| Title: | A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor |
|---|---|
| Description: | Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters. |
| Authors: | Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut] |
| Maintainer: | Aaron Lun <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.36.0 |
| Built: | 2026-10-04 17:12:22 UTC |
| Source: | https://github.com/bioc/simpleSingleCell |
Execute code to set up the compilation environment at the start of every chapter.
chapterPreamble(cache = FALSE)chapterPreamble(cache = FALSE)
cache |
Logical indicating whether to cache code chunks. |
Compilation is performed with no tolerance for errors, no printing of package start-up messages, and no printing of warnings.
Numbers are printed to 4 digits of precision.
The BiocStyle package is automatically attached.
HTML elements are defined using setupHTML.
See setupHTML.
Aaron Lun
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} pi # four digits! ``` ```{r} warning('ASDASD') # warnings and messages are not saved in the HTML. ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} pi # four digits! ``` ```{r} warning('ASDASD') # warnings and messages are not saved in the HTML. ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))
Compile a Rmarkdown file - typically a chapter of a book -
so that extractCached calls work correctly in other chapters.
compileChapter(path, cache = TRUE)compileChapter(path, cache = TRUE)
path |
String containing a path to an Rmarkdown file. |
cache |
Logical scalar indicating whether the compilation should be cached. |
Compilation is performed in an isolated session using r from the callr package.
This ensures that settings from one chapter do not affect the next chapter.
If an error is encountered during compilation of any Rmarkdown file,
the standard output of render leading up to the error is printed out before the function exists.
All files are (re)compiled to generate the corresponding *_cache directories.
NULL is invisibly returned.
Aaron Lun
extractCached, which calls this function.
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") compileChapter(tmp) file.exists(sub(".Rmd$", ".html", tmp)) # output HTML exists. file.exists(sub(".Rmd$", "_cache", tmp)) # output cache exists. exists("rodan") # FALSEtmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") compileChapter(tmp) file.exists(sub(".Rmd$", ".html", tmp)) # output HTML exists. file.exists(sub(".Rmd$", "_cache", tmp)) # output cache exists. exists("rodan") # FALSE
Extract specific R objects from the knitr cache of a previously compiled Rmarkdown file (the “donor”) so that it can be used in the compilation process of another Rmarkdown file (the “acceptor”).
extractCached(path, chunk, objects, envir = topenv(parent.frame()))extractCached(path, chunk, objects, envir = topenv(parent.frame()))
path |
String containing the path to the donor Rmarkdown file. |
chunk |
String containing the name of the requested chunk. |
objects |
Character vector containing variable names for one or more objects to be extracted. |
envir |
Environment where the loaded objects should be stored. |
Each R object is extracted in its state at the requested chunk and inserted into envir.
Note that the object does not have to be generated or even referenced in chunk,
provided it was generated in a previous chunk.
The parser in this function is rather limited, so the donor Rmarkdown file is subject to several constraints:
All chunks involved in generating the requested objects (indirectly or otherwise) should be named.
All named chunks should be executed; eval=FALSE is not respected.
All relevant code occurs within triple backticks, i.e., any inline code should be read-only.
Unnamed chunks are allowed but cannot be referenced and will not be shown in the output of this function.
This should not be used for code that might affect variables in the named chunks,
i.e., code in unnamed chunks should be “read-only” with respect to variables in the named chunks.
Chunks with names starting with unref- are considered to be the same as unnamed chunks and will be ignored;
this is useful for figure-generating chunks that need to be referenced inside the donor report.
Obviously, this entire process assumes that donor report has already been compiled with cache=TRUE.
If not, extractCached will compile it (and thus generate the cache) using compileChapter.
Variables with names objects are created in envir.
A markdown chunk (wrapped in a collapsible element) is printed that contains all commands needed to generate those objects,
based on the code in the named chunks of the donor Rmarkdown file.
Aaron Lun
setupHTML and chapterPreamble, to set up the code for the collapsible element.
compileChapter, to compile a Rmarkdown report to generate the cache.
# Mocking up an Rmarkdown report. donor <- tempfile(fileext=".Rmd") write(file=donor, "```{r some-monsters} destoroyah <- 1 mecha.king.ghidorah <- 2 ``` ```{r more-monsters} space.godzilla <- 3 ``` ```{r} msg <- 'I am not referenced.' ``` ```{r unref-figure} plot(1, 1, main='I am also not referenced.') ``` ```{r even-more-monsters} megalon <- 4 ```") # Extracting stuff from it in another report. acceptor <- tempfile(fileext=".Rmd") dpb <- deparse(basename(donor)) write(file=acceptor, sprintf("```{r, echo=FALSE, results='asis'} chapterPreamble() ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='more-monsters', objects=c('space.godzilla', 'destoroyah')) ``` ```{r} space.godzilla * destoroyah ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='even-more-monsters', objects=c('megalon', 'mecha.king.ghidorah')) ``` ```{r} mecha.king.ghidorah * megalon ```", dpb, dpb)) rmarkdown::render(acceptor) if (interactive()) browseURL(sub(".Rmd$", ".html", acceptor))# Mocking up an Rmarkdown report. donor <- tempfile(fileext=".Rmd") write(file=donor, "```{r some-monsters} destoroyah <- 1 mecha.king.ghidorah <- 2 ``` ```{r more-monsters} space.godzilla <- 3 ``` ```{r} msg <- 'I am not referenced.' ``` ```{r unref-figure} plot(1, 1, main='I am also not referenced.') ``` ```{r even-more-monsters} megalon <- 4 ```") # Extracting stuff from it in another report. acceptor <- tempfile(fileext=".Rmd") dpb <- deparse(basename(donor)) write(file=acceptor, sprintf("```{r, echo=FALSE, results='asis'} chapterPreamble() ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='more-monsters', objects=c('space.godzilla', 'destoroyah')) ``` ```{r} space.godzilla * destoroyah ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='even-more-monsters', objects=c('megalon', 'mecha.king.ghidorah')) ``` ```{r} mecha.king.ghidorah * megalon ```", dpb, dpb)) rmarkdown::render(acceptor) if (interactive()) browseURL(sub(".Rmd$", ".html", acceptor))
Wraps the session information output chunk in a collapsible HTML element so that it doesn't dominate the compiled chapter.
prettySessionInfo()prettySessionInfo()
Aaron Lun
setupHTML and chapterPreamble, to set up the code for the collapsible element.
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))
Scrape Rmarkdown reports in the book for all required dependencies.
scrapeDependencies(dir)scrapeDependencies(dir)
dir |
String containing the path to the directory containing Rmarkdown reports.
This is searched recursively for all files ending in |
The output of this should be added to the Suggests field of the book's DESCRIPTION,
to make it easier to simply install all of its required dependencies.
Note that dependencies in inline code sections are not detected, so these should be explicitly mentioned in a standalone code chunk to be captured.
Character vector of required packages.
Aaron Lun tmp <- tempfile(fileext=".Rmd") write(file=tmp, "“'r A::a() “'
“'r library(B) require(C) “'")
scrapeDependencies(tempdir())
Set up Javascript and CSS elements for the custom collapsible class.
setupHTML()setupHTML()
The custom collapsible class allows us to hide details until requested by the user. This improves readability by reducing the clutter in the compiled chapter.
Prints HTML to set up JS and CSS elements.
Aaron Lun
chapterPreamble, which calls this function.
extractCached and prettySessionInfo, which use the custom collapsible class.
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))