ningbioinfo commented 11 months ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/DavisLaboratory/hoodscanR

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 11 months ago

Hi @ningbioinfo

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: hoodscanR
Title: Spatial cellular neighbourhood scanning in R
Version: 0.99.0
Authors@R: 
    c(person(given = "Ning",
   family = "Liu",
   role = c("aut", "cre"),
   email = "liu.n@wehi.edu.au",
   comment = c(ORCID = "0000-0002-9487-9305")),
      person(given = "Jarryd",
   family = "Martin",
   role = c("aut"),
   email = "",
   comment = c(ORCID = "")))
Description: hoodscanR is an user-friendly R package providing functions to assist 
    cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. 
    All functions in the package are built based on the SpatialExperiment object, 
    allowing integration into various spatial transcriptomics-related packages from Bioconductor.
    The package can result in cell-level neighborhood annotation output, along with funtions to
    perform neighborhood colocalization analysis and neighborhood-based cell clustering.
biocViews: Spatial, Transcriptomics, SingleCell, Clustering
License: GPL-3 + file LICENSE
URL: https://github.com/DavisLaboratory/hoodscanR, https://davislaboratory.github.io/hoodscanR/
BugReports: https://github.com/DavisLaboratory/hoodscanR/issues
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports:
    knitr,
    rmarkdown,
    SpatialExperiment,
    SummarizedExperiment,
    circlize,
    ComplexHeatmap,
    scico,
    rlang,
    utils,
    ggplot2,
    grid,
    methods,
    stats,
    RANN,
    Rcpp (>= 1.0.9)
LinkingTo:
    Rcpp
Suggests:
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Depends: 
    R (>= 4.3)
VignetteBuilder: knitr

vjcitn commented 10 months ago

vignette must include prose introduction explaining purpose of package and relation to bioconductor

ningbioinfo commented 10 months ago

Hi @vjcitn , the vignette has been updated with including a paragraph of introduction of the package at the front.

bioc-issue-bot commented 10 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: hoodscanR_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): hoodscanR_0.99.0.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/hoodscanR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 10 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d7d91bd1ba3dc3a21a4fa1abeb07e32d76bb75c4

bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): hoodscanR_0.99.1.tar.gz macOS 12.6.5 Monterey: hoodscanR_0.99.1.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/hoodscanR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

HelenaLC commented 10 months ago

Hey, thanks for your submission, it is nice to see some development on spatial analyses and also directly leveraging existing Bioc infrastructure. A couple thoughts below, but nothing major. Please report back with what has/has not been addressed, or if you have any questions/need for clarity.

code

[ ] Avoid the use of sapply() and use vapply() instead (see build report). Specifically, in plot_heatmap.R line 112 numeric_cols <- sapply(df, is.numeric) should be vapply(df, is.numeric, logical(1)).
[ ] I would highly encourage implementing some minimal validity checks on input arguments, e.g., many functions expect a SpatialExperiment object with certain information (e.g., spatial coordinates). So something like is(..., "SpatialExepriment"), !is.null(spatialCoordsNames(spe)) etc. would be nice, throwing informative messages when minimal requirements aren't met. Similarly for other non-SPE arguments.

vignette

[ ] I feel the vignette currently contains only a quick start, demoing all functions with a brief comment on what they do. It would be appreciated if there was a little more explanation on what different computations are trying to achieve and how they are to be interpreted (see also comment below); less statistically inclined users may be interest in these methods from a biological perspective, but may let the know-how of what different metrics/plots mean exactly.
[ ] We encourage the use of `r BiocStyle::Biocpkg("BiocStyle")` for formatting with html_document as rendering target, i.e.,
```
output:
BiocStyle::html_document:
```
[ ] Considering making use of BiocStyle functionality to highlight/distinguish and hyperlink external package as to aid readability and directly users to these directly, e.g., `r BiocStyle::Biocpkg("SpatialExperiment")`.
[ ] Typo summarisatino -> summarisation

documentation

[ ] On the corresponding help-page, please provide a description and source information for the example dataset spe_test.
[ ] In the package help-(man-)page (?hoodscanR), it would be nice to direct users to key functions (via \code{\link{<function>}}) to grasp an idea of the main analysis workflow.
[ ] In the corresponding .man pages, more detail on theory/methodology of the underlying methods would be nice. E.g., calcMetrics(): (briefly!) what are entropy and perplexity, how are they calculated, what is there value range, how are they to be interpreted etc. (same for others).

other

[ ] In the READEME, please provide Bioconductor installation instructions using BiocManager::install().
[ ] Please properly track changes in the NEWS file; it is currently listing version 1.0.0, which never should have existed, while the DESCRIPTION is at 0.99.1.
[ ] Unit testing looks quite all right (70% overall coverage), but might be worth improving on (there's currently only 1-11 hits per line according to devtools::test_coverage()).
[ ] The LICENSE contains placeholders from the template (e.g., "<one line to give the program's name and a brief idea of what it does.> Copyright (C) "); please provide a proper one.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 77d383368456dfde6fec37e4ce8b817727520a09

bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: hoodscanR_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): hoodscanR_0.99.2.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/hoodscanR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 959bae5dcf4f296181adb03d7d91b8324bb476ef

ningbioinfo commented 10 months ago

Hi @HelenaLC , Thanks for the feedbacks.

Here are the report after addressing the feedbacks/suggestions.

Code

[x] sapply change to vapply.
[x] validity checks on inputs are now added to all functions using either is(spe, "SpatialExperiment") or is(m, "matrix") etc.

vignette

[x] Explanation of plots and algorithm inside different functions are now added to the vignette briefly.
[x] BiocStyle are now used.
[x] BiocStyle to hyperlink packages are now used.
[x] Typo summarisatino is now fixed.

documentation

[x] data description of the test data has been added.
[x] cross-link key function have added to the package help page.
[x] the equation and theory of the calcMetrics are now added in the help page.

other

[x] Bioconductor installation instructions is now added to the readme file.
[x] NEWS file is now currently listing v 0.99.1.
[x] code coverage is now almost 85%.
[x] The LICENSE placeholders is now edited.

bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): hoodscanR_0.99.3.tar.gz macOS 12.6.5 Monterey: hoodscanR_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 git@git.bioconductor.org:packages/hoodscanR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

HelenaLC commented 10 months ago

Thanks for the prompt addressing of these points. It's looking fairly good to me. On a quick glance, I have a couple suggestions to improve some parts of the code as well as "user perspective/experience"-related bits, but nothing major.

[ ] Again, please try to properly track changes in the NEWS file. It is now at 0.99.3, however, changes for previous versions are gone. Ideally, each version should be listed with a couple of bullet points briefly tracking bug fixes, additional features, general changes (e.g., "documentation revision"") etc. Perhaps have a look at how other packages do this, but of course find your own style!
[ ] For anything adding information to the input SPE and returning that, I'd be happy to see in the documentation (under "Value"/@value) where that's gone. E.g., clustByHood() stores results in the cluster slot of colData.
[ ] Complementary to the above, any function adding data should check that that slot is empty and/or expose an argument that let's them control where to store results, otherwise the user's data might be unintentionally overwritten. E.g., cluster might be something that users have already used up previously.
[ ] I'd suggest to check that spatial coordinates are actually defined in the input SPE (i.e., !is.null(spatialCoordsNames(spe))) everywhere they are needed, as their absence gives a quite confusing error, specially to novice users, e.g.:
```
> spatialCoords(spe) <- NULL
> findNearCells(spe, k = 100)
Error in dimnames(x) <- dn : 
length of 'dimnames' [2]
not equal to array extent
```
[ ] calc_metrics.R lines 53+ could be written as colData(spe)[colnames(result)] <- result
[ ] utils.R line 10+ argument rn="rwoname" should be "rowname"
[ ] merge_by_group.R lines 38+ initializes an empty data.frame that's filled with a for-loop. That sort of thing can be written as (also note the conversion of a logial to numeric matrix via 1*):
```
out_df <- vapply(uniquegroups, \(g) {
mask <- 1 * (group_df == g)
rowSums(mask * pm)[rownames(df)]
}, numeric(nrow(df)))
```

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4665e5b75872a2e98b1369fe5e358212ea24d321

ningbioinfo commented 10 months ago

Hi @HelenaLC , thanks for the comments, quite useful!

[x] NEWS file updated, listed what I've changed since the first submission.
[x] output values are now all specified in the value slot of the documentation.
[x] parameter val_names is added to relevant functions now, allowing user to define output names if necessary.
[x] spatialCoordsNames check is now added to both findNearCells() and readHoodData().
[x] for loop is now gone. Same as in the mergeHoodSpe().
[x] typo is fixed.
[x] Thanks for this vapply, works really good, have replaced the for loop.

bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): hoodscanR_0.99.4.tar.gz macOS 12.6.5 Monterey: hoodscanR_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 git@git.bioconductor.org:packages/hoodscanR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

HelenaLC commented 10 months ago

Fantastic. Note that merge_by_group.R lines 38-40 can be dropped now, and any commented out code should also be removed eventually. - happy to accept.

bioc-issue-bot commented 10 months ago

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.

bioc-issue-bot commented 10 months ago

cannot build unless issue is open and has the 'pre-review' label or '2. review in progress' label, or is closed and has the 'TESTING' label.

lshep commented 10 months ago

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/ningbioinfo.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

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(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("hoodscanR"). 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.

Bioconductor / Contributions

hoodscanR #3117

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