Joss-reviews: [REVIEW]: qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Created on 10 May 2018 · 34Comments · Source: openjournals/joss-reviews

Submitting author: @stephenturner (Stephen Turner)
Repository: https://github.com/stephenturner/qqman/
Version: v0.1.6
Editor: @leeper
Reviewer: @tgerke
Archive: 10.5281/zenodo.591547

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/da6fe875ac2679d7a56b6dea4181e7fe"><img src="http://joss.theoj.org/papers/da6fe875ac2679d7a56b6dea4181e7fe/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/da6fe875ac2679d7a56b6dea4181e7fe/status.svg)](http://joss.theoj.org/papers/da6fe875ac2679d7a56b6dea4181e7fe)

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) 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

@tgerke, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leeper know.

Review checklist for @tgerke

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v0.1.6)?
[x] Authorship: Has the submitting author (@stephenturner) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

accepted published recommend-accept review

Source

whedon

Most helpful comment

@tgerke - many thanks for your review here and to @leeper for editing this submission :sparkles:

@stephenturner - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00731 :zap: :rocket: :boom:

arfon on 19 May 2018

🎉1 👍1

All 34 comments

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @tgerke it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

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

notifications

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

@whedon commands

whedon on 10 May 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 10 May 2018

PDF failed to compile for issue #731 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:52:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

whedon on 10 May 2018

@tgerke I think you know how this works, but let me know if you have any questions along the way.

leeper on 10 May 2018

@whedon generate pdf

leeper on 10 May 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 10 May 2018

PDF failed to compile for issue #731 with the following error:

whedon on 10 May 2018

@stephenturner Two quick things:

I suspect the paper compilation issue is due to the jpeg image file. Can you convert to PNG perhaps?
Please add DOIs for all articles in your .bib file.

leeper on 10 May 2018

@whedon generate pdf

stephenturner on 10 May 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 10 May 2018

PDF failed to compile for issue #731 with the following error:

whedon on 10 May 2018

I think it's because the repository might be pointing to https://github.com/stephenturner/qqman/tree/master/misc/paper instead of to the top level https://github.com/stephenturner/qqman/ ? @leeper

stephenturner on 10 May 2018

See #706 @arfon https://github.com/openjournals/joss-reviews/issues/706#issuecomment-384835018

stephenturner on 10 May 2018

@leeper also, updated .bib with DOI.

stephenturner on 10 May 2018

👍1

Review complete, all boxes checked. Great package; my lab has already used it multiple times in the past year with success.

Very minor comments (that I don't think should hold back acceptance in JOSS):
-- vignette on CRAN showing zscore as part of gwasResults object before the variable is created later in the vignette.
-- this could be related to CRAN still hosting v0.1.4. The GitHub version does sync with the JOSS paper though (v0.1.6).
-- in our previous use of the package, we sometimes wanted to annotate SNPs in a way that is not related to p-value (e.g. SNPs that were candidates from previous literature). To my knowledge, the package only lets you annotate by p threshold. The feature to highlight by a character vector of SNPs of interest is very useful to this end; the capacity to extend the highlight argument to similarly permit annotation by rsID (or similar) would be helpful in future versions.

tgerke on 17 May 2018

👍1

Thanks for the feedback, @tgerke.

I've never noticed that the vignette on CRAN shows the z-score before the object is created. I'm not sure how that even happened, unless I somehow had the object in my environment when I created the vignette without using devtools. In any case, I've ensured the vignette in 0.1.6 does not do this. I just submitted 0.1.6 to winbuilder. If that comes back okay, and once this is published, I'll add a CITATION file and release 0.1.6 to CRAN.

On the ability to annotate SNPs not related to p-values - I already have some code in place to highlight SNPs based on ID, so it shouldn't be too difficult to use this framework to label them. I've been putting this off because I really want to move this back to ggplot2, to be able to take advantage of the ggrepel package for doing this. That might be version 0.2.0.

stephenturner on 17 May 2018

👍1

@whedon generate pdf

stephenturner on 17 May 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 17 May 2018

PDF failed to compile for issue #731 with the following error:

whedon on 17 May 2018

@whedon commands

stephenturner on 17 May 2018

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

whedon on 17 May 2018

Looks like it's still failing to generate the PDF because the repo points to https://github.com/stephenturner/qqman/tree/master/misc/paper instead of the top level https://github.com/stephenturner/qqman

stephenturner on 17 May 2018

@whedon generate pdf

arfon on 17 May 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 17 May 2018

--> Check article proof :page_facing_up: <--

whedon on 17 May 2018

@tgerke Thanks for another great (and fast) review!

leeper on 18 May 2018

@stephenturner Thanks for your package. Everything looks good. Can you please create a DOI for the package using, for example, figshare or zenodo and post the DOI for the archive here?

leeper on 18 May 2018

done https://doi.org/10.5281/zenodo.591547 @leeper

stephenturner on 18 May 2018

@whedon set 10.5281/zenodo.591547 as archive

leeper on 18 May 2018

OK. 10.5281/zenodo.591547 is the archive.

whedon on 18 May 2018

@stephenturner Great. That's it then - congrats on a quick review and acceptance!

leeper on 18 May 2018

@arfon Over to you.

leeper on 18 May 2018

@tgerke - many thanks for your review here and to @leeper for editing this submission :sparkles:

@stephenturner - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00731 :zap: :rocket: :boom:

arfon on 19 May 2018

🎉1 👍1

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00731/status.svg)](https://doi.org/10.21105/joss.00731)

This is how it will look in your documentation:

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
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whedon on 19 May 2018

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