Submission: colocr

[MahShaaban]

Summary

• What does this package do? (explain in 50 words or less):
  Conduct Co-localization Analysis of Fluorescence Microscopy Images

• Paste the full DESCRIPTION file inside a code block below:

Package: colocr
Type: Package
Title: Conduct Co-localization Analysis of Fluorescence Microscopy Images
Version: 0.1.0
License: GPL-3
Authors@R: person("Mahmoud", "Ahmed",
    email = "mahmoud.s.fahmy@students.kasralainy.edu.eg",
    role = c("aut", "cre"))
URL: https://github.com/MahShaaban/colocr
BugReports: https://github.com/MahShaaban/colocr/issues
Description: Automate the co-localization analysis of fluoresence microscopy 
  images. Selecting regions of interest, extract pixel intensities from 
  the image channels and calculate different co-localization statistics.
Encoding: UTF-8
LazyData: true
Suggests: testthat,
    covr,
    knitr,
    rmarkdown,
    devtools
RoxygenNote: 6.0.1
Imports: imager,
  shiny,
  scales
VignetteBuilder: knitr

• URL for the package (the development repository, not a stylized html page):
  https://github.com/MahShaaban/colocr

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

[e.g., "data extraction, because the package parses a scientific data file format"]
data extraction

•   Who is the target audience and what are scientific applications of this package?  
  Biologists (no advanced R required)

• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?
  The EBImage and the imager packages contain the algorithms for dealing with images. This package uses imager but is focused only on the functionality needed for conducting co-localization of multichannel images. In addition, the package provide a shiny app to inteactively perform the same analysis.

•   If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
  A pre-submission, Pre-submisstion Inquiry: colocr #241

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

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• Do you intend for this package to go on CRAN?
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  • (Do not submit your package separately to JOSS)
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• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

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[maelle]

Thanks @MahShaaban! 😀

Before I proceed with regular checks since the package has a Shiny app could you have a look at our brand new specific guidance for Shiny apps especially their testing?

https://ropensci.github.io/dev_guide/building.html#interactivegraphical-interfaces

https://ropensci.github.io/dev_guide/building.html#testing

You can ask any question here / on discuss.ropensci.org / Slack (had you gotten an invite to our Slack yet?)

[MahShaaban]

Hey, @maelle

I had a look at links.

• I am already using the shinytest in the app
• Code auto-generation sounds like a great idea, do you recommend any resource to get started on that? For the time being, the app optionally returns the final output in the R session and/or save it to a file. I will add to that all the intermediate values.

I don't think I've received any invites on slack.

[maelle]

👋 @MahShaaban

I am already using the shinytest in the app

Ah sorry! But I don't see where in the tests? In particular, "shinytest" isn't written in DESCRIPTION like "testthat" is?

Code auto-generation sounds like a great idea, do you recommend any resource to get started on that?
No, I'll research that and update this thread (and the guide, good point!)

I've now sent you an invite to the Slack.

[MahShaaban]

Thanks for the slack invite, @maelle

Regarding the shiny tests. The tests are in the app directory, inst/colocr_app/tests/. The reason is I wanted to test the app on Travis separately. If necessary, I will move the tests to run with the package testing.

[maelle]

To be honest I am very new to the testing ofShiny apps inside packages, and once your package is onboarded it'll probably be an example linked from the gitbook. 😸 Why test the app separately? What does it mean exactly? Your Travis config file looks normal to me 🤔

[MahShaaban]

I am also new to shinytest.

I wanted to test the app separately cuz I intended to make it stand-alone and I have a prototype of it on shinyapps.io, here.

I have the app as a separate repo on github, here. This repo is added to the package repo as a submodule. The app repo contains separate .travis.yml and tests/. This way I can link the app as a regular repo on Travis and it runs the tests in with every commit.

[maelle]

Ah interesting! Could you ask in the forum/Slack what best practice is? One thing that I still wonder about is whether your package's README should include a badge of the app's build status.

I'll make other checks as soon as I can.

[MahShaaban]

Alright. Will do.
I think I can add the build status badge from travis, if this what you mean.

Thanks

[maelle]

Do you want to look into code generation before your package undergoes review? I tagged you in a commit, see links to apps generating code here.

[maelle]

goodpractice output

  ✖ use '<-' for assignment instead of '='. '<-' is
    the standard, and R users and developers are used it and it
    is easier to read your code for them if you use '<-'.

    R\methods.R:367:12
    R\methods.R:368:12
    R\methods.R:369:5

  ✖ avoid long code lines, it is bad for readability.
    Also, many people prefer editor windows that are about 80
    characters wide. Try make your lines shorter than 80
    characters

    inst\extdata\manual_analysis.R:6:1
    R\methods.R:378:1
    R\methods.R:379:1
    R\methods.R:380:1
    R\methods.R:381:1

and devtools::spell_check

WORD          FOUND IN
caculated     coloc_test.Rd:23
determin      roi_select.Rd:42
differen      roi_show.Rd:19
fluoresence   description:1
indecies      intensity_get.Rd:15
indicies      roi_show.Rd:16
manders       coloc_test.Rd:12
pearsons      coloc_test.Rd:12
reslution     roi_show.Rd:24
Thes          roi_select.Rd:36