[REVIEW]: APackOfTheClones: Visualization of clonal expansion with circle packing

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[REVIEW]: APackOfTheClones: Visualization of clonal expansion with circle packing #6868

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@Qile0317@skanwal<!--end-editor-- Reviewers: @ncborcherding, @jspaezp Archive: Pending

Status

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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

@ncborcherding & @jspaezp, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

📝 Checklist for @ncborcherding

editorialbot commented 1 month ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1779.7 files/s, 225713.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               51           1198           1370           4856
SVG                             14              0              0           1158
C/C++ Header                     5            202             53            695
C++                              8             96             48            563
Rmd                              6            282            561            414
Markdown                         7            154              0            338
TeX                              1             26              0            259
YAML                             6             36             12            212
JSON                             1              0              0             23
-------------------------------------------------------------------------------
SUM:                            99           1994           2044           8518
-------------------------------------------------------------------------------

Commit count by author:

   241  Qile0317
   182  Qile

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1056

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.21769/BioProtoc.4735 is OK
- 10.1137/141000671 is OK
- 10.21769/BioProtoc.4735 is OK
- 10.18637/jss.v040.i08 is OK

MISSING DOIs

- 10.1016/j.imlet.2014.10.011 may be a valid DOI for title: The activation of the adaptive immune system: cros...
- 10.1016/j.jaccao.2022.08.012 may be a valid DOI for title: The role of single-cell profiling and deep immunop...
- 10.1038/s41587-023-01767-y may be a valid DOI for title: Dictionary learning for integrative, multimodal an...
- No DOI given, and none found for title: Single-cell analysis pinpoints distinct population...
- No DOI given, and none found for title: Recombinant multimeric dog allergen prevents airwa...
- 10.1016/j.imlet.2014.10.011 may be a valid DOI for title: The activation of the adaptive immune system: cros...
- 10.37473/dac/10.1101/2020.04.10.035865 may be a valid DOI for title: Scirpy: a Scanpy extension for analyzing single-ce...
- 10.1016/j.jaccao.2022.08.012 may be a valid DOI for title: The role of single-cell profiling and deep immunop...
- 10.1038/s41587-023-01767-y may be a valid DOI for title: Dictionary learning for integrative, multimodal an...
- No DOI given, and none found for title: Tutorial: guidelines for the computational analysi...
- No DOI given, and none found for title: Single-cell analysis pinpoints distinct population...
- No DOI given, and none found for title: Recombinant multimeric dog allergen prevents airwa...
- No DOI given, and none found for title: Integrated analysis of multimodal single-cell data
- 10.12688/f1000research.22139.1 may be a valid DOI for title: scRepertoire: An R-based toolkit for single-cell i...
- 10.1038/s41577-020-0307-4 may be a valid DOI for title: Clonal expansion of innate and adaptive lymphocyte...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- 10.1038/s41421-021-00280-3 may be a valid DOI for title: Single-cell transcriptome and TCR profiling reveal...
- No DOI given, and none found for title: Integrated analysis of multimodal single-cell data
- 10.1038/s42003-020-01625-6 may be a valid DOI for title: Mapping the immune environment in clear cell renal...
- 10.1038/s41577-020-0307-4 may be a valid DOI for title: Clonal expansion of innate and adaptive lymphocyte...
- 10.1038/s41421-021-00280-3 may be a valid DOI for title: Single-cell transcriptome and TCR profiling reveal...
- No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis

INVALID DOIs

- None

editorialbot commented 1 month ago

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

jspaezp commented 1 month ago

Review checklist for @jspaezp

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

[ ] Repository: Is the source code for this software available at the https://github.com/Qile0317/APackOfTheClones?
[ ] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@Qile0317) 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
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[ ] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[ ] 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?

jspaezp commented 1 month ago

@Qile0317 Would you mind fixing the DOIs flagged by the editorial bot?

Qile0317 commented 1 month ago

@Qile0317 Would you mind fixing the DOIs flagged by the editorial bot?

soz for the late reply - will get on that this weekend.

Here is my personal checklist for each doi to fix - if it is ticked then I've checked and either made sure to add it to my paper.bib file, or the source was a duplicate, or the source has no DOI (Like R and ggplot):

[x] 10.1016/j.imlet.2014.10.011 may be a valid DOI for title: The activation of the adaptive immune system: cros...
[x] 10.1016/j.jaccao.2022.08.012 may be a valid DOI for title: The role of single-cell profiling and deep immunop...
[x] 10.1038/s41587-023-01767-y may be a valid DOI for title: Dictionary learning for integrative, multimodal an...
[x] No DOI given, and none found for title: Single-cell analysis pinpoints distinct population...
[x] No DOI given, and none found for title: Recombinant multimeric dog allergen prevents airwa...
[x] 10.1016/j.imlet.2014.10.011 may be a valid DOI for title: The activation of the adaptive immune system: cros...
[x] 10.37473/dac/10.1101/2020.04.10.035865 may be a valid DOI for title: Scirpy: a Scanpy extension for analyzing single-ce...
[x] 10.1016/j.jaccao.2022.08.012 may be a valid DOI for title: The role of single-cell profiling and deep immunop...
[x] 10.1038/s41587-023-01767-y may be a valid DOI for title: Dictionary learning for integrative, multimodal an...
[x] No DOI given, and none found for title: Tutorial: guidelines for the computational analysi...
[x] No DOI given, and none found for title: Single-cell analysis pinpoints distinct population...
[x] No DOI given, and none found for title: Recombinant multimeric dog allergen prevents airwa...
[x] No DOI given, and none found for title: Integrated analysis of multimodal single-cell data
[x] 10.12688/f1000research.22139.1 may be a valid DOI for title: scRepertoire: An R-based toolkit for single-cell i...
[x] 10.1038/s41577-020-0307-4 may be a valid DOI for title: Clonal expansion of innate and adaptive lymphocyte...
[x] No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
[x] 10.1038/s41421-021-00280-3 may be a valid DOI for title: Single-cell transcriptome and TCR profiling reveal...
[x] No DOI given, and none found for title: Integrated analysis of multimodal single-cell data
[x] 10.1038/s42003-020-01625-6 may be a valid DOI for title: Mapping the immune environment in clear cell renal...
[x] 10.1038/s41577-020-0307-4 may be a valid DOI for title: Clonal expansion of innate and adaptive lymphocyte...
[x] 10.1038/s41421-021-00280-3 may be a valid DOI for title: Single-cell transcriptome and TCR profiling reveal...
[x] No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis

Qile0317 commented 4 weeks ago

@editorialbot check references

editorialbot commented 4 weeks ago

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

OK DOIs

- 10.1016/j.imlet.2014.10.011 is OK
- 10.1016/j.jaccao.2022.08.012 is OK
- 10.1038/s41587-023-01767-y is OK
- 10.1126/sciimmunol.abg6356 is OK
- 10.1111/all.15399 is OK
- 10.3389/fimmu.2019.00360 is OK
- 10.37473/dac/10.1101/2020.04.10.035865 is OK
- 10.1016/j.jaccao.2022.08.012 is OK
- 10.1038/s41596-020-00409-w is OK
- 10.12688/f1000research.22139.2 is OK
- 10.1038/s41577-020-0307-4 is OK
- 10.1137/141000671 is OK
- 10.1038/s41421-021-00280-3 is OK
- 10.21769/BioProtoc.4735 is OK
- 10.1038/s42003-020-01625-6 is OK
- 10.21769/BioProtoc.4735 is OK
- 10.18637/jss.v040.i08 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis

INVALID DOIs

- None

Qile0317 commented 4 weeks ago

@jspaezp DOIs are now all fixed where available - lemme know if there's anything else I could help with to speed up the process

ncborcherding commented 3 weeks ago

Review checklist for @ncborcherding

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 https://github.com/Qile0317/APackOfTheClones?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Qile0317) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

ncborcherding commented 3 weeks ago

@Qile0317 Grammar/Quality of Writing issue per below issue.

https://github.com/Qile0317/APackOfTheClones/issues/10#issue-2375632966

Qile0317 commented 3 weeks ago

Grammar issues have been fixed to the best of my efforts.

A question to both @ncborcherding and @jspaezp - if you check the comments on the sourcecode of my paper - would you think it is nessecary to have further discussions on the other features of the package? Though it may not be the most useful, there are functions for getting and filtering clone sizes, highlighting clonotypes, and adding links between shared clones.

Additionally, should the code used to reproduce the main figure be included in the paper? Although I'm unsure if this aligns with JOSS's principles? @skanwal

skanwal commented 3 weeks ago

@Qile0317 - can you please elaborate - why do you think this won't align with JOSS principles?

jspaezp commented 2 weeks ago

@editorialbot generate pdf

editorialbot commented 2 weeks ago

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