tidytof

[keyes-timothy]

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[bioc-issue-bot]

Hi @keyes-timothy

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:

Type: Package
Package: tidytof
Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
Version: 0.99.0
Authors@R: 
    c(person(given = "Timothy",
   family = "Keyes",
   role = c("cre"),
   email = "tkeyes@stanford.edu", 
   comment = c(ORCID = "0000-0003-0423-9679")),
      person(given = "Kara", 
   family = "Davis", 
   role = c("rth", "own"),
   email = "kldavis@stanford.edu"), 
      person(given = "Garry", 
   family = "Nolan", 
   role = c("rth", "own"), 
   email = "gnolan@stanford.edu"))    
Description: This package implements an interactive, scientific analysis
    pipeline for high-dimensional cytometry data built using tidy data principles.  
    It is specifically designed to play well with both the tidyverse and 
    Bioconductor software ecosystems, with functionality for reading/writing 
    data files, data cleaning, preprocessing, clustering,
    visualization, modeling, and other quality-of-life functions. tidytof 
    implements a "grammar" of high-dimensional cytometry data analysis.
License: MIT + file LICENSE
Depends: 
    R (>= 4.3)
Imports:
    doParallel,
    dplyr,
    flowCore,
    foreach,
    ggplot2,
    ggraph,
    glmnet,
    methods,
    parallel,
    purrr,
    readr,
    recipes,
    rlang,
    stringr,
    survival,
    tidygraph,
    tidyr,
    tidyselect,
    yardstick,
    Rcpp,
    tibble,
    stats,
    utils,
    RcppHNSW
Suggests:
    ConsensusClusterPlus,
    Biobase,
    broom,
    covr,
    diffcyt,
    emdist,
    FlowSOM,
    forcats,
    ggrepel,
    HDCytoData,
    knitr,
    markdown,
    philentropy,
    rmarkdown,
    Rtsne,
    statmod,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    lmerTest,
    lme4,
    ggridges,
    spelling,
    scattermore,
    preprocessCore,
    SingleCellExperiment,
    Seurat,
    SeuratObject,
    embed,
    rsample
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1
LinkingTo: 
    Rcpp
URL: https://keyes-timothy.github.io/tidytof,
    https://keyes-timothy.github.io/tidytof/
VignetteBuilder: knitr
Language: en-US
biocViews: SingleCell, FlowCytometry

[keyes-timothy]

(This is my first submission to Bioconductor - thank you for your help and patience in the review process! I'm sure I will learn a lot through this first experience.)

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[hpages]

Thanks @keyes-timothy for this submission.

Given the amount of vignettes (11 in total), it's gonna be a challenge for a newcomer like me to navigate them:

There's a "Getting started with tidytof" vignette, so I suppose that users will be able to figure out where to start but then it's not clear where to go after that. Can the other vignettes be read in any order or is there an order that you recommend?

It would be nice if the introduction vignette could be made more prominent, maybe by using uppercase in the title (e.g. "GETTING STARTED with tidytof"), and if the introduction vignette had a "where to go next" section -- or something like that -- that lists the other vignettes in the recommended order of reading and provides a short description for each of them.

Also what does tof stand for? It's part of the package name and is the prefix of a bunch of function names defined in the package, but I can't figure out where it's comming from. I'm curious why you didn't choose tidycyto for the package name since it would have made the package's relationship with cytometry immediately obvious. Anyways would be nice to explain the tof acronym in the introduction vignette.

Thanks,
H.

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Received a valid push on git.bioconductor.org; starting a build for commit id: f94e11af10f6a3840e25462d488ce07ef287e070

[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 22.04.3 LTS): tidytof_0.99.7.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
git@git.bioconductor.org:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[keyes-timothy]

Hi @hpages,

Thanks for your comments, and for your patience waiting on my responses. I've just pushed some changes to incorporate your feedback, and I've replied to your comments with specific in-line responses below. Please let me know if you have any other thoughts, concerns, or suggestions!

Timothy

Thanks @keyes-timothy for this submission.

Given the amount of vignettes (11 in total), it's gonna be a challenge for a newcomer like me to navigate them:

There's a "Getting started with tidytof" vignette, so I suppose that users will be able to figure out where to start but then it's not clear where to go after that. Can the other vignettes be read in any order or is there an order that you recommend?

It would be nice if the introduction vignette could be made more prominent, maybe by using uppercase in the title (e.g. "GETTING STARTED with tidytof"),

I've made this change! The vignette title is now "GETTING STARTED with tidytof", which I think helps it stand out in the list of vignettes.

and if the introduction vignette had a "where to go next" section -- or something like that -- that lists the other vignettes in the recommended order of reading and provides a short description for each of them.

To your point, I've added a "Where to go next" section to the introductory vignette that includes a suggested order for visiting the remainder of the vignettes. The schema that I've proposed starts small (at the cell-level) and works its way up to higher-order (i.e. cluster and then sample-level) operations.

I've also added references to the tidytof manuscript and the manuscript describing the larger "tidyomics" project

Also what does tof stand for? It's part of the package name and is the prefix of a bunch of function names defined in the package, but I can't figure out where it's comming from. I'm curious why you didn't choose tidycyto for the package name since it would have made the package's relationship with cytometry immediately obvious. Anyways would be nice to explain the tof acronym in the introduction vignette.

This is a great question, and at some point in the future I've been considering building a next-generation version of tidytof (that would probably have the name "tidycyto"). The "tof" in "tidytof" comes from CyTOF (mass cytometry), which is a high-dimensional cytometry technology that much of the field focuses on (including myself). tidytof works for high-dimensional cytometry platforms other than CyTOF, but the implicit focus is on CyTOF (where there is less tidy tooling, compared to tidyFlowCore that essentially works right out-of-the-box for any cytometry platform that can be analyzed with flowCore.)

To this point, I've added a brief parenthetical that explains the naming in the introductory vignette. It reads as follows:

{tidytof} ("tidy" as in "tidy data"; "tof" as in "CyTOF", a flagship high-dimensional cytometry technology) implements a concise, integrated "grammar" of single-cell data analysis capable of answering a variety of biological questions.

Thanks, H.

[vjcitn]

Just a quick comment concerning the number of vignettes, I had a look at the pkgdown site and was impressed by:

[vjcitn]

I don't know how to do that (substructuring the articles tab content) and will look at the sources for guidance. It would be great if R's HTML help pages could incorporate such substructure but that's likely a ways down the road.