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

[whedon]

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

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Markdown: [![status](https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536/status.svg)](https://joss.theoj.org/papers/bba2b08ac88581cfd5cf446686183536)

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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:

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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

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• 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?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• 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?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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]

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

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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:

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

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]

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

 Can't find any papers to compile :-(

[osorensen]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[wiljnich]

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]

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]

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]

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]

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

[jonjoncardoso]

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 <#4074 (comment)>, 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]

@whedon generate pdf from branch paper

[whedon]

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

[osorensen]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[osorensen]

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]

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]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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]

@whedon generate pdf from branch paper

[osorensen]

@whedon set <v1.0.0> as versino

[whedon]

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

@whedon commands

[osorensen]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[osorensen]

@whedon recommend-accept from branch paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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]

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

Check final proof 👉 openjournals/joss-papers#2923

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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]

@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]

@whedon accept deposit=true from branch paper

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04074 joss-papers#2931
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04074
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

Congratulations @rhenkin on getting this work published in JOSS! 🎉

Thanks for editing @osorensen, and thanks @jonjoncardoso and @wiljnich for your review efforts.

[Kevin-Mattheus-Moerman]

@openjournals/dev the DOI link does not show the paper pdf for me yet. It is taking longer than usual. I'll check in again later.

[danielskatz]

It's working for me now

[rhenkin]

Congratulations @rhenkin on getting this work published in JOSS! 🎉

Thanks for editing @osorensen, and thanks @jonjoncardoso and @wiljnich for your review efforts.

Thanks @Kevin-Mattheus-Moerman! Also many thanks to @osorensen @jonjoncardoso @wiljnich

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04074/status.svg)](https://doi.org/10.21105/joss.04074)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04074">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04074/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04074/status.svg
   :target: https://doi.org/10.21105/joss.04074

This is how it will look in your documentation:

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