Remove software carpentries logo

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

diff --git a/bin/chunk-options.R b/bin/chunk-options.R
index 5836973226adfab41d0423143aa0cccc09317c43..8e0d62af7eed10817d7c3c4d2bc3534a8c2a2b2b 100644 (file)
--- a/bin/chunk-options.R
+++ b/bin/chunk-options.R
@@ -8,7 +8,19 @@ library("knitr")
 
 fix_fig_path <- function(pth) file.path("..", pth)
 
-## We use the rmd- prefix for the figures generated by the lssons so
+
+## We set the path for the figures globally below, so if we want to
+## customize it for individual episodes, we can append a prefix to the
+## global path. For instance, if we call knitr_fig_path("01-") in the
+## first episode of the lesson, it will generate the figures in
+## `fig/rmd-01-`
+knitr_fig_path <- function(prefix) {
+    new_path <- paste0(opts_chunk$get("fig.path"),
+                      prefix)
+    opts_chunk$set(fig.path = new_path)
+}
+
+## 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,
@@ -17,30 +29,42 @@ fix_fig_path <- function(pth) file.path("..", pth)
 
 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.
 
 hook_in <- function(x, options) {
+  lg <- tolower(options$engine)
+  style <- paste0(".language-", lg)
+
   stringr::str_c("\n\n~~~\n",
-                 paste0(x, collapse="\n"),
-                 "\n~~~\n{: .r}\n\n")
+    paste0(x, collapse="\n"),
+    "\n~~~\n{: ", style, "}\n\n")
 }
 
 hook_out <- function(x, options) {
   x <- gsub("\n$", "", x)
   stringr::str_c("\n\n~~~\n",
-                   paste0(x, collapse="\n"),
-                 "\n~~~\n{: .output}\n\n")
+    paste0(x, collapse="\n"),
+    "\n~~~\n{: .output}\n\n")
 }
 
 hook_error <- function(x, options) {
   x <- gsub("\n$", "", x)
   stringr::str_c("\n\n~~~\n",
-                 paste0(x, collapse="\n"),
-                 "\n~~~\n{: .error}\n\n")
+    paste0(x, collapse="\n"),
+    "\n~~~\n{: .error}\n\n")
+}
+
+hook_warning <- function(x, options) {
+  x <- gsub("\n$", "", x)
+  stringr::str_c("\n\n~~~\n",
+    paste0(x, collapse = "\n"),
+    "\n~~~\n{: .warning}\n\n")
 }
 
-knit_hooks$set(source = hook_in, output = hook_out, warning = hook_error,
-               error = hook_error, message = hook_out)
+knit_hooks$set(source = hook_in, output = hook_out, warning = hook_warning,
+  error = hook_error, message = hook_out)