[PRE REVIEW]: funkyheatmap: Visualising data frames with mixed data types

[editorialbot]

Submitting author: @LouiseDck (Louise Deconinck)
Repository: https://github.com/funkyheatmap/funkyheatmap
Branch with paper.md (empty if default branch):
Version: 0.5.0
Editor: Pending
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/4345bc25b2c78ea510e09b51fa1ef990/status.svg)](https://joss.theoj.org/papers/4345bc25b2c78ea510e09b51fa1ef990)

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1585.8 files/s, 234964.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              0           3950
R                               43            327            737           2919
YAML                             8             67             12            400
Markdown                         5            122              0            313
Rmd                              5            149            292            296
TeX                              2             14              0            151
JSON                             1              1              0             14
Bourne Shell                     1              3              2             10
-------------------------------------------------------------------------------
SUM:                            66            683           1043           8053
-------------------------------------------------------------------------------

Commit count by author:

   120	Robrecht Cannoodt
     5	Louise Deconinck
     1	Luke Zappia
     1	dependabot[bot]

[editorialbot]

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

✅ OK DOIs

- 10.1007/978-0-387-98141-3 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/TVCG.2011.185 is OK
- 10.1038/s41587-019-0071-9 is OK
- 10.1038/s41592-021-01336-8 is OK
- 10.1038/s41587-020-0469-4 is OK
- 10.1101/642926 is OK
- 10.1093/bioinformatics/btac805 is OK
- 10.1101/2023.03.22.533802 is OK
- 10.48550/arXiv.2110.11494 is OK
- 10.1038/s41467-023-37168-7 is OK
- 10.21203/rs.3.rs-4181617/v1 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 902

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Robrecht Cannoodt*, perhaps the affiliations index need quoting?.

[danielskatz]

👋 @LouiseDck - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[LouiseDck]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[danielskatz]

👋 @LouiseDck - please add countries to all affiliations.

I'm also unsure why you use "{funkyheatmap}" in your paper in a number of places. Are the {}s coming from some type of formatting instruction?

Also, there is a References heading missing at the end of the paper, so the references look like they are part of the Acknowledgments. Please add this.

Finally, I am going to ask the JOSS editors to take a look at this, as it's not clear to me that this is research software as defined by JOSS. You should hear back in a couple of weeks or so, due to the holidays.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[LouiseDck]

@editorialbot generate pdf

Thanks @danielskatz for the speed of your reply! I've adapted the references and added the references section. I hope this will be fine now 🤞

The curly-brace thing is a convention in the R community, and is used to denote the name of a package. I don't know where this convention originated, but it is common and still in use, e.g: here

If I may make a case for this piece of software: I think benchmarking is a key part of the scientific process, and software like this enhances the usability of these benchmarks -- For big benchmarks it's a very useful way to communicate results clearly (you simply can't do this effectively with only a huge table full of numbers). For that reason I do think it fits within "extracting knowledge from data" or "supports the execution of research experiments" (as a benchmarking study is a kind of research experiment.)
But of course I will await the editorial review, thanks for the consideration!

[editorialbot]

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

[editorialbot]

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[LouiseDck]

@editorialbot generate pdf

Sorry, this should be fine now 😅

[editorialbot]

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

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[rcannood]

@danielskatz Thanks for being the managing EiC for this submission!

Finally, I am going to ask the JOSS editors to take a look at this, as it's not clear to me that this is research software as defined by JOSS. You should hear back in a couple of weeks or so, due to the holidays.

Just to weigh in on this -- I would argue it definitely falls under JOSS' definition of research software:

JOSS publishes articles about research software. This definition includes software that: solves complex modeling problems in a scientific context (physics, mathematics, biology, medicine, social science, neuroscience, engineering); supports the functioning of research instruments or the execution of research experiments; extracts knowledge from large data sets; offers a mathematical library, or similar. While useful for many areas of research, pre-trained machine learning models and notebooks are not in-scope for JOSS.

Since this package was developed and specifically catered to being able to showcase results from (bioinformatics) benchmarking studies. Therefore it supports the execution of research experiments, and extracts knowledge from the raw benchmarking results. A showcase of which studies (derivatives of) funkyheatmap have been used in is shown here.

An example of how funkyheatmap extracts knowledge from large datasets: on the openproblems website funkyheatmap is used to summarise the results ( https://openproblems.bio/results/label_projection/ ) based on the raw data from the benchmark ( https://openproblems.bio/results/label_projection/data/results.json ).

One final note, it was originally part of a repository from a different study ( https://github.com/dynverse/dynbenchmark/blob/master/package/R/funky_heatmap.R ) but we decided to turn into a standalone package since there was a lot of interest from the research community.

🙇 Thank you for taking this into consideration and hope for a positive response.