[REVIEW]: MitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell datasets

[editorialbot]

Submitting author: @gabrielelubatti (Gabriele Lubatti)
Repository: https://github.com/ScialdoneLab/MitoHEAR
Branch with paper.md (empty if default branch): master
Version: v1.0.1
Editor: @csoneson
Reviewers: @BatoolMM, @juanvillada
Archive: 10.5281/zenodo.6598821

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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

@BatoolMM & @sahilseth & @juanvillada, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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

Checklists

📝 Checklist for @BatoolMM

📝 Checklist for @sahilseth

📝 Checklist for @juanvillada

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (375.8 files/s, 96005.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               10            746            439           1607
Rmd                              4            602            398            445
Markdown                         2             70              0            197
TeX                              1             10              0             83
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            18           1428            837           2333
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1101/2021.03.08.434450 is OK
- 10.1016/j.cell.2019.01.022 is OK
- 10.1093/bioinformatics/btab358 is OK
- 10.1101/2020.11.23.394569 is OK
- 10.1038/s42255-021-00422-7 is OK
- 10.15252/embr.201949612 is OK
- 10.1038/s41556-017-0017-8 is OK

MISSING DOIs

- None

INVALID DOIs

- doi.org/10.1038/nrg3966 is INVALID because of 'doi.org/' prefix

[editorialbot]

Wordcount for paper.md is 641

[editorialbot]

Failed to discover a valid open source license

[sahilseth]

Review checklist for @sahilseth

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 https://github.com/ScialdoneLab/MitoHEAR?
• 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 (@gabrielelubatti) 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?

[csoneson]

👋🏼 @gabrielelubatti, @BatoolMM, @sahilseth, @juanvillada - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

[editorialbot]

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

[BatoolMM]

Review checklist for @BatoolMM

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 https://github.com/ScialdoneLab/MitoHEAR?
• 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 (@gabrielelubatti) 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?

[csoneson]

👋🏻 Hi all - just wanted to check in on how the reviews are coming along? Don't hesitate to let me know if you have questions. Thanks!

[BatoolMM]

@csoneson Apologies for the delay, I expect to finish my review by the 18th of April, if that's OK!

[csoneson]

That's perfect, thanks @BatoolMM!

[juanvillada]

Hi @csoneson, thanks for the reminder. I am aiming to be done this weekend. Best!

[juanvillada]

Review checklist for @juanvillada

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 https://github.com/ScialdoneLab/MitoHEAR?
• 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 (@gabrielelubatti) 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?

[BatoolMM]

Did anyone of the reviewers have a piece of luck in installing the package MitoHEAR! I can't seem to install it in my local machine - I was going to open an issue in the repository but checking with @sahilseth and @juanvillada beforehand! It can be something with my local environment and R version!

[BatoolMM]

I managed to install it from GitHub - checking now the tests and quality!

[juanvillada]

1. On installation

Hi all, I managed to install MitoHEAR in Debian (linux kernel 5.10.104) with the latest R v4.1.3. I used a Docker container so I could track potential installation issues faced by users that have no pre-installed R libraries.

The issue I found was regarding the libraries required by MitoHEAR:

ERROR: dependencies ‘Biostrings’, ‘ComplexHeatmap’, ‘GenomicRanges’, ‘IRanges’, ‘rlist’, ‘Rsamtools’ are not available for package ‘MitoHEAR’

---

Note: I had to make sure curl and xml were properly installed in the system to avoid further error messages. I am in Debian, so in my case I used:

apt-get install libcurl4-gnutls-dev
apt-get install libxml2-dev

---

I then tried to install the dependencies:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")
BiocManager::install("ComplexHeatmap")
BiocManager::install("GenomicRanges")
BiocManager::install("rlist")
BiocManager::install("Rsamtools")

And I finally was able to successfully install MitoHEAR with:

install.packages("MitoHEAR")

@gabrielelubatti it would be great if you could add the dependencies to the installation instructions as suggested in https://joss.readthedocs.io/en/latest/review_criteria.html#installation-instructions.

[juanvillada]

2. On functionality

Most functionality could be reproduced. It is great the authors provided the reproducible notebooks, thanks!

Other comments:

2.1. Function: get_raw_counts_allele ⚠️

I could not reproduce the example for the function get_raw_counts_allele. I think this example/test should be better automated. I can load the input and inspect the input data, I can load the expected output and inspect the output data; but it is difficult to generate the output from the input with the instructions given in the documentation.

@gabrielelubatti there moght better options but I am thinking if it would be possible to host the required .bam and .bai files in a .tar.gz file? and then use the R functions download.file() and untar() to download and extract these data? I believe this can help potential users to have the testing data ready in a more automated way rather to having to download the files manually to test this function?

2.2. Function: get_heteroplasmy ✅

• Rewording

starts from the output of get_raw_counts and performs a two step (...)

should be

starts from the output of get_raw_counts*_allele* and performs a two step (...)

I was able to reproduce the example provided for this function.

Vignettes

I took advantage of the availability of these cool vignettes/notebooks to further test the functionality of MitoHEAR, here are some notes:

2.3. Notebook: cell_competition_mt_example_notebook.Rmd ✅⚠️

Please be explicit with the dependencies for this notebook, I found these issues:

⚠️ Dependency karyoploteR and regioneR

  Package karyoploteR and regioneR needed for this function to work. Please install them: BiocManager::install('karyoploteR') and BiocManager::install('regioneR')

⚠️ Dependency gam

Error in dpt_test(heteroplasmy_matrix_ci[, relevant_bases], time, index_ci,  :
  Package gam needed for method==gam. Please install it: install.packages('gam')

⚠️ Dependency fmsb

Error in plot_spider_chart(colnames(sum_matrix_qc)[1], cluster_ci, heteroplasmy_matrix_ci,  :
  Package fmsb needed for this function. Please install it: install.packages('fmsb')

2.4. Notebook: cell_competition_bulk_data_mt_example_notebook.Rmd ⚠️

⚠️ bulk_data_competition[[5]] is NULL

index_bulk <- bulk_data_competition[[5]]
index_bulk
# NULL

2.5. Notebook: lineage_tracing_example_notebook.Rmd ⚠️

⚠️ Line 81: sc_data[[5]] is NULL

index_sc <- sc_data[[5]]
index_sc
# NULL

⚠️ Line 130: sc_data[[5]] is NULL

index_sc <- sc_data[[5]]
index_sc
# NULL

⚠️ Line 234: sc_data[[5]] is NULL

index_sc <- sc_data[[5]]
index_sc
# NULL

2.6. Notebook: Ludwig_et_al_example_notebook.Rmd

⚠️ Line 73: tfi_fig_2[[5]] is NULL

index_ci <- tfi_fig_2[[5]]
index_ci
# NULL

✅ Line 291: Here donor_1_2[[5]] is NOT NULL. I am wondering if this has something to do with the fact that in this case:

"We don't execute the function get_raw_counts_allele here and we directly load his output. "

index_ci <- donor_1_2[[5]]
index_ci
# Juan's note: Output looks as expected

I was able to test this notebook til Line 356 (Unsupervised cluster analysis among cells based on allele frequency values). My session is killed after a while and I have not found the reason, but I guess is due to my RAM availabity, I will try this again with more RAM soon.

[juanvillada]

3. On references:

It would be nice to use consistent journal names. Some are abbreviated and some are not.

• Nat Cell Biol
• Nat Metab
• EMBO Rep
• Nat Rev Gen

[BatoolMM]

Thank you @juanvillada - The License is also listed differently in two places: Artistic-2.0 in DESCRIPTION whereas it says GPL-3 in the main GitHub repo.

[juanvillada]

🐳

I have created a public Docker image with all the required dependencies in case we need it to further test MitoHEAR.

https://hub.docker.com/r/biovillada/r-base-mitohear

[gabrielelubatti]

Dear @juanvillada and @BatoolMM , thanks for your comments and feedback! I will work on these soon and let you know.
Regarding the problem with the fifth element of the output given by function get_heteroplasmy (that in some notebooks is NULL), this is something expected.
In the documentation for the get_heteroplasmy, in the section value, for the fifth element is written "Indices of the samples that cover a base, for all bases and samples that pass the two consequentially filtering steps; if all the samples cover all the bases, then index is NULL". So basically if the parameter "filtering" in function get_heteroplasmy is equal to 1, then the fifth element of the output is NULL, if filtering is equal to 2, then the fifth element is not NULL.

[gabrielelubatti]

Regarding the comments from @juanvillada:

• On installation

1. Using BiocManager::install("MitoHEAR") instead of install.packages("MitoHEAR") should resolve the issue with installation (since the error arises for libraries on Bioconductor). I added an example in the installation section of the README file in the GitHub repo.

• On functionality

1. I modified the example for the function get_raw_counts_allele, using download.file() and untar() functions in order to make the test more automated.

• Vignettes

1. For the notebook "cell_competition_mt_example_notebook.Rmd" I added a sentence and a chunk of code at the beginning of the script, specifying the dependencies.
2. For the problem with the fifth element of the output given by function get_heteroplasmy, in addition to what I wrote in my previous comment, I slightly changed the documentation of get_heteroplasmy, in order to make things clearer.

• On references

1. Regarding the references, I abbreviated them in order to keep consistency.

[gabrielelubatti]

Regarding the comments from @BatoolMM:
I changed the license in the DESCRIPTION file, in order to be consistent with the one in the main GitHub repo (GPL-3).

[csoneson]

Excellent, thanks. I'm going to hand off now to the associate EiC on rotation for the last steps. Thanks for submitting to JOSS!

[csoneson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/s41587-022-01210-8 is OK
- 10.1016/j.cell.2019.01.022 is OK
- 10.1093/bioinformatics/btab358 is OK
- 10.1186/s12864-021-07974-8 is OK
- 10.1038/s42255-021-00422-7 is OK
- 10.15252/embr.201949612 is OK
- 10.1038/nrg3966 is OK
- 10.1038/s41556-017-0017-8 is OK
- 10.1093/bioinformatics/btu483 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error prepararing paper acceptance. The generated XML metadata file is invalid.

ID figU003Aflowshart already defined
ID figU003Aflowshart already defined

[csoneson]

@gabrielelubatti - looks like there is an issue with the figure labels - all the figures have \label{fig:flowshart}. Could you rename them to have different labels, and we'll try again.

[gabrielelubatti]

Hello @csoneson I should have renamed the labels of the figures.

[csoneson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/s41587-022-01210-8 is OK
- 10.1016/j.cell.2019.01.022 is OK
- 10.1093/bioinformatics/btab358 is OK
- 10.1186/s12864-021-07974-8 is OK
- 10.1038/s42255-021-00422-7 is OK
- 10.15252/embr.201949612 is OK
- 10.1038/nrg3966 is OK
- 10.1038/s41556-017-0017-8 is OK
- 10.1093/bioinformatics/btu483 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3253

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3253, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

👋 @gabrielelubatti - I'm the AEiC on duty this week, handing the rest of the publication process for your paper. I have some suggested changes in ScialdoneLab/MitoHEAR#6 - please merge this or let me know what you disagree with, then we can proceed.

[gabrielelubatti]

Dear @danielskatz, thanks for your suggestions. I merged the changes.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/s41587-022-01210-8 is OK
- 10.1016/j.cell.2019.01.022 is OK
- 10.1093/bioinformatics/btab358 is OK
- 10.1186/s12864-021-07974-8 is OK
- 10.1038/s42255-021-00422-7 is OK
- 10.15252/embr.201949612 is OK
- 10.1038/nrg3966 is OK
- 10.1038/s41556-017-0017-8 is OK
- 10.1093/bioinformatics/btu483 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3255

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3255, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04265 joss-papers#3256
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04265
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...

[danielskatz]

Congratulations to @gabrielelubatti (Gabriele Lubatti) and co-authors!!

And thanks to @BatoolMM and @juanvillada for reviewing, and @csoneson for editing!
We couldn't do this without you

[editorialbot]

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[gabrielelubatti]

Thanks @BatoolMM and @juanvillada for the very useful comments and feedbacks and @csoneson for editing!