cont. rknit

R/rknit/rknit.sh

@@ -4,32 +4,29 @@
 rknit(){
     ## rscript=/projects/project-raphael/Rcode/misc/DivisionPerpendicularity.R
     ## rscript=/home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R
+    ## rscript=/Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_example.R
     rscript=$1
+
 #    tmdRmd=$(mktemp  --suff .Rmd)
     tmdRmd=$(basename $rscript .R).Rmd
 
-    echo '# '$(basename $rscript .R) > $tmdRmd
+#    echo '# '$(basename $rscript .R) > $tmdRmd
 
     ## alternatively we could use the header argument for knit2html
     echo '
-
 <style type="text/css">
-
-body {
- max-width: 80%;
-}
+    body {
+        max-width: 80%;
+    }
 </style>
-
 ```{r}
-    ' >> $tmdRmd
-    cat $rscript | grep -Fv "#!" | Rscript  -e 'require(stringr); require(dplyr); readLines(file("stdin")) %>% str_replace("##> ([^{]*)[{](.*)[}]", "```\n\\1\n```{r \\2}") %>% writeLines(stdout()) ' >> $tmdRmd
+    ' > $tmdRmd
+
+#    cat $rscript | grep -Fv '#!' | Rscript --vanilla  - 'require(stringr); require(dplyr); readLines(file("stdin")) %>% str_replace("^#([#]*)> ([^{]*)([{]+.+[}])?", "```\n\\1 \\2\n```{r \\3}") %>% collapsewriteLines(stdout())' # >> $tmdRmd
+    cat $rscript | grep -Fv '#!' | Rscript --vanilla -e 'source("/Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_preprocessor.R")'  >> $tmdRmd
+
     echo '```' >> $tmdRmd
 
     echo 'require(knitr); options(width=150); opts_knit$set(cache = TRUE); knit2html("'$tmdRmd'", output="'$(basename $rscript .R)'")' | R --vanilla -q
 }
 
-echo '
-
-##> # Prepare elongation data
-
-' | Rscript  -e 'require(stringr); require(dplyr); readLines(file("stdin")) %>% str_replace("##> ([^{]*)[{](.*)[}]", "```\n\\1\n```{r \\2}") %>% writeLines(stdout()) '

R/rknit/rknit_example.R

+#> {message=F, echo=F}
 require(dplyr)
-require(gplot)
+require(ggplot2)
 
-##> test
+###> test heading
+
+#> ... followed by some markup
+head(iris)
+
+#> some markup
 ggplot(iris, aes(Species, Sepal.Length, fill=Species)) + geom_boxplot() + scale_fill_discrete(guide=F)
 
 
+#> {fig.width=14}
+## just chunk definition without markdown text or header
+
+ggplot(iris, aes(Species, Sepal.Length, fill=Species)) + geom_boxplot() + scale_fill_discrete(guide=F)
 
-# source /Users/brandl/Dropbox/Public/datautils/R/rknit/rknit.sh ; rknit /Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_example.R
\ No newline at end of file
+# source /Users/brandl/Dropbox/Public/datautils/R/rknit/rknit.sh ;
+# rknit /Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_example.R

R/rknit/rknit_preprocessor.R

+require(stringr);
+require(dplyr);
+
+#readLines(file("stdin")) %>%
+mdRegex <- "^#([#]*)> ([^{]*)([{]+(.+)[}])?"
+
+
+#str_match("##> test heading", mdRegex)
+#str_match("##> test heading {fig.width=10}", mdRegex)
+#str_match("#> simple markup", mdRegex)
+#str_match("#>  {fig.width=10}", mdRegex)
+
+readLines(file("/Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_example.R")) %>%
+    str_replace(mdRegex, "```\n\\1 \\2\n```{r \\4}") %>% paste(collapse="\n") %>% cat(stdout())
+