R/plotSpectraJS.R

In bryanhanson/ChemoSpec: Exploratory Chemometrics for Spectroscopy

#'
#' Plot a Spectra Object Interactively
#'
#' This function uses the d3.js JavaScript library by Mike Bostock to plot a \code{\link{Spectra}}
#' object interactively.  This is most useful for data exploration.  For high
#' quality plots, consider \code{\link{plotSpectra}}.
#'
#' The spectral data are incorporated into the web page. Keep in mind that very large
#' data sets, like NMR spectra with 32K points, will bog down the browser.
#' In these cases, you may need to limit the number of samples in passed to this function.
#' See \code{\link{removeSample}} or use argument \code{which}.
#'
#' @param spectra `r .writeDoc_Spectra1()`
#'
#' @param which Integer.  If not \code{NULL}, specifies by number which spectra to plot.
#' If greater control is needed, use \code{\link{removeSample}} which is more flexible
#' before calling this function.
#'
#' @param browser Character.  Something that will make sense to your OS.  Only
#' necessary if you want to override your system specified browser as
#' understood by \code{R}.  See below for further details.
#'
#' @param minify Logical.  Shall the JavaScript be minified?  This improves
#' performance.  However, it requires package \code{js} which in turn requires
#' package \code{V8}.  The latter is not available on all platforms.  Details
#' may be available at \url{https://github.com/jeroen/V8}
#'
#' @return None; side effect is an interactive web page.  The temporary
#' directory containing the files that drive the web page is written to the
#' console in case you wish to use those files.  This directory is deleted when
#' you quit R.  If you wish to read the file, don't minify the code, it will be
#' unreadable.
#'
##' @section Browser Choice: The browser is called by
##' \code{\link[utils]{browseURL}}, which
##' in turn uses \code{options("browser")}.  Exactly how this is handled
##' is OS dependent.
##'
##' @section RStudio Viewer: If browser is \code{NULL}, you are using RStudio, and a
#' viewer is specified, this will be called.  You can stop this by with
#' \code{options(viewer = NULL)}.
##'
##' @section Browser Choice (Mac): On a Mac, the default browser is called
##' by \code{/bin/sh/open}
##' which in turn looks at which browser you have set in the system settings.  You can
##' override your default with
##' \code{browser = "/usr/bin/open -a 'Google Chrome'"} for example.
##'
##' @section Browser Choice & Performance:  You can check the performance of
##' your browser at peacekeeper.futuremark.com  The most relevant score
##' is the rendering category.
#'
#' @author `r .writeDoc_Authors("BH")`
#'
#' @seealso \code{\link{plotSpectra}} for non-interactive plotting.  Details
#' about \code{d3.js} are at \url{https://d3js.org}. Additional documentation at
#' \url{https://bryanhanson.github.io/ChemoSpec/}
#'
#'
#' @keywords plot
#'
#' @examples
#'
#' if (interactive()) {
#'   require("jsonlite")
#'   require("js")
#'   data(metMUD2)
#'   plotSpectraJS(metMUD2)
#' }
#' @export plotSpectraJS
#'
#' @importFrom utils browseURL
#'
plotSpectraJS <- function(spectra, which = NULL, browser = NULL, minify = TRUE) {

  # This is the R front end controlling everything

  .chkArgs(mode = 11L)
  chkSpectra(spectra)

  if (!is.null(which)) {
    which <- as.integer(which)
    which2 <- setdiff(1:length(spectra$names), which)
    spectra <- removeSample(spectra, rem.sam = which2)
  }

  if (!requireNamespace("jsonlite", quietly = TRUE)) {
    stop("You need install package jsonlite to use this function")
  }

  # Check to see if spectra$freq is increasing - if not, the scales will be inverted
  # Silently reverse things
  if (is.unsorted(spectra$freq)) {
    spectra$freq <- rev(spectra$freq)
    spectra$data <- spectra$data[, ncol(spectra$data):1]
  }

  if (requireNamespace("jsonlite", quietly = TRUE)) {

    # Break the pieces of the Spectra object out into
    # separate JSON entities
    # These will be global variables in the JavaScript

    Freq <- jsonlite::toJSON(spectra$freq)
    D0 <- jsonlite::toJSON(spectra$data)
    D1 <- jsonlite::toJSON(spectra$data)
    Names <- jsonlite::toJSON(paste(" ", spectra$names, sep = "  "))
    Groups <- jsonlite::toJSON(spectra$groups)
    Colors <- jsonlite::toJSON(spectra$colors)
    xUnit <- jsonlite::toJSON(spectra$unit[1])
    Desc <- jsonlite::toJSON(spectra$desc)
    Dx <- jsonlite::toJSON(range(spectra$freq))
    Dy <- jsonlite::toJSON(range(spectra$data))

    # Note: D1 is a copy of the data which will be modified for plotting
    # D0, the original data, and will not be changed

    # This vector will keep track of which spectra are to be plotted
    sampleBOOL <- c(1L, rep(0, length(spectra$names) - 1))
    sampleBOOL <- jsonlite::toJSON(sampleBOOL)

    # Prepare for writing
    # Groups commented out as it is not currently used

    data1 <- paste("var Freq = ", Freq, sep = "")
    data2 <- paste("var D0 = ", D0, sep = "")
    data3 <- paste("var D1 = ", D1, sep = "")
    data4 <- paste("var Names = ", Names, sep = "")
    data5 <- paste("var Groups = ", Groups, sep = "")
    data6 <- paste("var Colors = ", Colors, sep = "")
    data7 <- paste("var xUnit = ", xUnit, sep = "")
    data8 <- paste("var Desc = ", Desc, sep = "")
    data9 <- paste("var Dx = ", Dx, sep = "")
    data10 <- paste("var Dy = ", Dy, sep = "")
    data11 <- paste("var sampleBOOL = ", sampleBOOL, sep = "")

    # Get the JavaScript modules & related files

    td <- tempdir()
    fd <- system.file("extdata", package = "ChemoSpec")
    pSfiles <- c(
      "pS.css", "pS_globals.js", "pS_controls.js",
      "pS_brushNguides.js", "pS_main.js", "plotSpectraJS.html", "pS_spectra.js"
    )
    chk2 <- file.copy(
      from = file.path(fd, pSfiles), to = file.path(td, pSfiles),
      overwrite = TRUE
    )
    if (!all(chk2)) stop("Copying to temporary directory failed")

    js1 <- readLines(con = file.path(td, "pS_globals.js"))
    js2 <- readLines(con = file.path(td, "pS_brushNguides.js"))
    js3 <- readLines(con = file.path(td, "pS_controls.js"))
    js4 <- readLines(con = file.path(td, "pS_spectra.js"))
    js5 <- readLines(con = file.path(td, "pS_main.js"))

    # The following are used to wrap the entire JS code in a
    # scoping function so that performance is improved.

    # scopeFunHeader <- "(function() {"
    # scopeFunTail <- "})();"

    # Combine, then optionally minify for faster performance, write

    text <- c(
      data1, data2, data3, data4,
      data5, data6, data7, data8, data9, data10, data11,
      js1, js2, js3, js4, js5
    )

    if (minify) {
      if (requireNamespace("js", quietly = TRUE)) {
        text <- js::uglify_optimize(text, unused = FALSE)
      }
      if (!requireNamespace("js", quietly = TRUE)) {
        stop("You need install package js to minify the JavaScript code")
      }
    }


    writeLines(text, sep = "\n", con = file.path(td, "pS.js"))

    # Open the file in a browser

    pg <- file.path(td, "plotSpectraJS.html")
    if (!is.null(browser)) {
      browseURL(pg, browser = browser)
    } else {
      # open in RStudio if viewer is not null
      # similar to htmltools::html_print
      viewer <- getOption("viewer")
      if (is.null(browser) && !is.null(viewer)) {
        viewer(pg)
      } else {
        browseURL(pg)
      }
    }

    message("The plotSpectraJS web page is in the following\ntemp directory which is deleted when you quit R: ")
    message(td)
    return(invisible())
  }
}