## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = FALSE, comment = "#>", eval=TRUE ) ## ---- eval=FALSE-------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("easyreporting") ## ----------------------------------------------------------------------------- library("easyreporting") ## ----------------------------------------------------------------------------- proj.path <- file.path(tempdir(), "bioinfo_report") er <- easyreporting(filenamePath=proj.path, title="example_report", author=c("Dario Righelli")) ## ----------------------------------------------------------------------------- mkdTitle(er, title="Code Chunks", level=1) mkdGeneralMsg(er, "A simple paragraph useful to describe my code chunk...") ## ----------------------------------------------------------------------------- mkdTitle(er, title="Manual code chunk", level=2) mkdCodeChunkSt(er) variable <- 1 mkdVariableAssignment(er, "variable", `variable`, show=TRUE) mkdCodeChunkEnd(er) ## ----------------------------------------------------------------------------- optList <- makeOptionsList(echoFlag=TRUE, includeFlag=TRUE) mkdCodeChunkSt(er, optionList=optList) mkdCodeChunkEnd(er) ## ----------------------------------------------------------------------------- ## moreover I can add a list of files to source in che code chunk RFilesList <- list.files(system.file("script", package="easyreporting"), full.names=TRUE) mkdCodeChunkSt(er, optionList=optList, sourceFilesList=RFilesList) mkdGeneralMsg(er, message="v <- fakeFunction(10)") mkdCodeChunkEnd(er) ## ----------------------------------------------------------------------------- mkdCodeChunkComplete(er, message="v <- fakeFunction(11)") ## ----------------------------------------------------------------------------- optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE) mkdCodeChunkCommented(er, commentMsg="This is the comment of the following code chunk", codeMsg="v <- fakeFunction(12)", optionList=optList, sourceFilesList=NULL) ## ----------------------------------------------------------------------------- compile(er) ## ----------------------------------------------------------------------------- sessionInfo()