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[rnaseq-cwl-training.git] / bin / chunk-options.R

diff --git a/bin/chunk-options.R b/bin/chunk-options.R
index f9435842034b264d147ef9549eab7ed94b595dff..6bd4aefaeb72ba14d2765e8dfffc8fa5592d91c9 100644 (file)
--- a/bin/chunk-options.R
+++ b/bin/chunk-options.R
@@ -20,7 +20,7 @@ knitr_fig_path <- function(prefix) {
     opts_chunk$set(fig.path = new_path)
 }
 
-## We use the rmd- prefix for the figures generated by the lssons so
+## We use the rmd- prefix for the figures generated by the lessons so
 ## they can be easily identified and deleted by `make clean-rmd`.  The
 ## working directory when the lessons are generated is the root so the
 ## figures need to be saved in fig/, but when the site is generated,
@@ -29,7 +29,9 @@ knitr_fig_path <- function(prefix) {
 
 opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
                fig.align = "center", fig.path = "fig/rmd-",
-               fig.process = fix_fig_path)
+               fig.process = fix_fig_path,
+               fig.width = 8.5, fig.height = 8.5,
+               fig.retina = 2)
 
 # The hooks below add html tags to the code chunks and their output so that they
 # are properly formatted when the site is built.
@@ -43,7 +45,7 @@ hook_in <- function(x, options) {
 hook_out <- function(x, options) {
   x <- gsub("\n$", "", x)
   stringr::str_c("\n\n~~~\n",
-                   paste0(x, collapse="\n"),
+                 paste0(x, collapse="\n"),
                  "\n~~~\n{: .output}\n\n")
 }