[REVIEW]: visxhclust: An R Shiny package for visual exploration of hierarchical clustering

whedon commented 2 years ago

Submitting author: @rhenkin (Rafael Henkin) Repository: https://github.com/rhenkin/visxhclust Version: v1.0.0 Editor: @osorensen Reviewer: @jonjoncardoso, @wiljnich Archive: 10.5281/zenodo.5946818

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536"><img src="https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536/status.svg)](https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jonjoncardoso & @wiljnich, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @jonjoncardoso

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rhenkin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @wiljnich

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rhenkin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jonjoncardoso, @wiljnich it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (987.6 files/s, 126289.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            42           1950            523           5693
R                               27            183            611           1769
Markdown                        14            160              0            611
CSS                              5             99             60            432
JavaScript                       5             68             39            290
Rmd                              4             62            116             60
YAML                             2              8              2             39
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           100           2530           1352           8905
-------------------------------------------------------------------------------

Statistical information for the repository '461a88a6a5a2935929606363' was
gathered on 2022/01/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Rafael Henkin                    4           538              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Rafael Henkin               538          100.0          0.8               11.52

whedon commented 2 years ago

PDF failed to compile for issue #4074 with the following error:

 Can't find any papers to compile :-(

osorensen commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

wiljnich commented 2 years ago

I'm pleased with this work and have no acceptance-blocking comments. The only outstanding concern I have is the lack of a reference to the documentation page (rhenkin.github.io/visxhclust/) in the README, because several of the key elements of the documentation (e.g. how to open an issue, examples analyses) are exclusively on that site. I would recommend either referring the user to that site via your README, or duplicating several of those elements in the README.

This is great work and I'm happy to see it move towards publication.

jonjoncardoso commented 2 years ago

This is a great package, the installation and example worked and it is a useful dashboard to explore data visually.

The only thing I felt lacking was a CONTRIBUTING.md so as to adhere to the journal's checklist: Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Other than that, I am happy to accept this work.

osorensen commented 2 years ago

Thanks for your reviews @jonjoncardoso and @wiljnich.

@rhenkin, please consider the point raised by @jonjoncardoso in his review, and let us now when it has been addressed.

rhenkin commented 2 years ago

Thanks for the feedback! @wiljnich I have updated the README.md, having fixed the links to the documentation guides while also changing a bit how it's structured (added a getting started section). @jonjoncardoso I added a CONTRIBUTING.md file and I also linked to do it in the README.md file. @osorensen I addressed the main issue and @wiljnich's comment, all changes are in the main repo (not the paper branch).

whedon commented 2 years ago

:wave: @jonjoncardoso, please update us on how your review is going (this is an automated reminder).

jonjoncardoso commented 2 years ago

All good from me.

On Wed, 2 Feb 2022 at 06:52 whedon @.***> wrote:

👋 @jonjoncardoso https://github.com/jonjoncardoso, please update us on how your review is going (this is an automated reminder).

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4074#issuecomment-1027638240, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG2Z7WQ63QKPBCA3PHM7H3UZDID7ANCNFSM5MJC3VEQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Jonathan Cardoso-Silva, PhD Data Science Institute/Department of Methodology London School of Economics and Political Science

osorensen commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

osorensen commented 2 years ago

@whedon check references from branch paper

whedon commented 2 years ago

Attempting to check references... from custom branch paper

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btv428 is OK
- 10.1007/978-3-540-70956-5_7 is OK
- 10.1111/1467-9868.00293 is OK
- 10.1093/nar/gkv468 is OK

MISSING DOIs

- 10.1093/bioinformatics/btw313 may be a valid DOI for title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data

INVALID DOIs

- None

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btv428 is OK
- 10.1007/978-3-540-70956-5_7 is OK
- 10.1111/1467-9868.00293 is OK
- 10.1093/nar/gkv468 is OK

MISSING DOIs

- 10.1093/bioinformatics/btw313 may be a valid DOI for title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data

INVALID DOIs

- None

@rhenkin, could you please check if the DOI suggested by whedon is correct, and if so, add it to the paper?

osorensen commented 2 years ago

Next, @rhenkin, could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

Meanwhile I will read through the paper once more, and get back to you if I have any further comments.

rhenkin commented 2 years ago

@whedon check references from branch paper

whedon commented 2 years ago

Attempting to check references... from custom branch paper

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btv428 is OK
- 10.1007/978-3-540-70956-5_7 is OK
- 10.1111/1467-9868.00293 is OK
- 10.1093/bioinformatics/btw313 is OK
- 10.1093/nar/gkv468 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rhenkin commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

@rhenkin, there is a typo in the first word of the Summary section "visxchlust --> visxhclust"

osorensen commented 2 years ago

@rhenkin, the same typo is also on line 26. Please do a find-and-replace to see if there are more.

osorensen commented 2 years ago

@rhenkin, on line 38, it says "see figure Figure 1". Please de-duplicate.

osorensen commented 2 years ago

@rhenkin, some correction of the reference list:

Please make sure R is spelled with a capital letter. Adding curly brackets around the word "R" in your .bib file should fix it. For example, change the reference to Shiny to

@Manual{Shiny,
title = {shiny: Web Application Framework for {R}},
author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
year = {2021},
note = {R package version 1.7.1},
url = {https://CRAN.R-project.org/package=shiny},
}

This also applies to

Galili, T. (2015). Dendextend: An r package for visualizing, adjusting, and comparing trees of hierarchical clustering. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv428

and

Nijs, V. (2021). Radiant: Business analytics using r and shiny. https://cran.r-project.org/ web/packages/radiant/index.html

rhenkin commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rhenkin commented 2 years ago

@osorensen the release version is v1.0.0, the DOI on Zenodo is 10.5281/zenodo.5946818 https://doi.org/10.5281/zenodo.5946817 I fixed the typos and references and generated the PDF again above

osorensen commented 2 years ago

@whedon set doi as 10.5281/zenodo.5946818

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

osorensen commented 2 years ago

@whedon set 10.5281/zenodo.5946818 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5946818 is the archive.

osorensen commented 2 years ago

@whedon set <v1.0.0> as versino

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

osorensen commented 2 years ago

@whedon set v1.0.0 as version

whedon commented 2 years ago

OK. v1.0.0 is the version.

osorensen commented 2 years ago

@whedon recommend-accept from branch paper

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btv428 is OK
- 10.1007/978-3-540-70956-5_7 is OK
- 10.1111/1467-9868.00293 is OK
- 10.1093/bioinformatics/btw313 is OK
- 10.1093/nar/gkv468 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2923

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2923, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper

Kevin-Mattheus-Moerman commented 2 years ago

@rhenkin @osorensen I have read the paper and inspected the archive and all seems in order to proceed with acceptance in JOSS.

Kevin-Mattheus-Moerman commented 2 years ago

@whedon accept deposit=true from branch paper

whedon commented 2 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

openjournals / joss-reviews