iheatmapr

[AliciaSchep]

Summary

• What does this package do? (explain in 50 words or less):

Makes complex, interactive heatmaps. The package includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap function for making relatively standard heatmaps.

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

Package: iheatmapr
Type: Package
Title: Interactive Complex Heatmaps
Version: 0.2.4
Authors@R: c(person("Alicia", "Schep", email = "aschep@gmail.com",
                  role = c("aut", "cre")),
              person("Sarah","Kummerfeld", email = "kummerfeld.sarah@gene.com",
                  role = c("aut")),
              person("Genentech", role = "cph"))
Description: iheatmapr is a package for making complex, interactive heatmaps.
    The package includes a modular system for iteratively building up complex
    heatmaps, as well as the iheatmap function for making relatively standard
    heatmaps.
License: MIT + file LICENSE
Depends:
    plotly (>= 4.1.1),
    R (>= 2.10)
Imports:
    methods,
    plyr,
    utils,
    magrittr,
    S4Vectors,
    stats,
    ggdendro,
    fastcluster,
    RColorBrewer,
    htmlwidgets,
    jsonlite,
    scales,
    knitr
Suggests:
    htmltools,
    datasets,
    shiny,
    testthat,
    rmarkdown,
    reshape2,
    roxygen2,
    covr
biocViews: Visualization
RoxygenNote: 6.0.1
VignetteBuilder: knitr
URL: https://github.com/AliciaSchep/iheatmapr
BugReports: https://github.com/AliciaSchep/iheatmapr/issues
Collate:
    'AllClasses.R'
    'AllGenerics.R'
    'annotations.R'
    'as_plotly.R'
    'axes.R'
    'axis_labels.R'
    'axis_titles.R'
    'barplot.R'
    'clustering.R'
    'clusters.R'
    'colorbars.R'
    'colors.R'
    'components.R'
    'dendogram.R'
    'generic_subplots.R'
    'groups.R'
    'main_heatmap.R'
    'iheatmap.R'
    'iheatmapr.R'
    'layout.R'
    'shiny_click_test.R'
    'signal.R'
    'subplot.R'
    'summary.R'
    'utils.R'

• URL for the package (the development repository, not a stylized html page):

https://github.com/AliciaSchep/iheatmapr

• Who is the target audience?

Anyone who wants to visualize data using heatmaps. Package is not intended to be domain specific, although some fields tend to use heatmaps more than others.

• Are there other R packages that accomplish the same thing? If so, what is different about yours?

There are great tools in R for creating relatively simple interactive heatmaps (plotly, d3heatmap, heatmaply) or creating static complex heatmaps (ComplexHeatmap). However, there are no tools (that I am aware of) facilitating easy creation of complex, interactive heatmaps.

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 with Travis CI and/or another service.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package contains a paper.md with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

[maelle]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for your submission @AliciaSchep! 😀 Currently looking for reviewers.

A few comments:

• The repository doesn't have a DOI yet but I guess you'd archive it after the review?

• Here is the output from goodpractice::gp() that can help you and the reviewers

It is good practice to

  ✖ write unit tests for all functions, and all package code in
    general. 78% of code lines are covered by test cases.

    R/AllGenerics.R:93:NA
    R/AllGenerics.R:96:NA
    R/AllGenerics.R:141:NA
    R/AllGenerics.R:144:NA
    R/AllGenerics.R:201:NA
    ... and 587 more lines

  ✖ not use "Depends" in DESCRIPTION, as it can cause name clashes,
    and poor interaction with other packages. Use "Imports" instead.
  ✖ 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

    R\AllGenerics.R:34:1
    R\axes.R:389:1
    R\axes.R:390:1
    R\axes.R:510:1
    R\axes.R:630:1
    ... and 37 more lines

  ✖ not import packages as a whole, as this can cause name clashes
    between the imported packages. Instead, import only the specific
    functions you need.
  ✖ fix this R CMD check NOTE: Namespace in Imports field not
    imported from: 'fastcluster' All declared Imports should be
    used.
  ✖ fix this R CMD check NOTE: add_col_clustering,Iheatmap: no
    visible global function definition for 'hclust'
    add_row_clustering,Iheatmap: no visible global function
    definition for 'hclust' Undefined global functions or variables:
    hclust Consider adding importFrom("stats", "hclust") to your
    NAMESPACE file.

• Using devtools::spell_check() I found the following typos
  • pallette add_main_heatmap.Rd:37
  • heirarchical add_col_clustering.Rd:17, add_row_clustering.Rd:17
  • annotion add_col_annotation.Rd:26, add_row_annotation.Rd:26

---

Reviewers: @andeek @carlganz
Due date: 2017-04-23

[AliciaSchep]

Thanks @maelle!

I have updated the typos, long lines, and some of the NAMESPACE issues.

For the use of DEPENDS, I think it is appropriate in this case to force user import of plotly. For importing the packages as whole, I am only importing S4Vectors and methods -- as I am using a lot of functions & classes from these packages I thought that might be appropriate, but am of course open to more guidance on this question.

I will work on adding more tests to get closer to 100% test coverage.

[maelle]

Great but note that 100% coverage isn't compulsory 😉

[maelle]

@AliciaSchep the reviewers are now assigned! 😀

Thanks for agreeing to review this package @andeek @carlganz! 😃

As a reminder here are links to the recently updated reviewing and packaging guides and to the review template.

[carlganz]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README

  Consider adding a more concrete statement of need in the readme. The paper.md and the vignette both provide good statements of need.

• Installation instructions: for the development version of package and any non-standard dependencies in README

  Consider mentioning the dependency on BiocInstaller since there may be users who are not familiar with how to install packages from BioConductor.

• Vignette(s) demonstrating major functionality that runs successfully locally

  Excellent vignette

• Function Documentation: for all exported functions in R help

• Examples for all exported functions in R Help that run successfully locally

  setup_colorbar_grid and save_iheatmap do not include examples.

• Community guidelines including contribution guidelines in the README or CONTRIBUTING, and URL, Maintainer and BugReports fields in DESCRIPTION

Paper (for packages co-submitting to JOSS)

The package contains a paper.md with:

• A short summary describing the high-level functionality of the software
• Authors: A list of authors with their affiliations
• A statement of need clearly stating problems the software is designed to solve and its target audience.
• References: with DOIs for all those that have one (e.g. papers, datasets, software).

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software been confirmed.
• Performance: Any performance claims of the software been confirmed.
• Automated tests: Unit tests cover essential functions of the package
  and a reasonable range of inputs and conditions. All tests pass on the local machine.
• Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 3

---

Review Comments

This package provides R users with a collection of easy-to-use functions for iteratively building complex interactive heatmaps. The iheatmap function initiates a heatmap, and a variety of function of the form add_* allow thee user to include annotations, barplots, clustering, grouping, dendrograms, labels, plots, titles, and summaries to both the rows, and columns as well as additional heatmaps. The package makes nice use of magrittr pipes, and plotly graphics, which gives it a nice modern feel.

The package is extremely well documented with an extensive vignette, and examples for almost every function. The package is also well tested with 79% code coverage. It contains a library of graphs, which are recreated, and then compared to in the tests.

Overall the package is very well done, and meets all the rOpenSci packaging guidelines. Functions have proper names, and documentation. Use of plotly in depends makes sense.

A few suggestions:

• Add clearer statement of need in readme. The first paragraph nicely explains what iheatmapr does, but I don't think it is a clear statement of need. The JOSS paper, and the vignette both make clearer statements of need.

• Consider mentioning how to install BiocInstaller in the installation instructions. I'll confess, I had to google how to install BioConductor packages because I hadn't done it before.

• Add examples for setup_colorbar_grid and save_iheatmap (you already fixed Small typo in documentation iheatmapr#1)

• Add DOIs for references in paper.md if they exist

• Consider adding Travis tests for Mac, and App-Veyor tests for Windows.

• Consider adding a badge in readme for minimum R version (i.e. badgecreatr::minimal_r_version_badge("2.10"))

• The vignette is very well done. Only suggestion is to maybe explain the differences between clustering vs clusters vs groups since they all seem like similar concepts to me.

Hope that helps.

Kind Regards,
Carl

[maelle]

Thanks a lot for your review @carlganz !

[AliciaSchep]

@carlganz thank you for the review and helpful suggestions! I will follow up on all the suggestions and post an update to this thread when that is complete.