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[REVIEW]: graphsim: An R package for simulating gene expression data from graph structures of biological pathways #2161

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @TomKellyGenetics (S. Thomas Kelly) Repository: https://github.com/TomKellyGenetics/graphsim Version: v1.0.0-joss Editor: @majensen Reviewer: @rcannood, @corybrunson Archive: 10.5281/zenodo.3931288

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whedon commented 4 years ago

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

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1186/gb-2014-15-2-r29 is OK
- 10.1186/1752-0509-3-41 is OK
- 10.1093/bioinformatics/btm639 is OK
- 10.1016/j.copbio.2007.11.005 is OK
- 10.1515/jib-2017-0027 is OK
- 10.1093/imanum/22.3.329 is OK
- 10.1186/s13062-015-0086-1 is OK
- 10.1101/gad.11.13.1748 is OK
- 10.1093/bioinformatics/btp174 is OK
- 10.1093/bioinformatics/btu736 is OK
- 10.1093/hmg/ddu309 is OK
- 10.1016/0022-2836(75)90213-2 is OK
- 10.1016/j.socnet.2004.11.008 is OK
- 10.1007/BF01386390 is OK
- 10.1177/1558689812454457 is OK
- 10.1111/j.1651-2227.2006.00178.x is OK
- 10.1016/j.patrec.2005.10.010 is OK
- 10.1124/jpet.103.064824 is OK
- 10.1016/j.cell.2009.02.024 is OK
- 10.1103/PhysRevLett.87.198701 is OK
- 10.1039/C3MB25589A is OK
- 10.1186/gb-2010-11-3-r25 is OK
- 10.1186/1471-2407-14-552 is OK
- 10.1016/j.fob.2012.04.003 is OK
- 10.1200/JCO.2008.18.1370 is OK
- 10.1016/S0169-7552(98)00110-X is OK
- 10.1093/nar/gkt1102 is OK
- 10.1093/bioinformatics/btl633 is OK
- 10.1093/annonc/mdg486 is OK
- 10.1093/hmg/ddp046 is OK
- 10.1016/S0968-0004(98)01343-7 is OK
- 10.1016/S1357-4310(99)01461-6 is OK
- 10.1016/S0959-8049(00)00158-1 is OK
- 10.1053/gast.2001.29611 is OK
- 10.1001/jama.297.21.2360 is OK
- 10.1371/journal.pgen.1003254 is OK
- 10.1186/1479-5876-7-43 is OK
- 10.1038/nrd3374 is OK
- 10.1158/1078-0432.ccr-13-3116 is OK
- 10.1016/j.ddtec.2013.12.002 is OK
- 10.1038/nrg3899 is OK
- 10.1016/j.cell.2015.11.015 is OK
- 10.1186/gb-2004-5-10-r80 is OK

MISSING DOIs

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- https://doi.org/10.1016/j.ctrv.2011.11.005 may be missing for title: Molecular biology in breast cancer: intrinsic subtypes and signaling pathways
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- https://doi.org/10.1200/jco.2006.09.1066 may be missing for title: Meta-analysis of BRCA1 and BRCA2 penetrance
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- https://doi.org/10.1038/452788b may be missing for title: James Watson’s genome sequenced at high speed
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- https://doi.org/10.1073/pnas.70.12.3581 may be missing for title: The Nucleotide Sequence of the lac Operator
- https://doi.org/10.1158/1535-7163.mct-14-0845 may be missing for title: Functional Genetic Screen Identifies Increased Sensitivity to WEE1 Inhibition in Cells with Defects in Fanconi Anemia and HR Pathways
- https://doi.org/10.1200/jco.2008.16.0812 may be missing for title: A synthetic lethal therapeutic approach: poly(ADP) ribose polymerase inhibitors for the treatment of cancers deficient in DNA double-strand break repair
- https://doi.org/10.1016/j.cell.2011.03.020 may be missing for title: Genetic interactions in cancer progression and treatment
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INVALID DOIs

- None
majensen commented 4 years ago

Replicating @arfon comment here regarding trimming bibtex entries:

@TomKellyGenetics - you might want to truncate your bibtex entries to only those that are cited in the JOSS paper to prevent Whedon responses like this one: #2137 (comment)

https://github.com/openjournals/joss-reviews/issues/2137#issuecomment-597923101

majensen commented 4 years ago

@TomKellyGenetics - in the first paragraph of Methodology and software, there is a sentence:

...of the popular package, which is often used...

Seems like the package name is missing here, or I'm missing something.

TomKellyGenetics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

TomKellyGenetics commented 4 years ago

This should build with updates from minor (formatting) corrections from errors found while submitting to CRAN and bioRxiv. I’ll look into removing unneeded references from the bibtex file. An updated submission with corrected documentation has been re-uploaded to CRAN and is pending manual confirmation.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

TomKellyGenetics commented 4 years ago

Dear Arfon,

Thank you for informing us on your policy. I'm currently based in Japan (which is considering to declare a state of emergency) so we're acutely aware of the developing situation here. I understand completely if reviews will take longer than usual during this time. I am safely able to work from home so can still respond to reviewers if they are able to.

Thank you,

Tom Kelly, Postdoctoral researcher at RIKEN IMS, Yokohama

corybrunson commented 4 years ago

@TomKellyGenetics the submission looks pretty cool, as i'm just starting my review. I have some comments on the paper before i begin exploring the software. Sorry if you've already caught some of these but not yet updated the PDF.

corybrunson commented 4 years ago

@TomKellyGenetics a couple of other comments, specifically on the code in the paper:

corybrunson commented 4 years ago

@TomKellyGenetics one last point on the paper:

rcannood commented 4 years ago

Sorry for my late response, I didn't manage to find any spare time until now. @majensen I wanted to start the review just now, but I see I missed the opportunity to accept whedon's invitation to the repository. (I thought I had retained the rights since my previous review, but apparently they get removed after the review is done.) Could I somehow be invited again?

TomKellyGenetics commented 4 years ago

Thanks @corybrunson, I'll take a look at Issues as they come into the package repo (I think the problem with plot_directed is resolved).

I can reformat the Statement of Need if this is required explicitly by JOSS. I made it a separate section (as done by other recent submissions) so it would be clear for the editorial process.

Sorry it seems that some text formatting for language and package names weren't handled well when exporting LaTeX to whedon-compatible markdown. I've fixed these on the biorXiv version and I'll update the JOSS submission accordingly.

Wang et al (2018) also simulate gene expression counts as a log-normal distribution. This package was originally developed before this publication. The approach to simulate based on graph structures is our original design. To my knowledge, there are no pre-existing implementations for this procedure in R.

The second author is my PhD supervisor. He was involved in planning, overseeing the project and preparing the manuscript. He has tested the software and given feedback on it.

I'll update the PDF once I've corrected the issues mentioned with the markdown document.

arfon commented 4 years ago

@whedon re-invite @rcannood

whedon commented 4 years ago

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

@whedon commands
arfon commented 4 years ago

@whedon re-invite @rcannood as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

@rcannood please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

rcannood commented 4 years ago

Thanks @arfon @whedon!

majensen commented 4 years ago

Thanks @arfon; WB @rcannood !

majensen commented 4 years ago

@corybrunson - my opinion as editor (which will be addressed by @arfon if I'm wrong) is that the paper should be sure to include the rationale for writing the software and why there is a niche for it. Not necessary to have a heading (personally, I think that would be stylistically gauche-- but that's only my opinion!).

corybrunson commented 4 years ago

@TomKellyGenetics no problem, i'll come back to the PDF after the next update.

Regarding the Statement of Need, i'll be fine with the current formatting (above the Summary with its own header) if you want to keep it (thank you @majensen for your comment); my concern is that it says only what the software does, not what need it satisfies. The first three paragraphs of the Introduction do this quite well, so i'd suggest encapsulating them into 2 or 3 sentences for that purpose.

Onward to the software itself. : )

TomKellyGenetics commented 4 years ago

@majensen @corybrunson Thanks for your advice, I agree. I thought a separate Statement of Need section was required by JOSS. I'd prefer to merge it into the Summary and avoid repetition so I'll do this as no one seems to object to this.

corybrunson commented 4 years ago

@TomKellyGenetics what do you think about incorporating the summary statement of need you're preparing into the DESCRIPTION and/or README as well? This would resolve the criterion for the software documentation as well as for the paper.

TomKellyGenetics commented 4 years ago

Hi @corybrunson, that sounds like a good idea. I'm planning update the manuscript and documentation in the next few days to make the the changes discussed so far.

TomKellyGenetics commented 4 years ago

@whedon generate pdf

TomKellyGenetics commented 4 years ago

Minor changes to the manuscript to aid further review.

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

corybrunson commented 4 years ago

@TomKellyGenetics i see your recent responses and will get to the repo issues next. I see only a few remaining issues with the paper:

corybrunson commented 4 years ago

@TomKellyGenetics sorry, one more:

TomKellyGenetics commented 4 years ago

Thanks @corybrunson, you've explained what is required very clearly. I've updated the manuscript as suggested.

The "igraph.extensions" library isn't so important at this stage, I've migrated all required functions into "graphsim" to satisfy CRAN requirements (no remote dependencies). It's for convenience to install other packages similar to the initial release of "tidyverse". I've updated the text to clarify this but I can remove it if it is not relevant (i.e., if JOSS submissions should only describe software on CRAN or similar repositories).

corybrunson commented 4 years ago

@TomKellyGenetics That sounds fine! No need to drop the extensions library if you find it useful; i was just unclear about it at first.

majensen commented 4 years ago

@corybrunson @rcannood can I get a progress report here? Are we stalled due to pandemic or ...? thanks

corybrunson commented 4 years ago

@majensen thanks for checking. There are a few issues that remain open on the repo, and @TomKellyGenetics has been making some revisions to the paper. (They may wish to comment.) I expect to be done with my review once these changes are made. (I don't expect to be slowed by the pandemic.)

rcannood commented 4 years ago

Same here. I am waiting for TomKellyGenetics/graphsim#13 to tick the final two checkboxes on my review checklist.

TomKellyGenetics commented 4 years ago

@majensen Sorry for the delays. I'm balancing childcare at home and a new position not related to this work. I'm still able work during the pandemic but revisions are taking longer than I'd have liked.

I expect the most time-consuming aspect will be revising the vignettes. The reviewers made good suggestions and I will make the requested revisions. Overall, I'm impressed by the JOSS review process and feel it will genuinely improve the package and paper.

It is a holiday period here in Japan next week. I will get back onto it after that and update you when it is ready. Thanks all for your patience.

rcannood commented 4 years ago

I understand your situation very well :smile: Enjoy your family and your holidays!

majensen commented 4 years ago

Thanks @TomKellyGenetics , no pressure at all, just checking if all was well.

majensen commented 4 years ago

How are things @TomKellyGenetics? Hope they are settling down for you.

TomKellyGenetics commented 4 years ago

Thanks for following up, it's taken longer than I'd planned but you can see most of the recent progress here: https://github.com/TomKellyGenetics/graphsim/issues/13

The main update is that the paper has been migrated to Rmarkdown format (with a few changes to the figure formatting that I've yet to test on Whedon). https://github.com/TomKellyGenetics/graphsim/blob/master/paper/paper.Rmd

I've also made changes to the computation of the state parameter which addresses this. Figures have been updated to reflect this change.

I'm unable to exactly reproduce the heatmaps displayed in the paper. They're based on the graph with inhibitions, and i'm also not clear on how to incorporate the vector state into these calculations, after looking into the code only a slight bit. (For issues running examples, etc. in the package itself, i'll open issues on the GitHub repo.)

I've started on the vignettes which was raised by both reviewers. This includes reformatting the vignettes in similar style to the Rmarkdown paper and including examples from the data directory as suggested. https://github.com/TomKellyGenetics/graphsim/issues/11 https://github.com/TomKellyGenetics/graphsim/issues/6

As discussed on the issue I'll update the manuscript text after the documentation. I should have some time to finish the biggest changes to the vignettes soon. I'll update this thread when the revised package and manuscript and ready for further review.

arfon commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #2161 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in initialize': No such file or directory @ rb_sysopen - tmp/2161/paper/paper.yml (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:123:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:63:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

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arfon commented 4 years ago

@TomKellyGenetics - a few comments on your paper:

The fact that paper.md and paper.tex exist in your repository confuses Whedon (hence the errors above).

The compiled paper compiled here is very long (15 pages currently) and much longer than we normally expect at JOSS (~1000 words is the guidance on length). Could you take a look at reducing the length, for example, by moving some of the long code examples to other documentation?

TomKellyGenetics commented 4 years ago

Thanks @arfon. I was unsure if Whedon would handle the new format. I'll look into that (I think adding the paper.tex to .gitignore and removing it from the repository) will avoid this.

I realise the manuscript is longer than recommended for the journal, I contacted @karthik about this before submitting. As suggested by reviewers, migrating to Rmarkdown format and including examples of empirical networks aids readers to understand and reproduce the results. Unfortunately the Rmarkdown format does make the manuscript even longer (to include all code needed to produce the figures).

I'll consider removing some of it (e.g., Figures 2 and 3), when the vignettes have been updated to cover this material. As suggested here, removing warning messages in Rmarkdown would also make it shorter.

I'll check if panes of different sizes (e.g., Figure 2E) are compatible with Whedon. Since LaTeX many packages are not supported, it was difficult to include subcaptions on the figures, is it possible to add this functionality? The code to add captions in R also makes the manuscript longer than otherwise needed.

TomKellyGenetics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

TomKellyGenetics commented 4 years ago

Here's a preview of the manuscript in Rmarkdown form with the code examples simplified (I'll add more details in the vignettes). This is a work-in-progress.

I've contacted my coauthor to discuss to reducing the length of the paper.

arfon commented 4 years ago

Here's a preview of the manuscript in Rmarkdown form with the code examples simplified (I'll add more details in the vignettes). This is a work-in-progress.

I've contacted my coauthor to discuss to reducing the length of the paper.

Thanks for working on this @TomKellyGenetics.

I'll check if panes of different sizes (e.g., Figure 2E) are compatible with Whedon. Since LaTeX many packages are not supported, it was difficult to include subcaptions on the figures, is it possible to add this functionality?

I don't believe a subcaption is possible with Pandoc and this template sorry.

karthik commented 4 years ago

Unfortunately the Rmarkdown format does make the manuscript even longer (to include all code needed to produce the figures).

Have you considered just hiding those blocks?