstream tasks. Just a suggestion...

There are some benefits of only using magick when necessary (and moved to Suggests) and perhaps this should be handled in the SpatialExperiment package (@drighelli).
I chose to use SpatialExperiment because the components match the data type closely. FWIW, the user also has the option to do as(spe, "SingleCellExperiment") so creating an import method that returns SingleCellExperiment may be more work than what it is worth.

• Somewhat related, TENxXenium() currently defaults to realizing data from .parquet into memory. Per my understanding, one of the perks of using arrow is not do this, but instead work with a Table that allows dplyr-style ops. E.g., one could filter for a subset of genes (.parquet = molecules) or cell types (.parquet = boundaries) before realizing. Any way to expose an argument that would let the user control this? I usually don't realize these, just stash the pointer, and realize what I need when I need it.

This would be nice to have but currently, the SpatialExperiment constructor does not handle Table classes in the colData and these get coerced to DFrame by the constructor further down the line.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e6ac63b6ea0bc526a5f440cc0e2b4e86038e8f76

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): XeniumIO_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/XeniumIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0fe98eb899e46670f15fc86fce17237d8a492f9f

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): XeniumIO_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/XeniumIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[drighelli]

sorry to jump in this, but thanks @LiNk-NY for pointing this out, indeed this is a pending issue in SpatialExperiment that we need to solve.
Suggesting the magick package is something that I'd be happy to let it take place in the next release

[vjcitn]

wget --no-check-certificate https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenDemo/Xenium_V1_human_Breast_2fov_outs.zip

will get one of the slim Xenium outputs (mentioned as lightweight by Helena above), substitute 'Lung' for 'Breast' for a second example

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9bcc803184a84951bf20e83008509e42ca1fe408

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): XeniumIO_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/XeniumIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Update : With the help from Vince and Alex, I uploaded the demo data to https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenDemo%2FXenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip (seen at https://mghp.osn.xsede.org/bir190004-bucket01/index.html#BiocXenDemo/) and changed the URLs in the package to point to that. Note that IMO the suggested dataset is a bit too big to use in the examples.