dandelionR #3680

zktuong · 2024-12-13T04:50:32Z

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bioc-issue-bot · 2024-12-13T04:50:36Z

Hi @zktuong

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: dandelionR
Title: Single-cell Immune Repertoire Trajectory Analysis in R
Version: 0.99.0
Authors@R:
    c(person(given="Jiawei", family="Yu", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0009-0005-9170-7881")),
      person(given="Nicholas", family="Borcherding", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0003-1427-6342")),
      person(given="Kelvin", family="Tuong", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6735-6808")))
Description: dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell
Collate:
    'check.R'
    'constructMarkovChain.R'
    'data.R'
    'determMultiscaleSpace.R'
    'terminalStateFromMarkovChain.R'
    'differentiationProbabilities.R'
    'filterCells.R'
    'getPbs.R'
    'projectProbability.R'
    'maxMinSampling.R'
    'minMaxScale.R'
    'markovProbability.R'
    'miloUmap.R'
    'projectPseudotimeToCell.R'
    'setupVdjPseudobulk.R'
    'splitCTgene.R'
    'vdjPseudobulk.R'
Imports:
    BiocGenerics,
    bluster,
    destiny, 
    igraph,
    MASS,
    Matrix,
    methods,
    miloR,
    purrr,
    rlang,
    S4Vectors,
    SingleCellExperiment,
    spam,
    stats,
    SummarizedExperiment,
    uwot
Suggests:
    BiocStyle,
    knitr,
    RColorBrewer,
    scater,
    scRepertoire,
    testthat
VignetteBuilder: knitr
URL: https://www.github.com/tuonglab/dandelionR/
BugReports: https://www.github.com/tuonglab/dandelionR/issues
Depends: 
    R (>= 4.4.0)

lshep · 2024-12-18T14:57:40Z

I currently cannot get the package to build for local testing

R CMD build dandelionR 
* checking for file 'dandelionR/DESCRIPTION' ... OK
* preparing 'dandelionR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette_from_scRepertoire.Rmd’ using rmarkdown

Quitting from lines 77-86 [unnamed-chunk-6] (vignette_from_scRepertoire.Rmd)
Error: processing vignette 'vignette_from_scRepertoire.Rmd' failed with diagnostics:
unused argument (filterNonproductive = TRUE)
--- failed re-building ‘vignette_from_scRepertoire.Rmd’

--- re-building ‘vignette_reproduce_original.rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Reproducing the original dandelion method/paper"", and the latter is "Reproducing the original dandelion method/paper". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘vignette_reproduce_original.rmd’

SUMMARY: processing the following file failed:
  ‘vignette_from_scRepertoire.Rmd’

Error: Vignette re-building failed.
Execution halted

zktuong · 2024-12-19T06:54:28Z

hi @lshep, i'm told that it should work – as the bioconcductor 3.20 release has that argument in scRepertoire: https://code.bioconductor.org/browse/scRepertoire/blob/RELEASE_3_20/R/combineContigs.R#L55

In anycase, we have since gona back to edit the vignette to exclude the argument filterNonproductive = TRUE as that was the default anyway.

lshep · 2024-12-19T11:54:31Z

Your package is building against devel not release_3_20 and that argument does not exist there https://code.bioconductor.org/browse/scRepertoire/blob/devel/R/combineContigs.R#L52 . Through this review process make sure you are testing against R-devel and Bioc devel (soon to be 3.21)

zktuong · 2024-12-19T13:07:38Z

ok thanks for that!

seems like the Bioc-devel version of scRepertoire is an outdated (different) version compared to the released version and that's causing the build to fail. i will work with @ncborcherding to resolve that first.

zktuong · 2024-12-21T06:14:13Z

Hi @lshep, we are ready for this to be reviewed again. our tests are passing when built against R-devel and Bioc-devel https://github.com/tuonglab/dandelionR/actions/runs/12441168543

bioc-issue-bot · 2025-01-02T16:21:22Z

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mireia-bioinfo · 2025-02-10T08:16:00Z

Hi @zktuong, could you please provide a point-by-point response to my review? This will help me efficiently verify how each comment has been addressed. Thank you!

zktuong · 2025-02-10T09:06:07Z

Hi @mireia-bioinfo, sure thing. Please see below for our response:

General

Remove LICENSE.md, it is not necessary to provide two license files, copyright info is already included in LICENSE.

We removed LICENSE.md.

We prefer the master branch be clean of other application files like _pkgdown.yml. Please move the file to a different branch or remove it.

We removed _pkgdown.yml.

README

Please update README.md to display installation instructions from Bioconductor. See Bioconductor package installation instructions on any current Bioconductor package landing page.

We included in the README.md and dandelionR.Rmd to now include

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dandelionR")

NAMESPACE

You seem to be importing the miloR package as a whole, while also importing specific functions with importFrom. We encourage selective imports using importFrom than importing all using import.

We have removed where we were importing miloR and used @importFrom miloR [function] wherever possible, except for nhoods<- which we couldn't get it to work, so we had to use miloR::nhoods directly.

Man pages

Add a package-level man page (https://contributions.bioconductor.org/docs.html#package-level-documentation)

Done

R code

Wherever message() or warning() calls are used, consider adding a verbose = TRUE/FALSE argument to allow users to control whether progress messages are printed to the console.

Done. Now there's a verbose option with Default as TRUE.

requireNamespace() is only necessary for packages listed under Suggests: in the DESCRIPTION file, as they are not automatically installed or loaded. If a package is in Imports:, it is ensured to be installed when the package is installed, so there is no need to check for its availability with requireNamespace(). Instead, you should import specific functions using @importFrom package function in the documentation or call them explicitly with package::function(). Please check all your calls to requireNamespace and remove those that are unnecessary:

R/./projectProbability.R:    requireNamespace("stats")
R/./constructMarkovChain.R:    requireNamespace("Matrix")
R/./miloUmap.R:    requireNamespace("miloR")
R/./miloUmap.R:    requireNamespace("igraph")
R/./vdjPseudobulk.R:    requireNamespace("stats")
R/./getPbs.R:    requireNamespace("rlang")
R/./getPbs.R:        requireNamespace("stats")
R/./getPbs.R:        requireNamespace("Matrix")
R/./check.R:    requireNamespace("methods")
R/./check.R:    requireNamespace("methods")

We have went through and removed all requireNamespace() and used @importFrom. As mentioned above, we have to call miloR::nhoods explicitly as @importFrom miloR nhoods<- (or any variations of it) doesn't seem to work.

We encourage the use the various apply family functions over for loops (https://contributions.bioconductor.org/r-code.html#code-syntax-and-efficiency). Here are some examples of functions that use for loops:

R/./projectProbability.R:    for (i in seq_len(n)) {
R/./projectProbability.R:        for (j in seq_len(n)) {
R/./constructMarkovChain.R:    for (i in seq_len(length(waypoints))) {
R/./maxMinSampling.R:    for (ind in colnames(data)) {
R/./maxMinSampling.R:        for (k in 2:no.iterations - 1) {
R/./vdjPseudobulk.R:        for (col_n in extract_cols) {
R/./getPbs.R:        for (anno_col in col_to_take) {
R/./terminalStateFromMarkovChain.R:    for (i in cells) {
R/./splitCTgene.R:            for (item in sublist) {

We have changed all of these to using apply family functions accordingly.

To improve clarity and ensure the function’s behavior is explicit, make sure that all functions use return() to specify the value being returned. Some functions that do not explicitly return are: projectPseudotimeToCell, .maxMinSampling, miloUmap, .minMaxScale, etc.

We have added return to all of the functions.

Check

Please address as many of the remaining BiocCheck notes as possible:

ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
The longest 5 functions are:
• setupVdjPseudobulk() (R/setupVdjPseudobulk.R): 262 lines
• ...
• markovProbability() (R/markovProbability.R): 70 lines
✔ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne…
ℹ NOTE: Consider shorter lines; 267 lines (14%) are 80 characters long.
First few lines:
• R/constructMarkovChain.R#L74 aff <- exp(-(ids$x^2) / ([adaptive.st](http://adaptive.st/) ...
• ...
• vignettes/vignette_reproduce_original.rmd#L176 And that's it! We have
successfully infe ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 6 lines (0%) are not.
First few lines:
• R/vdjPseudobulk.R#L61 "v_call_ab ...
• ...
• R/vdjPseudobulk.R#L66 ), col_to_take ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.

We have fixed all of the notes and there's no more BiocCheck Notes.

Vignette

It is not entirely clear which vignette users should refer to when getting started with the package. I assume vignette_from_scRepertoire.Rmd serves this purpose, as it includes a brief package description and installation instructions. To improve clarity, I recommend renaming this vignette to dandelionR.Rmd, making it more intuitive for users to access the introductory vignette with vignette("dandelionR").

We have renamed the notebook accordingly to dandelionR.Rmd.

Style vignettes with BiocStyle and include table of contents (see https://contributions.bioconductor.org/docs.html#vignettes).

We have added this to the top of the two markdown documents.

dandelionR.md

---
title: "Starting From scRepertoire"
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
    number_sections: true
knitr:
  opts_chunk:
    dev: 'png'
    fig.align: 'left'
date: "`r Sys.Date()`"
vignette: >
  %\VignetteIndexEntry{Starting From scRepertoire}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

vignette_reproduce_original.rmd

---
title: "Reproducing the original dandelion method/paper"
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
    number_sections: true
knitr:
  opts_chunk:
    dev: 'png'
    fig.align: 'left'
date: "`r Sys.Date()`"
vignette: >
  %\VignetteIndexEntry{Reproducing the original dandelion method/paper}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

No code chunks necessary for running the vignette should be hidden for the user. Please remove include=FALSE from the chunk loading the destiny package or, since it is being loaded later, remove this specific chunk.

This is now removed completely and evaluated properly later when the destiny section comes on.

`vignette_from_scRepertoire.Rmd`

Update to display installation instructions from Bioconductor. See Bioconductor package installation instructions on any current Bioconductor package landing page.

Added now as per above.

When you mention “Check out the other vignette for an example dataset” it would be useful to include the code for accessing it: vignette("vignette_reproduce_original")

Done and added to the vignette!

mireia-bioinfo · 2025-02-14T13:44:44Z

Hi @zktuong,

Thank you for addressing all the points in my review. I just have a few remaining minor comments:

Vignette dandelionR.Rmd

When I mentioned that it would be useful to include the code for accessing the second vignette in the main one, I meant to make it visible to the users reading the vignette, so they can easely acess it if they're interested. Something like:

Check out the other vignette for an example dataset that starts from the original dandelion output associated with the original manuscript: vignette("vignette_reproduce_original").

You included the code but in a chunk with include=FALSE, which means that it doesn't appear in the rendered vignette and thus it is not visible to the people following the vignette.
The hierarchy of sections in the vignette is not well-structured. Currently, everything is placed under the 'Foreword' section. Please adjust the section headings to properly reflect the content structure.
Could you also make the vignette title more descriptive? It currently is "Starting From scRepertoire", which is a bit vague. For example, it could be something like "Single-cell immune repertoire trajectory analysis with dandelionR".

As soon as these are addressed I will proceed with accepting the package.

bioc-issue-bot · 2025-02-14T21:15:38Z

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bioc-issue-bot · 2025-02-14T21:27:01Z

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zktuong · 2025-02-14T21:34:47Z

hi @mireia-bioinfo, thanks again. I've fixed all of the below.

Vignette dandelionR.Rmd

[x] When I mentioned that it would be useful to include the code for accessing the second vignette in the main one, I meant to make it visible to the users reading the vignette, so they can easely acess it if they're interested. Something like:

Check out the other vignette for an example dataset that starts from the original dandelion output associated with the original manuscript: vignette("vignette_reproduce_original").
You included the code but in a chunk with include=FALSE, which means that it doesn't appear in the rendered vignette and thus it is not visible to the people following the vignette.

include=FALSE has been removed

[x] The hierarchy of sections in the vignette is not well-structured. Currently, everything is placed under the 'Foreword' section. Please adjust the section headings to properly reflect the content structure.

This has been fixed/reordered.

[x] Could you also make the vignette title more descriptive? It currently is "Starting From scRepertoire", which is a bit vague. For example, it could be something like "Single-cell immune repertoire trajectory analysis with dandelionR".

Yes sorry this is fixed now.

mireia-bioinfo · 2025-02-17T09:30:27Z

Hi @zktuong,

Thank you for addressing my comments. I'll go ahead and accept the package now. Thank you for your contribution to Bioconductor!

bioc-issue-bot · 2025-02-17T09:30:41Z

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

lshep · 2025-02-18T18:48:00Z

The default branch of your GitHub repository has been added to Bioconductor's
git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/zktuong.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("dandelionR"). The package 'landing page' will be created at

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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Dec 13, 2024

lshep added the 3e. pending pre-review changes review has indicated blocking concern that needs attention label Dec 18, 2024

zktuong mentioned this issue Dec 18, 2024

Fix vignette tuonglab/dandelionR#48

Merged

lshep added pre-check passed pre-review performed and ready to be added to git and removed 3e. pending pre-review changes review has indicated blocking concern that needs attention labels Jan 2, 2025

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lshep added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean labels Jan 14, 2025

bioc-issue-bot added WARNINGS and removed OK labels Feb 8, 2025

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mireia-bioinfo added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Feb 17, 2025

lshep closed this as completed Feb 18, 2025

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dandelionR #3680

dandelionR #3680

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dandelionR #3680

dandelionR #3680

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General

README

NAMESPACE

Man pages

R code

Check

Vignette

vignette_from_scRepertoire.Rmd

mireia-bioinfo commented Feb 14, 2025

Vignette dandelionR.Rmd

bioc-issue-bot commented Feb 14, 2025

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zktuong commented Feb 14, 2025

Vignette dandelionR.Rmd

mireia-bioinfo commented Feb 17, 2025

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lshep commented Feb 18, 2025

lshep commented Dec 19, 2024 •

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`vignette_from_scRepertoire.Rmd`