R/buildChapterGraph.R

In rebook: Re-using Content in Bioconductor Books

#' Build the chapter dependency graph
#'
#' Build the dependency graph between chapter based on their \code{\link{extractCached}} calls to each other.
#'
#' @inheritParams scrapeDependencies
#'
#' @return A directed \link[igraph]{graph} object from the \pkg{igraph} package,
#' where each node is a chapter and is connected to its dependencies by an edge.
#'
#' @author Aaron Lun
#'
#' @examples
#' dir <- tempfile()
#' dir.create(dir)
#'
#' tmp1 <- file.path(dir, "alpha.Rmd")
#' write(file=tmp1, "```{r, echo=FALSE, results='asis'}
#' rebook::chapterPreamble()
#' ```
#' 
#' ```{r}
#' rodan <- 1
#' ```")
#'
#' tmp2 <- file.path(dir, "bravo.Rmd")
#' write(file=tmp2, "```{r, echo=FALSE, results='asis'}
#' rebook::chapterPreamble()
#' ```
#' 
#' ```{r}
#' extractCached('alpha.Rmd')
#' ```")
#' 
#' # Building the chapter graph:
#' g <- buildChapterGraph(dir)
#' plot(g)
#'  
#' @export
#' @importFrom CodeDepends readScript scriptInfo
buildChapterGraph <- function(dir, recursive=TRUE, pattern="\\.Rmd$") {
    # CodeDepends uses the current WD to check whether a string corresponds to
    # a file path, hence the need to keep it happy by changing the WD.
    old <- getwd()
    setwd(dir)
    on.exit(setwd(old))

    all.rmds <- list.files(".", recursive=recursive, pattern=pattern)
    collated <- list()
    
    for (i in seq_along(all.rmds)) {
        txt <- readScript(all.rmds[i], type="Stangled")
        all.info <- scriptInfo(txt)
        dependencies <- character(0)

        for (j in seq_along(all.info)) {
            current <- all.info[[j]]
            if ("extractCached" %in% names(current@functions)) {
                dependencies <- union(dependencies, current@files)
            }
        }

        collated[[all.rmds[i]]] <- intersect(dependencies, all.rmds)
    }

    all.upstream <- unlist(collated)
    X <- rbind(all.upstream, rep(names(collated), lengths(collated)))
    igraph::make_graph(X, isolates=setdiff(all.rmds, X))
 }