## ----install_rmarkdown, eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## install.packages("rmarkdown")


## ----render_rmarkdown, eval=FALSE, message=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## rmarkdown::render("sample.Rmd", clean=TRUE, output_format="BiocStyle::html_document")


## $ Rscript -e "rmarkdown::render('sample.Rmd', output_format='BiocStyle::html_document', clean=TRUE)"


## $ make -B


## ----kable----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(knitr)
kable(iris[1:12,])


## ----dt-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(DT)
datatable(iris)


## ----some_jitter_plot, eval=TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(ggplot2)
dsmall <- diamonds[sample(nrow(diamonds), 1000), ]
ggplot(dsmall, aes(color, price/carat)) + geom_jitter(alpha = I(1 / 2), aes(color=color))


## ----some_custom_inserted_plot, eval=TRUE, warning=FALSE, message=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------
png("myplot.png")
ggplot(dsmall, aes(color, price/carat)) + geom_jitter(alpha = I(1 / 2), aes(color=color))
dev.off()


## ----rmarkdown_symbolic_link, eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## cd ~/.html
## ln -s ~/bigdata/today/rmarkdown/sample.html sample.html


## ----sessionInfo----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
sessionInfo()