[PRE REVIEW]: ggoncoplot: an R package for interactive visualisation of somatic mutation data from cancer patient cohorts

[editorialbot]

Submitting author: @selkamand (Sam El-Kamand)
Repository: https://github.com/selkamand/ggoncoplot
Branch with paper.md (empty if default branch):
Version: v0.1.0
Editor: @ppxasjsm
Reviewers: @zainabarshad
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bff5bd8f5c6aa0b55b83b5d7b7eb1d1f/status.svg)](https://joss.theoj.org/papers/bff5bd8f5c6aa0b55b83b5d7b7eb1d1f)

Author instructions

Thanks for submitting your paper to JOSS @selkamand. Currently, there isn't a JOSS editor assigned to your paper.

@selkamand if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1002/imt2.43 is OK
- 10.1101/gr.239244.118 is OK
- 10.1093/bioinformatics/btw325 is OK
- 10.1038/s41587-020-0546-8 is OK
- 10.1016/j.cels.2018.03.002 is OK

MISSING DOIs

- 10.32614/cran.package.ggiraph may be a valid DOI for title: ggiraph: Make ’ggplot2’ Graphics Interactive
- 10.32614/cran.package.patchwork may be a valid DOI for title: patchwork: The Composer of Plots
- No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1205.6 files/s, 248581.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               12            321           1473           1267
XML                              1              0              0           1122
CSV                              3              0              0            824
Markdown                         4             97              0            299
Rmd                              3            198            283            255
YAML                             5             25              7            112
TeX                              1              9              0             98
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                            31            650           1763           3979
-------------------------------------------------------------------------------

Commit count by author:

    64	Sam El-Kamand
    36	Sam
    29	selkamand
    19	unknown

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 932

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@selkamand Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

[selkamand]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1002/imt2.43 is OK
- 10.1101/gr.239244.118 is OK
- 10.1093/bioinformatics/btw325 is OK
- 10.32614/CRAN.package.ggiraph is OK
- 10.32614/cran.package.patchwork is OK
- 10.32614/CRAN.package.ggplot2 is OK
- 10.1038/s41587-020-0546-8 is OK
- 10.1016/j.cels.2018.03.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[selkamand]

Thanks @Kevin-Mattheus-Moerman. Missing DOIs and a CONTRIBUTING.md have been added

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@selkamand thanks for making those changes. I've just added the query-scope label which will trigger a scope review by the editorial board. The objective of the scope review is to determine if the functionality offered by the work is substantial enough, is research software, and conforms to our substantial scholarly effort criteria. This is normal for projects that are on the small side and also for projects that appear to focus on visualization. The scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@selkamand I am pleased to inform the board has concluded this work may be in scope for JOSS. We will now proceed to seek a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @ppxasjsm as editor

[editorialbot]

Invitation to edit this submission sent!

[ppxasjsm]

@editorialbot assign @ppxasjsm as editor

[editorialbot]

Assigned! @ppxasjsm is now the editor

[ppxasjsm]

@selkamand I'll be editing your submission.
If you could check suggestions for potential reviewers I would appreciate it as it will make the search easier for me. Please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission. Thanks for your help!

[selkamand]

Hi @ppxasjsm,

I've listed some potential reviewers (* next to those from the list linked above). Hope this helps
Jianhui Gong*
Nicola Cosgrove
Lei Chen
Kim-Anh Lê Cao

[ppxasjsm]

Hi @@duncanjunegong would you be willing to review this JOSS submission?

[lpantano]

Hi, I am editor for joss (and I saw this), and my colleague @zainabarshad, can be a reviewer for this tool.

[ppxasjsm]

Hi @zainabarshad that would be amazing if you could review this submission!

[ppxasjsm]

HI @kelly-sovacool, I was wondering if you were available to review this submission. I am not sure if this fits your remit.

[zainabarshad]

Hi @ppxasjsm, Great! I'll begin reviewing the code shortly. Are there any specific instructions I should keep in mind in my review?

[kelly-sovacool]

HI @kelly-sovacool, I was wondering if you were available to review this submission. I am not sure if this fits your remit.

Sorry, I am too busy to review at this time

[ppxasjsm]

@editorialbot add @zainabarshad as reviewer

[editorialbot]

@zainabarshad added to the reviewers list!

[ppxasjsm]

Hi @yafeiwang89, is there any chance you'd be available to review this JOSS submission?

[ppxasjsm]

Hi @allaway, is there any chance you are available to review this submission for JOSS?

[ppxasjsm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7390.