diff --git a/R/utils.R b/R/utils.R index 30df041..2d4b6db 100644 --- a/R/utils.R +++ b/R/utils.R @@ -177,8 +177,9 @@ ipdf <- function(file, ...) { #' plot(1:5) #' dev.off() #' +#' pngfile <- file.path(tmpdir, "test.png") #' pdf2png(pdffile) -#' pdf2png(pdffile, outfile="test.png") +#' pdf2png(pdffile, outfile=pngfile) #' #' testfile <- system.file("/doc/intro.pdf", package="limma") #' if(file.exists(testfile)) { diff --git a/man/pdf2png.Rd b/man/pdf2png.Rd index 8256fae..1ea1aa9 100644 --- a/man/pdf2png.Rd +++ b/man/pdf2png.Rd @@ -48,8 +48,9 @@ dpi) PNG files. plot(1:5) dev.off() + pngfile <- file.path(tmpdir, "test.png") pdf2png(pdffile) - pdf2png(pdffile, outfile="test.png") + pdf2png(pdffile, outfile=pngfile) testfile <- system.file("/doc/intro.pdf", package="limma") if(file.exists(testfile)) { diff --git a/vignettes/cascadePlot.Rmd b/vignettes/cascadePlot.Rmd deleted file mode 100644 index 57dc5df..0000000 --- a/vignettes/cascadePlot.Rmd +++ /dev/null @@ -1,65 +0,0 @@ ---- -title: "Cascade plot" -author: "Jitao David Zhang" -date: "`r Sys.Date()`" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Cascade plot in ribiosPlot} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -```{r setup, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>" -) -``` - -Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format: - -- Never uses retina figures -- Has a smaller default figure size -- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style - -## Vignette Info - -Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette. - -## Styles - -The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows: - - output: - rmarkdown::html_vignette: - css: mystyles.css - -## Figures - -The figure sizes have been customised so that you can easily put two images side-by-side. - -```{r, fig.show='hold'} -plot(1:10) -plot(10:1) -``` - -You can enable figure captions by `fig_caption: yes` in YAML: - - output: - rmarkdown::html_vignette: - fig_caption: yes - -Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**. - -## More Examples - -You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`. - -```{r, echo=FALSE, results='asis'} -knitr::kable(head(mtcars, 10)) -``` - -Also a quote using `>`: - -> "He who gives up [code] safety for [code] speed deserves neither." -([via](https://twitter.com/hadleywickham/status/504368538874703872))