No major adaptations are needed for ggplot2 s7 #104
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…ve README formatting for better readability. Enhance ggplot method for compatibility with ggplot2 4.0.0 using S7 methods.
…xperiment into adapt-ggplot-S7
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Pull Request Overview
This PR adapts ggplot() methods for S7 compatibility by updating documentation, adding a conditional S7 registration function, and reflecting these changes in NEWS, README, and package metadata.
- Updated manual and R documentation to reference
SummarizedExperimentinstead oftidyseurat - Introduced an S7-compatible
ggplotmethod withregister_s7_ggplot_method() - Updated NEWS, bumped version, and adjusted README examples and tables
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| man/ggplot.Rd | Removed old alias and updated title to reference SummarizedExperiment |
| inst/NEWS.rd | Added section for version 1.16.0 with S7 compatibility notes |
| README.md | Reformatted links, example calls, and table headers |
| README.Rmd | Updated example call to use unqualified ggplot() |
| R/ggplot2_methods.R | Added S7 method registration in .onLoad() and updated title in roxygen |
| DESCRIPTION | Bumped package version to 1.19.1 and added S7 to Suggests |
Comments suppressed due to low confidence (4)
man/ggplot.Rd:8
- Removing the S3 alias for
ggplot.SummarizedExperimentmay prevent users from finding help for the original method. Consider re-adding\alias{ggplot.SummarizedExperiment}to preserve lookup compatibility.
}
README.md:49
- The table header separator was updated but the column titles were removed. Please restore the header row (e.g.,
| SummarizedExperiment-compatible Functions | Description |).
|----|----|
R/ggplot2_methods.R:44
- The unqualified call to
map()(andenquos()) may fail ifpurrr(andrlang) are not imported. Consider using namespace prefixes (e.g.,purrr::map,rlang::enquos) or ensure these packages are listed in Imports.
map(~ quo_name(.x)) %>% unlist()
DESCRIPTION:4
- The package version was bumped to 1.19.1 but the NEWS entry only documents version 1.16.0. Please synchronize the version number and NEWS sections to reflect all intermediate releases.
Version: 1.19.1
|
Tagging for knowledge @teunbrand @almahmoud @mblue9 |
teunbrand
reviewed
Jul 10, 2025
…3.22 release, enhance documentation for as_tibble and ggplot methods, and add new import for cli package.
…proved clarity and compatibility with ggplot2.
…by removing S7 method registration. Update DESCRIPTION to remove S7 as a suggested dependency and enhance NEWS documentation for clarity.
stemangiola
changed the title
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