gg4way #3129

ben-laufer · 2023-08-30T20:14:57Z

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bioc-issue-bot · 2023-08-30T20:15:01Z

Hi @ben-laufer

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: gg4way
Title: 4way Plots of Differential Expression
Version: 0.99.0
Authors@R: c(
    person(given = "Ben",
 family = "Laufer",
 role = c("aut", "cre"),
 email = "blaufer@gmail.com",
 comment = c(ORCID = "0000-0002-7558-1335")),
    person(given = "Brad",
 family = "Friedman",
 role = c("aut")))
Description: 4way plots enable a comparison of two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.
License: MIT + file LICENSE
URL: https://github.com/ben-laufer/gg4way
BugReports: https://github.com/ben-laufer/gg4way/issues
biocViews: 
    Software,
    Visualization,
    DifferentialExpression,
    GeneExpression,
    Transcription,
    RNASeq,
    SingleCell,
    Sequencing
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
    R (>= 4.3.0),
    ggplot2
Imports: 
    DESeq2,
    dplyr,
    ggrepel,
    glue,
    janitor,
    limma,
    magrittr,
    methods,
    purrr,
    rlang,
    scales,
    stats,
    stringr,
    tibble,
    tidyr
Suggests: 
    airway,
    BiocStyle,
    edgeR,
    knitr,
    org.Hs.eg.db,
    rmarkdown,
    testthat
VignetteBuilder: knitr
Config/testthat/edition: 3
LazyData: false

bioc-issue-bot · 2023-09-14T14:56:51Z

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bioc-issue-bot · 2023-09-14T16:45:56Z

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bioc-issue-bot · 2023-09-15T02:03:33Z

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PeteHaitch · 2023-09-28T00:25:52Z

Hi @ben-laufer,

Thank you for submitting gg4way to Bioconductor.
It's a nice, simple package with a clear purpose, which made for an straightforward review.
Thank you!

The package is largely fine as is, but I did want to ask whether you considered implementing gg4way() as a generic with specific methods for MArrayLM, DESeqDataSet, and (a list of) DESeqResults objects, along with a default version for the general 'tidyList' format?
The Glimma package does something similar (custom plots of DE analysis results) and uses the S3 object oriented programming system to implement this.
This would slightly simplify the user-interface and obviate the need to export the tidyDGE() function.
To be clear, this isn't a requirement for acceptance, but I thought it worth raising in case it is helpful to you.

In my review below I have separated the issues into Required and Recommended points that I would ask you to address before the package can be accepted.
Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.

I'll be on leave (and offline) from today until October 9.
The deadline for new packages to be accepted is October 18 (see https://www.bioconductor.org/developers/release-schedule/).
I think the requested changes will be fairly straightforward for you implement and I will then be able to accept the package soon after returning from leave.
But if while I'm away you do have any urgent concerns or questions, please post to this issue and tag @vjcitn or @lshep to bring it to their attention.

Cheers,
Pete

Required

library(gg4way)
#> Loading required package: ggplot2

data("airwayFit")
airwayFit |>
    tidyDGE() |>
    gg4way(x = "N61311 vs N052611",
           y = "N061011 vs N052611",
           # Force all genes to be 'significant'.
           FDRcutoff = 1,
           logFCcutoff = 0)
#> Warning: Removed 1 rows containing missing values (`geom_label()`).

Session info

sessioninfo::session_info()
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#>  ctype    en_US.UTF-8
#>  tz       Australia/Melbourne
#>  date     2023-09-28
#>  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
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"A commonly used approach is to apply FDR and logFC cutoffs simultaneously. However this tends to favor lowly expressed genes, and also fails to control the FDR correctly.".
Instead, the authors developed limma::treat() and edgeR::glmTreat(); see their documentation for further details.
DESeq2 may have similar functionality but I'm not as familiar with that package. ↩

bioc-issue-bot · 2023-10-08T22:30:55Z

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bioc-issue-bot · 2023-10-08T22:38:43Z

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The following are build products from R CMD build on the Bioconductor Build
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Linux (Ubuntu 22.04.2 LTS): gg4way_0.99.1.tar.gz

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ben-laufer · 2023-10-08T22:44:24Z

Hi @PeteHaitch,

Thanks for reviewing gg4way. All the required changes have been made. See below for a point-by-point response about the improvements.

The package is largely fine as is, but I did want to ask whether you considered implementing gg4way() as a generic with specific methods for MArrayLM, DESeqDataSet, and (a list of) DESeqResults objects, along with a default version for the general 'tidyList' format? The Glimma package does something similar (custom plots of DE analysis results) and uses the S3 object oriented programming system to implement this. This would slightly simplify the user-interface and obviate the need to export the tidyDGE() function. To be clear, this isn't a requirement for acceptance, but I thought it worth raising in case it is helpful to you.

gg4way() is now a generic with specific methods for: MArrayLM, list, and DESeqDataSet. The list method can recognize lists of DGELRT, DESeqResults, and data.frame objects. The tidyDGE() function has been removed.

Required

The man page for gg4way needs a little fleshing out. Some thoughts/questions I had when reading it are listed below. Some of these can be addressed with small changes to the current text, but I think the addition of a 'Details' section would be helpful.

The man page for gg4way now clarifies these points.

The format of tidyList must be explicitly documented, particularly since it's not a formal class.

The tidyList argument has been renamed to DGEdata. The argument now contains details about the supported objects. The details section of the documentation also shows the format for a data.frame.

It could be made clearer that x and y must be the actual names of the results in the tidyList object rather than some names being added just for the purposes of axis labels on the plots.

This has been clarified in the argument descriptions.

Why are both symbol and ID required by gg4way()? It seems only symbol is used in the plot (as the optional labels).

The "other packages" section of the vignette (and function documentation) mention that the symbol column is optional and used for the plot labels. It enables cases where not every feature has a (unique) gene ID. The ID column is how unique features are defined.

Do you have any guidance on interpreting the correlation? For example, if the 2 contrasts 'overlap' (i.e. include a common factor), as they do in the vignette, then that would seem to induce a non-zero correlation whereas if the 2 contrasts do not overlap then I imagine the correlation does not have this 'bias'?

I have added a note about this to the details section of the man page for gg4way.

What does "sums" mean in "textSize Numeric specifying size of text with sums" and this "textOffset Numeric specifying offset of text with sums"?

The documentation for the arguments now mention that this is referring to the DEG totals for each category of gene overlap, which is shown by the numeric text in the plot.

What's actually plotted could be made more explicit. E.g., I assume it is the logFC from each comparison that's plotted on the x and y axes, but it's not actually stated.

Added to the description section of the man page and mentioned in the vignette.

In the vignette, the numbers sometimes differ between the text and figures, e.g., "71 DEGs" in text" vs. "72"" in bottom-left of first figure. Perhaps you can include the in-text values via inline evaluated R code (i.e. using r ) rather than hardcoding them.

In-text values are now obtained from inline R code.

All exported data in data/ must be documented, i.e. airwaysFit needs a man page; see https://contributions.bioconductor.org/citation.html.

Let me know if it's missing any key details.

The numbers reported in the quadrants seem to incorrect if a user forces all genes to be significant. Does this indicate deeper problems with this calculations or just a pathological corner case?

This has been fixed and additional error checks have been added.

Support has been added for the output of the limma::treat() and edgeR::glmTreat() functions mentioned in the link as replacements for limma::eBayes() and edgeR::glmQLFTest(), respectively. The vignette now also mentions that gg4way() works with these and a similar approach in DESeq2. This should help with leaving the decision of the statistical approach up to the user. It also seems like the default of gg4way(logFCcutoff = 1) remains acceptable.

Regarding the label argument of gg4way(), and this is a pathological case, but what if there was a gene symbol called "shared"? Perhaps use label = TRUE instead of label = "shared" to denote that option (since the default is shared = FALSE)?

label = TRUE now replaces label = "shared".

Consider adding captions for figures in the vignette.

Added.

Perfectionist nitpicking: For the first figure in vignette, for example, that the %<-->% expression is not centered around x=0 (whereas it is for y=0) is slightly jarring. I'm not sure of a general solution to this, and so I apologise for even bringing it up, but I can't unsee it!

.tidyLabel() uses spacers to help with this, but it's only perfectly aligned when the limits of the axis are identical. The vignette details how a user can customize the axis titles through ggplot2 afterwards.

Once accepted, you could add a link from the README to the BioC landing page (which will be https://bioconductor.org/packages/gg4way/) and even the the rendered vignette (https://bioconductor.org/packages/release/bioc/vignettes/gg4way/inst/doc/gg4way.html) for where you write "See the package vignette." for examples.

These links will be added upon acceptance.

Consider adding a inst/CITATION file.

The description file has been modified to generate a better default citation.

Good job on including unit tests. Take a look at running covr::report() on your package for gaps in the test coverage.

An additional unit test has been added.

Recommend running a spell check (if you use R Studio there is one built in). E.g., stop("Format not **suppourted**") in tidyDGE().

That one slipped through my R Studio spell check.

Footnotes

"A commonly used approach is to apply FDR and logFC cutoffs simultaneously. However this tends to favor lowly expressed genes, and also fails to control the FDR correctly.".
Instead, the authors developed limma::treat() and edgeR::glmTreat(); see their documentation for further details.
DESeq2 may have similar functionality but I'm not as familiar with that package. ↩

PeteHaitch · 2023-10-12T02:22:46Z

I'm happy to mark gg4way as accepted.
Thank you for your engaging constructively in the review process, @ben-laufer, and for your contribution to Bioconductor!

A few final, minor things to address:

Once accepted, you could add a link from the README to the BioC landing page (which will be https://bioconductor.org/packages/gg4way/) and even the the rendered vignette (https://bioconductor.org/packages/release/bioc/vignettes/gg4way/inst/doc/gg4way.html) for where you write "See the package vignette." for examples.
It's worth documenting that the output of edgeR::glmLRT() is also supported since it is the same format as the output of edgeR::glmQLFTest().
Why not show the results in 'Plot by contrast' section of vignette (i.e. why is fig.show = "hide")?

bioc-issue-bot · 2023-10-12T02:23:01Z

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lshep · 2023-10-13T17:09:00Z

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bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Aug 30, 2023

vjcitn added the pre-check passed pre-review performed and ready to be added to git label Sep 12, 2023

bioc-issue-bot added the ERROR label Sep 14, 2023

lshep added the 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place label Sep 14, 2023

bioc-issue-bot assigned PeteHaitch Sep 14, 2023

bioc-issue-bot removed the pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean label Sep 14, 2023

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lshep removed the pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean label Sep 14, 2023

bioc-issue-bot added the pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean label Sep 15, 2023

lshep closed this as completed Oct 13, 2023

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gg4way #3129

gg4way #3129

ben-laufer commented Aug 30, 2023

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PeteHaitch commented Sep 28, 2023

bioc-issue-bot commented Oct 8, 2023

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ben-laufer commented Oct 8, 2023

Footnotes

PeteHaitch commented Oct 12, 2023 •

edited

bioc-issue-bot commented Oct 12, 2023

lshep commented Oct 13, 2023

gg4way #3129

gg4way #3129

Comments

ben-laufer commented Aug 30, 2023

bioc-issue-bot commented Aug 30, 2023

bioc-issue-bot commented Sep 14, 2023

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PeteHaitch commented Sep 28, 2023

Required

Recommended

Footnotes

bioc-issue-bot commented Oct 8, 2023

bioc-issue-bot commented Oct 8, 2023

ben-laufer commented Oct 8, 2023

Required

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Footnotes

PeteHaitch commented Oct 12, 2023 • edited

bioc-issue-bot commented Oct 12, 2023

lshep commented Oct 13, 2023

PeteHaitch commented Oct 12, 2023 •

edited