Optimisations
Kevin Rue-Albrecht
University of Oxfordkevin.rue-albrecht@imm.ox.ac.uk
16 March 2026
Optimisations.RmdLibraries
Attach packages used in this vignettes.
library("BiocPkgTools")
#> Loading required package: htmlwidgets
library("BiocPkgToolsPlus")
#> Loading required package: biocViewsFirst step
Fetch the combined listing of packages from all Bioconductor repositories.
bioc_pkg_list <- get_all_biocpkglist(verbose = FALSE)
bioc_pkg_list
#> # A tibble: 3,753 × 49
#> Package Version Depends Suggests License MD5sum NeedsCompilation Title
#> <chr> <chr> <list> <list> <chr> <chr> <chr> <chr>
#> 1 a4 1.58.0 <chr [5]> <chr [7]> GPL-3 56d24… no "Aut…
#> 2 a4Base 1.58.0 <chr [2]> <chr [4]> GPL-3 5efa1… no "Aut…
#> 3 a4Classif 1.58.0 <chr [2]> <chr [4]> GPL-3 20d28… no "Aut…
#> 4 a4Core 1.58.0 <chr [1]> <chr [2]> GPL-3 bd94b… no "Aut…
#> 5 a4Preproc 1.58.0 <chr [1]> <chr [4]> GPL-3 2c56d… no "Aut…
#> 6 a4Reporting 1.58.0 <chr [1]> <chr [2]> GPL-3 9d31f… no "Aut…
#> 7 ABarray 1.78.0 <chr [1]> <chr [2]> GPL 6ad7c… no "Mic…
#> 8 abseqR 1.28.0 <chr [1]> <chr [1]> GPL-3 … 9ec04… no "Rep…
#> 9 ABSSeq 1.64.0 <chr [2]> <chr [1]> GPL (>… b12fd… no "ABS…
#> 10 acde 1.40.0 <chr [2]> <chr [2]> GPL-3 c04fa… no "Art…
#> # ℹ 3,743 more rows
#> # ℹ 41 more variables: Description <chr>, biocViews <list>, Author <list>,
#> # Maintainer <list>, git_url <chr>, git_branch <chr>, git_last_commit <chr>,
#> # git_last_commit_date <chr>, `Date/Publication` <chr>, source.ver <chr>,
#> # win.binary.ver <chr>, `mac.binary.big-sur-x86_64.ver` <chr>,
#> # `mac.binary.big-sur-arm64.ver` <chr>, vignettes <list>,
#> # vignetteTitles <list>, hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>, …Wordclouds
The ‘Getting started’ vignette demonstrated a single method for producing a wordcloud. This section offers alternatives.
Let’s start by getting the count of co-occurrences for each biocViews term with a query term, obtained as follows:
library("dplyr")
out <- get_view_cooccurrences(
view = "Spatial",
pkg_list = bioc_pkg_list
)
out |>
arrange(desc(value))
#> # A tibble: 65 × 2
#> package value
#> <chr> <int>
#> 1 Transcriptomics 51
#> 2 SingleCell 49
#> 3 GeneExpression 42
#> 4 DataImport 18
#> 5 RNASeq 15
#> 6 Clustering 14
#> 7 ImmunoOncology 10
#> 8 DataRepresentation 8
#> 9 CellBasedAssays 7
#> 10 QualityControl 7
#> # ℹ 55 more rowsIn contrast to the interactive workclouds produced by wordcloud2, the wordcloud package can be used to produce static wordclouds, with a little bit more work:
library(wordcloud)
library(RColorBrewer)
set.seed(1)
wordcloud(
words = out$package,
freq = out$value,
colors = brewer.pal(n = 8, name = "Dark2"),
random.color = TRUE,
rot.per=.2,
scale=c(3, .5)
)
Wordcloud.
Reproducibility
The BiocPkgToolsPlus package (kevinrue, 2026) was made possible thanks to:
- R (R Core Team, 2025)
- BiocStyle (Oleś, 2025)
- knitr (Xie, 2025)
- RefManageR (McLean, 2017)
- rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2025)
- sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2025)
- testthat (Wickham, 2011)
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("BiocPkgToolsPlus.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("BiocPkgToolsPlus.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2026-03-16 08:57:00 UTC"Wallclock time spent generating the vignette.
#> Time difference of 6.34 secsR session information.
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#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────Bibliography
This vignette was generated using BiocStyle (Oleś, 2025) with knitr (Xie, 2025) and rmarkdown (Allaire, Xie, Dervieux et al., 2025) running behind the scenes.
Citations made with RefManageR (McLean, 2017).
[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.30. 2025. URL: https://github.com/rstudio/rmarkdown.
[2] kevinrue. Demonstration of a Bioconductor Package. https://github.com/kevinrue/BiocPkgToolsPlus/BiocPkgToolsPlus - R package version 0.99.0. 2026. DOI: 10.18129/B9.bioc.BiocPkgToolsPlus. URL: http://www.bioconductor.org/packages/BiocPkgToolsPlus.
[3] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.
[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.38.0. 2025. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.
[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2025. URL: https://www.R-project.org/.
[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/articles/RJ-2011-002/.
[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.3. 2025. URL: https://github.com/r-lib/sessioninfo#readme.
[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.51. 2025. URL: https://yihui.org/knitr/.