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#' Display of a diagram representing the network structure of a GRiwrm object#'#' @param x \[GRiwrm object\] data to display. See [CreateGRiwrm] for details#' @param display [logical] if `TRUE` plots the diagram, returns the mermaid code otherwise#' @param orientation [character] orientation of the graph. Possible values are "LR" (left-right), "RL" (right-left), "TB" (top-bottom), or "BT" (bottom-top). "LR" by default#' @param box_colors [list] containing the color used for the different types of nodes#' @param defaultClassDef [character] default style apply to all boxes#' @param ... Not used#'#' @details This function only works inside RStudio because the HTMLwidget produced by DiagrammeR#' is not handled on some platforms#'#' @return Mermaid code of the diagram if display is `FALSE`, otherwise the function returns the diagram itself.#'#' @export#'#' @example man-examples/CreateGRiwrm.R#'plot.GRiwrm <- function(x, display = TRUE, orientation = "LR", box_colors = c(UpstreamUngauged = "#eef", UpstreamGauged = "#aaf", IntermediateUngauged = "#efe", IntermediateGauged = "#afa", Reservoir = "#9de", DirectInjection = "#faa"), defaultClassDef = "stroke:#333", ...) { stopifnot(inherits(x, "GRiwrm"), is.logical(display), length(display) == 1, is.character(orientation), length(orientation) == 1, is.character(box_colors), length(setdiff(names(box_colors), c("UpstreamUngauged", "UpstreamGauged", "IntermediateUngauged", "IntermediateGauged", "DirectInjection", "Reservoir"))) == 0) nodes <- sprintf("id_%1$s[%1$s]", x$id) g2 <- x[!is.na(x$down),] links <- paste( sprintf("id_%1$s", g2$id), "-->|", round(g2$length, digits = 0), "km|", sprintf("id_%1$s", g2$down) ) x$nodeclass <- sapply(x$id, getNodeClass, griwrm = x) node_class <- lapply(unique(x$nodeclass), function(nc) { x$id[x$nodeclass == nc] }) names(node_class) <- unique(x$nodeclass) node_class <- lapply(node_class, function(id) if (length(id) > 0) paste0("id_", id)) node_class <- paste("class", sapply(node_class, paste, collapse = ","), names(node_class)) css <- c( paste("classDef default", defaultClassDef), paste("classDef", names(box_colors), paste0("fill:", box_colors)), paste("classDef", paste0(names(box_colors[1:5]), "Diversion"), sprintf("fill:%s, stroke:%s, stroke-width:3px", box_colors[1:5], box_colors["DirectInjection"])) ) if (length(getDiversionRows(g2)) > 0) { css <- c(css, paste("linkStyle", getDiversionRows(g2) - 1, sprintf("stroke:%s, stroke-width:2px,stroke-dasharray: 5 5;", box_colors["DirectInjection"]))) } diagram <- paste(c(paste("graph", orientation), nodes, links, node_class, css),7172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
collapse = "\n\n")
class(diagram) <- c("mermaid", class(diagram))
if (display) {
plot(diagram)
} else {
return(diagram)
}
}
getNodeClass <- function(id, griwrm) {
props <- getNodeProperties(id, griwrm)
if (props$DirectInjection) {
nc <- "DirectInjection"
} else if (props$Reservoir) {
nc <- "Reservoir"
} else {
nc <- paste0(props$position, props$calibration)
}
if (props$Diversion) nc <- paste0(nc, "Diversion")
return(nc)
}
#' Generate a file from a mermaid diagram
#'
#' This function download the file from https://mermaid.ink which generates the image.
#' The file is downloaded only if it does not already exist.
#'
#' @details
#' Use this function with [knitr::include_graphics] to display a mermaid diagram
#' in a Rmarkdown document. Compared to the `diagrammeR::mermaid` function, the
#' generated image is not a HTMLwidget and can be knit in pdf through latex and
#' moreover, its size can be controlled with `fig.width` and `fig.height`.
#'
#' @param diagram Diagram in mermaid markdown-like language or file (as a connection or file name) containing a diagram specification
#' @param theme Mermaid theme (See https://mermaid.js.org/config/theming.html#available-themes)
#' @param format Image format (either `"jpg"`, or `"png"`, or `"svg"`)
#' @param dir.dest Destination folder for the downloaded image. This parameter is
#' ignored if `file.dest` contains a folder path.
#' @param file.dest Path to the downloaded image. It's combined with `dir.dest`
#' if it only contains the name of the file without a folder path.
#' @param link Link generated by [mermaid_gen_link]
#' @param server URL of the server used to generate the link
#'
#' @return The path to the downloaded image or `NA` if the download failed.
#' In this latter case, get the error message in the attribute "error".
#' @noRd
#' @rdname mermaid
#'
#' @examples
#' diagram <- "flowchart LR\n A --> B"
#' mermaid_gen_link(diagram)
#' f <- mermaid(diagram)
#' f
#' \dontrun{
#' # For displaying the diagram in Rmarkdown document
#' knitr::include_graphics(mermaid(diagram))
#' }
#'
#' # Clean temporary folder
#' unlink(f)
mermaid <- function(diagram,
format = "png",
theme = "default",
dir.dest = tempdir(),
file.dest = paste0(rlang::hash(link), ".", format),
link = mermaid_gen_link(diagram, theme = theme, format = format)) {
if (!dir.exists(dir.dest)) dir.create(dir.dest, recursive = TRUE, showWarnings = FALSE)
if (dirname(file.dest) == ".") file.dest <- file.path(dir.dest, file.dest)
if (!file.exists(file.dest)) {
ret <- tryCatch(
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utils::download.file(link, file.dest, quiet = TRUE, mode = "wb"),
error = function(e) e
)
if (inherits(ret, "error")) {
file.dest <- NA
attr(file.dest, "error") <- ret$message
}
}
return(file.dest)
}
#' Compress data in pako format
#'
#' @param data [character] data to compress
#'
#' @return Raw compresses data.
#' @source Translated from python script
#' https://github.com/mermaid-js/mermaid-live-editor/discussions/1291#discussioncomment-6837936
#' @noRd
pako_deflate <- function(data) {
# compress = zlib.compressobj(9, zlib.DEFLATED, 15, 8,zlib.Z_DEFAULT_STRATEGY)
compress <- zlib::compressobj(
level = 9,
method = zlib::zlib$DEFLATED,
wbits = 15,
memLevel = 8,
strategy = zlib::zlib$Z_DEFAULT_STRATEGY
)
compressed_data <- compress$compress(charToRaw(data))
compressed_data <- c(compressed_data, compress$flush())
return(compressed_data)
}
#' @noRd
mermaid_gen_link <- function(diagram, theme = "default", format = "png", server = "https://mermaid.ink") {
is_connection_or_file <- inherits(diagram[1], "connection") ||
file.exists(diagram[1])
if (is_connection_or_file) {
diagram <- readLines(diagram, encoding = "UTF-8", warn = FALSE)
}
if (length(diagram) > 1) {
diagram <- paste(diagram, collapse = "\n")
}
jGraph <-
list(code = diagram,
mermaid = list(theme = theme)) |> jsonlite::toJSON(auto_unbox = TRUE)
deflated <- pako_deflate(jGraph)
dEncode = gsub("\n", "", jsonlite::base64url_enc(deflated))
mode <- ifelse(format != "svg", "img", "svg")
link = sprintf("%s/%s/pako:%s", server, mode, dEncode)
if (format != "svg") {
link <- paste0(link, "?type=", format)
}
return(link)
}
#' Plot a PNG file
#'
#' @source From https://stackoverflow.com/a/28729601/5300212
#' @param path Path of the file
#' @param add [logical] Add the image to the existing plot
#' @param pic output of
#'
#' @return Nothing, used to side effect.
#' @noRd
#'
plot_png = function(path, add=FALSE)
{
# read the file
pic <- png::readPNG(path, native = TRUE)
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res <- dim(pic)[2:1] # get the resolution, [x, y]
if (!add) # initialize an empty plot area if add==FALSE
plot(1,1,xlim=c(1,res[1]),ylim=c(1,res[2]),asp=1,type='n',xaxs='i',yaxs='i',xaxt='n',yaxt='n',xlab='',ylab='',bty='n')
graphics::rasterImage(pic,1,1,res[1],res[2])
}
#' Plot a mermaid diagram
#'
#' @param x [character] mermaid diagram dialect
#' @param add [logical] to add the diagram on the existing plot
#' @param ... Not used
#'
#' @return Nothing, used for side effect.
#' @export plot.mermaid
#' @export
#'
#' @examples
#' s <- "flowchart LR
#' A -> B"
#' class(s) <- c("mermaid", class(s))
#' plot(s)
plot.mermaid <- function(x, add = FALSE, ...) {
file_mmd <- mermaid(x)
if (is.na(file_mmd)) {
warning("Mermaid diaagram generation failed with error:\n",
attr(file_mmd, "error"))
return(invisible())
}
plot_png(file_mmd, add = add)
unlink(file_mmd)
invisible()
}