CITEViz

[gartician]

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• Repository: https://github.com/maxsonBraunLab/CITEViz

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[bioc-issue-bot]

Hi @gartician

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: CITEViz
Title: CITEViz
Version: 0.99.0
Authors@R: c(
    person('Garth', 'Kong', email = '[email protected]', role = c('cre', 'aut'), comment = c(ORCID = '0000-0001-5262-5406')),
    person('Thai', 'Nguyen', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-8988-4003')),
    person('Wesley', 'Rosales', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-6381-9844')),
    person('Anjali', 'Panikar', email = '[email protected] ', role = 'aut', comment = c(ORCID = '0000-0002-5740-807X')),
    person('John', 'Cheney', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-6194-2745')),
    person('Sarah', 'Carratt', email = '[email protected]', role = 'rev', comment = c(ORCID = '0000-0003-2493-6789')),
    person('Brittany', 'Curtiss', email = '[email protected]', role = 'rev', comment = c(ORCID = '0000-0002-5274-8323')),
    person('Theodore', 'Braun', email = '[email protected]', role = 'rev', comment = c(ORCID = '0000-0002-6248-2143')),
    person('Julia', 'Maxson', email = '[email protected]', role = 'rev', comment = c(ORCID = '0000-0002-3871-7221'))
    )
Description: CITEViz is a single-cell visualization platform with a custom module that replicates the interactive flow cytometry workflow in CITE-Seq. Users can can isolate cell populations of interest using the protein assay in CITE-Seq with minimal computational training. Additional features of CITEViz includes assessment of quality control metrics, feature visualization (feature expression and co-expression), and evaluation of clusters.
License: MIT + file LICENSE
Imports:
    bslib,
    config (>= 0.3.1),
    dplyr,
    DT,
    ggplot2,
    golem (>= 0.3.1),
    grDevices,
    magrittr,
    methods,
    plotly,
    rlang,
    SeuratObject,
    shiny (>= 1.6.0),
    stats,
    tibble,
    vembedr
Encoding: UTF-8
RoxygenNote: 7.2.0
Suggests:
    knitr,
    BiocStyle,
    rmarkdown,
    spelling,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Language: en-US
VignetteBuilder: knitr
biocViews: SingleCell, ShinyApps, FlowCytometry, QualityControl, GeneExpression

[vjcitn]

I am seeing that you have a tarball exceeding 5MB with a lot of large nice gifs under inst. We have to keep our package tarball sizes low. If you run BiocCheck::BiocCheck you will see that it produces an error on tarball size. I have to remove the pre-check passed notice.

[gartician]

Thank you Vince, we replaced all the large GIFs with still images (PNGs). Our BiocCheck run on our GitHub Actions looks dandy: https://github.com/maxsonBraunLab/CITEViz/runs/7717115756?check_suite_focus=true

[gartician]

I pushed my changes to GitHub, but I am confused about how to push my new changes to bioconductor's git repository. I tried to set my upstream using the command git remote add upstream [email protected]:packages/CITEViz.git, but it didn't work. I noticed I could not find CITEViz in this link , is that why I can't set an upstream because it doesn't exist?

[vjcitn]

Thanks for dealing with the images. @lshep this can be moderated. Garth it usually takes some time to get into git.

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/CITEViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[gartician]

I'm going to pre-emptively address the warning that suggests me to evaluate more code chunks in the vignette.

One code chunk is used to show the readers how to install our program and run the app. Since this is a Shiny app, this makes the code chunk runs indefinitely which isn't ideal. One question though: should I instruct the users to install using the BioC method e.g. BiocInstall("CITEViz") as opposed to devtools?

Another code chunk shows how to do differential expression in gated cells, but that requires importing a 120MB test dataset. I didn't include that dataset here because that's not part of the app, but I did add links for the user to get these external files.

[PeteHaitch]

Thanks for your submission of CITEViz, @gartician. I'll be reviewing the package but won't be able to start the formal review until next week.

should I instruct the users to install using the BioC method e.g. BiocInstall("CITEViz") as opposed to devtools?

It is recommended to only refer to (or otherwise emphasise) the 'official' Bioconductor installation instructions, to avoid issues with people installing incompatible versions of software when using the 'GitHub' installation instructions.

I didn't include that dataset here because that's not part of the app, but I did add links for the user to get these external files.

I've not yet looked closely at the package, so I'm not sure which test dataset you are referring to, but please consider making the data available via AnnotationHub or ExperimentHub (https://contributions.bioconductor.org/data.html).

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a8e71ffbac7909b48827d17f4b4f70075a2880ab

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/CITEViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[gartician]

Hi @PeteHaitch, I hope you were able to take a look at this package during the week.

That last update was to replace devtools installation instructions with BiocManager::install("CITEViz").

How important is it to create an ExperimentHub/AnnotationHub for this dataset? The test dataset I mentioned is just a subset of of the data from this paper paper and this Seurat vignette. Since it's readily available for download as an RDS file, I wonder if it's more work than necessary to include into this package. If I am mistaken and there's good reason to include one, I will be glad to learn more about it.

[PeteHaitch]

@Bioconductor/core: could you please respond to @gartician's query:

How important is it to create an ExperimentHub/AnnotationHub for this dataset? The test dataset I mentioned is just a subset of of the data from this paper paper and this Seurat vignette. Since it's readily available for download as an RDS file, I wonder if it's more work than necessary to include into this package. If I am mistaken and there's good reason to include one, I will be glad to learn more about it.

[lshep]

Without looking closely at the package... You need to be able to run or test run the code of the package. If there are smaller datasets that are executed in tests and man page code than perhaps that is okay... but it depends on what is exported and how functions are run in the package. The other alternative too would be instead of using ExperimentHub, if the data is readily downloadable, you could download and use BiocFileCache to at least have runnable examples.

[PeteHaitch]

Hi @gartician,

I started to review CITEViz, but it needs substantial changes before it can be considered for Bioconductor.

One of the central aims of Bioconductor is to provide interoperable software, but CITEViz does not support SingleCellExperiment objects, the core Bioconductor data structure for storing single-cell data. Support for SingleCellExperiment objects is a requirement for inclusion into Bioconductor.

I don't mean to discourage the submission of CITEViz to Bioconductor but I want to be realistic about expectations and requirements (covered in detail in https://contributions.bioconductor.org/). If supporting SingleCellExperiment objects is beyond the current scope of the package, then CRAN might be a suitable repository for CITEViz since it has no such interoperability requirements.

If you intend to support SingleCellExperiment objects and would to proceed with the Bioconductor submission, please let us know. I do have some additional comments from my initial look but we won't proceed further with the review until this is resolved.

Cheers, Pete

[gartician]

Thank you @PeteHaitch for the initial review, I'll have a chat with my team to include support for SCE objects to provide interoperable software in BioConductor.

[gartician]

Hi @PeteHaitch, we are working to accept SCE objects into CITEViz. We plan to use a file format flag that determines how the data will be queried based on the input file. This should help us build things more hierarchically with a reasonable coding structure. Thank you for the feedback so far!

[gartician]

Hi @PeteHaitch, we were able to include SCE objects to CITEViz! For some new functions we added, should we include the tests into the next commit? We will definitely finish writing tests before the BioConductor 3.16 release, but one of our developers is out sick and may require an extra week or two to finish. Meanwhile, we are available to address additional comments if possible. Thank you for your input, let us know what you think.

[PeteHaitch]

Hi @gartician,

That's great news!

According to the Bioconductor 3.16 Release Schedule, we have until October 26 for the package to be accepted in order for it to make the 3.16 release. I'm confident we can achieve this and will work with you to help as best I can.

I'll do a complete review once the new version of the package is submitted and passing the automatic checks. In the meantime, here are some notes from my initial look at the package that will need to be addressed:

• I tried to use the app with the example data, but it was harder than it needed to be to find and download the example data. The vignette links to a paper, but the paper doesn't contain the example data as best I could tell, and it wasn't until the last line of the vignette that a link to a GitHub repo was mentioned. I dug around in that repo and found what I think is the right file (https://github.com/gartician/CITEVizWorkshop/blob/master/inst/extdata/small_pbmc_2.rds), albeit with a slightly different filename and without some metadata shown in the vignette screenshots (e.g., it doesn't seem to have the seurat_clusters shown in the 'Clustering' section of the vignette). This is where hosting the data as an ExperimentHub resource would simplify things for a Bioconductor user.
• Many figures in vignette were illegibly small.

[vjcitn]

I am looking at 0.99.4. The comments from Pete above seem to hold ... can't find example data readily when starting the app. I'd also add a few points

• the vignette does not mention accommodation of SingleCellExperiment objects; it just refers to Seurat
• "a custom module that replicates the flow-cytometry gating workflow" is not easy for me to understand. What does it mean for a module to replicate a workflow? Are all the steps of flow gating encoded in the rds file? That would seem to be important if there is indeed "replication" occurring with this tool. Or does the package permit one to explore the gating process with data that have or have not been gated?
• the app does not have an exit component, like a stop button
• the "installation" code fragment in the vignette asks the user to run the app, which does not seem to be part of installation

I hope these can be addressed along with Pete's comments in the near future.

[gartician]

Thank you for the additional comments! We have more documentation coming up soon, which should address most of the comments. I'll definitely rephrase the custom module sentence as it can be misinterpreted. I just wanted to see if I am pushing to the right places, and the changes are being tracked correctly. Thanks!

[gartician]

I do have a general question about ExperimentHub and data sharing. I was wondering if it's ethically okay for us to publish another EH package if we didn't generate the data ourselves? All I did was download the original RDS and down-sampled the data, which I don't feel warrants my name on it.

As an alternative, can we provide a link to a Google Drive similar to the vignette found in excluderanges? I did include a link to a Google Drive folder for the test data PBMC (120MB) in the original CITEViz preprint in the Supplementary Information section. Now that I am aware it is hard to find, what I can do is advertise it better.

As this is my first time submitting a package, I am still understanding how things are done efficiently so please excuse the newbie questions. Thank you in advanced!

[vjcitn]

@lshep will have the best advice here. As long as you make proper attributions I think there is no problem with you using EH for data that is integral to your package. As for Google Drive, I am not familiar with that approach, but if the resource is durable and open, it sounds OK. zenodo is probably a better option in terms of durability and cost.

[lshep]

We in generally don't allow or recommend using a google drive to distribute data and have asked maintainers to do this to move the data to a more permanent secure data distribution server. The excluderanges uses data from the hubs and not google drive in the package itself which I think why this slipped through the cracks.
As far as okay to publish the data. I agree with @vjcitn that you should give the original data credit and make sure you check the licensing of the data that you are down-sampling to make sure it allow redistribution.

[gartician]

AdditionalPackage: https://github.com/maxsonBraunLab/CITEVizTestData

[bioc-issue-bot]

Can't build unless issue is open and '2. review in progress' label is present, or issue is closed and 'TESTING' label is present.

[gartician]

Can anyone adjust the labels to start building the test data?

[lshep]

Please try again

[gartician]

AdditionalPackage: https://github.com/maxsonBraunLab/CITEVizTestData

[bioc-issue-bot]

Hi @gartician, Thanks for submitting your additional package: https://github.com/maxsonBraunLab/CITEVizTestData. We are taking a quick look at it and you will hear back from us soon.