R/mini_plots.R - IDS-Mannheim/kableExtra - Gitiles

 #' Helper functions to generate inline sparklines
 #'
 #' @description These functions helps you quickly generate sets of sparkline
 #' style plots using base R plotting system. Currently, we support histogram,
 #' boxplot, and line. You can use them together with `column_spec` to
 #' generate inline plot in tables. By default, this function will save images
 #' in a folder called "kableExtra" and return the address of the file.
 #'
 #' @param x Vector of values or List of vectors of values.
 #' @param width The width of the plot in pixel
 #' @param height The height of the plot in pixel
 #' @param res The resolution of the plot. Default is 300.
 #' @param same_lim T/F. If x is a list of vectors, should all the plots be
 #' plotted in the same range? Default is True.
 #' @param lim Manually specify plotting range in the form of
 #' `c(0, 10)`.
 #' @param xaxt On/Off for xaxis text
 #' @param yaxt On/Off for yaxis text
 #' @param ann On/Off for annotations (titles and axis titles)
 #' @param col Color for the fill of the histogram bar/boxplot box.
 #' @param border Color for the border.
 #' @param dir Directory of where the images will be saved.
 #' @param file File name. If not provided, a random name will be used
 #' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
 #' for HTML output
 #' @param ... extra parameters sending to `hist()`
 #'
 #' @export
 spec_hist <- function(x, width = 200, height = 50, res = 300,
                       breaks = "Sturges",
                       same_lim = TRUE, lim = NULL,
                       xaxt = 'n', yaxt = 'n', ann = FALSE,
                       col = "lightgray", border = NULL,
                       dir = if (is_latex()) rmd_files_dir() else tempdir(),
                       file = NULL,
                       file_type = if (is_latex()) "png" else "svg", ...) {
   if (is.list(x)) {
     if (same_lim & is.null(lim)) {
       lim <- base::range(unlist(x))
     }
     return(lapply(x, function(x_) {spec_hist(
       x = x_, width = width, height = height,
       breaks = breaks, same_lim = same_lim, lim = lim,
       xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, border = border,
       dir = dir, file = file, file_type = file_type, ...
     )}))
   }

   if (is.null(x)) return(NULL)

   if (is.null(lim)) {
     lim <- base::range(x)
   }

   file_type <- match.arg(file_type, c("svg", "png"))

   if (!dir.exists(dir)) {
     dir.create(dir)
   }

   if (is.null(file)) {
     file <- file.path(dir, paste0(
       "hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
   }

   if (file_type == "svg") {
     grDevices::svg(filename = file, width = width / res, height = height / res,
                    bg = 'transparent')
   } else {
     grDevices::png(filename = file, width = width, height = height, res = res,
                    bg = 'transparent')
   }

   graphics::par(mar = c(0, 0, 0.2, 0), lwd=0.5)
   graphics::hist(x, breaks = breaks, xlim = lim, border = border,
                  xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, ...)
   grDevices::dev.off()

   if (file_type == "svg") {
     svg_xml <- xml2::read_xml(file)
     svg_text <- as.character(svg_xml)
     unlink(file)
   } else {
     svg_text <- NULL
   }
   out <- list(path = file, dev = file_type, type = "hist",
               width = width, height = height, res = res,
               svg_text = svg_text)

   class(out) <- "kableExtraInlinePlots"
   return(out)
 }

 #' Helper functions to generate inline sparklines
 #'
 #' @description These functions helps you quickly generate sets of sparkline
 #' style plots using base R plotting system. Currently, we support histogram,
 #' boxplot, and line. You can use them together with `column_spec` to
 #' generate inline plot in tables. By default, this function will save images
 #' in a folder called "kableExtra" and return the address of the file.
 #'
 #' @param x Vector of values or List of vectors of values.
 #' @param width The width of the plot in pixel
 #' @param height The height of the plot in pixel
 #' @param res The resolution of the plot. Default is 300.
 #' @param add_label For boxplot. T/F to add labels for min, mean and max.
 #' @param label_digits If T for add_label, rounding digits for the label.
 #' Default is 2.
 #' @param same_lim T/F. If x is a list of vectors, should all the plots be
 #' plotted in the same range? Default is True.
 #' @param lim,xlim,ylim Manually specify plotting range in the form of
 #' `c(0, 10)`. `lim` is used in `spec_hist` and `spec_boxplot`; `xlim`
 #' and `ylim` are used in `spec_plot`.
 #' @param xaxt On/Off for xaxis text
 #' @param yaxt On/Off for yaxis text
 #' @param ann On/Off for annotations (titles and axis titles)
 #' @param col Color for the fill of the histogram bar/boxplot box.
 #' @param border Color for the border.
 #' @param boxlty Boxplot - box boarder type
 #' @param medcol Boxplot - median line color
 #' @param medlwd Boxplot - median line width
 #' @param dir Directory of where the images will be saved.
 #' @param file File name. If not provided, a random name will be used
 #' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
 #' for HTML output
 #' @param ... extraparameters passing to boxplot
 #'
 #' @export
 spec_boxplot <- function(x, width = 200, height = 50, res = 300,
                          add_label = FALSE, label_digits = 2,
                          same_lim = TRUE, lim = NULL,
                          xaxt = 'n', yaxt = 'n', ann = FALSE,
                          col = "lightgray", border = NULL,
                          boxlty = 0, medcol = "red", medlwd = 1,
                          dir = if (is_latex()) rmd_files_dir() else tempdir(),
                          file = NULL,
                          file_type = if (is_latex()) "png" else "svg", ...) {
   if (is.list(x)) {
     if (same_lim & is.null(lim)) {
       lim <- base::range(unlist(x))
     }
     return(lapply(x, function(x_) {spec_boxplot(
       x = x_, width = width, height = height,
       add_label = add_label, same_lim = same_lim, lim = lim,
       xaxt = xaxt, yaxt = yaxt, ann = ann,
       col = col, border = border,
       boxlty = boxlty, medcol = medcol, medlwd = medlwd,
       dir = dir, file = file, file_type = file_type, ...
     )}))
   }

   if (is.null(x)) return(NULL)

   if (is.null(lim)) {
     lim <- base::range(x)
     lim[1] <- lim[1] - (lim[2] - lim[1]) / 10
     lim[2] <- (lim[2] - lim[1]) / 10 + lim[2]
   }

   file_type <- match.arg(file_type, c("svg", "png"))

   if (!dir.exists(dir)) {
     dir.create(dir)
   }

   if (is.null(file)) {
     file <- file.path(dir, paste0(
       "hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
   }

   if (file_type == "svg") {
     grDevices::svg(filename = file, width = width / res, height = height / res,
                    bg = 'transparent')
   } else {
     grDevices::png(filename = file, width = width, height = height, res = res,
                    bg = 'transparent')
   }

   graphics::par(mar = c(0, 0, 0, 0))

   graphics::boxplot(x, horizontal = TRUE, ann = ann, frame = FALSE, bty = 'n', ylim = lim,
           col = col, border = border,
           boxlty = boxlty, medcol = medcol, medlwd = medlwd,
           axes = FALSE, outcex = 0.2, whisklty = 1,
           ...)
   if (add_label) {
     x_median <- round(median(x, na.rm = T), label_digits)
     x_min <- round(min(x, na.rm = T), label_digits)
     x_max <- round(max(x, na.rm = T), label_digits)
     graphics::text(x_median, y = 1.4, labels = x_median, cex = 0.5)
     graphics::text(x_min, y = 0.6, labels = x_min, cex = 0.5)
     graphics::text(x_max, y = 0.6, labels = x_max, cex = 0.5)
   }
   grDevices::dev.off()

   if (file_type == "svg") {
     svg_xml <- xml2::read_xml(file)
     svg_text <- as.character(svg_xml)
     unlink(file)
   } else {
     svg_text <- NULL
   }
   out <- list(path = file, dev = file_type, type = "boxplot",
               width = width, height = height, res = res,
               svg_text = svg_text)
   class(out) <- "kableExtraInlinePlots"
   return(out)
 }

 is_latex <- knitr::is_latex_output

 rmd_files_dir <- function(create = TRUE) {
   curr_file_name <- sub("\\.[^\\.]*$", "", knitr::current_input())
   dir_name <- paste0(curr_file_name, "_files")
   if (!dir.exists(dir_name) & create) dir.create(dir_name)
   fig_dir_name <- file.path(dir_name, "figure-latex/")
   if (!dir.exists(fig_dir_name) & create) dir.create(fig_dir_name)
   return(fig_dir_name)
 }

 #' Helper functions to generate inline sparklines
 #'
 #' @description These functions helps you quickly generate sets of sparkline
 #' style plots using base R plotting system. Currently, we support histogram,
 #' boxplot, and line. You can use them together with `column_spec` to
 #' generate inline plot in tables. By default, this function will save images
 #' in a folder called "kableExtra" and return the address of the file.
 #'
 #' @param x,y Vector of values or List of vectors of values. y is optional.
 #' @param width The width of the plot in pixel
 #' @param height The height of the plot in pixel
 #' @param res The resolution of the plot. Default is 300.
 #' @param same_lim T/F. If x is a list of vectors, should all the plots be
 #' plotted in the same range? Default is True.
 #' @param xlim,ylim Manually specify plotting range in the form of
 #' `c(0, 10)`.
 #' @param xaxt On/Off for xaxis text
 #' @param yaxt On/Off for yaxis text
 #' @param ann On/Off for annotations (titles and axis titles)
 #' @param col Color for the fill of the histogram bar/boxplot box.
 #' @param border Color for the border.
 #' @param frame.plot On/Off for surrounding box (`spec_plot` only). Default
 #' is False.
 #' @param lwd Line width for `spec_plot`; within `spec_plot`, the `minmax`
 #' argument defaults to use this value for `cex` for points. Default is 2.
 #' @param pch,cex Shape and size for points (if type is other than "l").
 #' @param type Passed to `plot`, often one of "l", "p", or "b", see
 #' [graphics::plot.default()] for more details. Ignored when 'polymin' is
 #' not 'NA'.
 #' @param polymin Special argument that converts a "line" to a polygon,
 #' where the flat portion is this value, and the other side of the polygon
 #' is the 'y' value ('x' if no 'y' provided). If 'NA' (the default), then
 #' this is ignored; otherwise if this is numeric then a polygon is
 #' created (and 'type' is ignored). Note that if 'polymin' is in the middle
 #' of the 'y' values, it will generate up/down polygons around this value.
 #' @param minmax,min,max Arguments passed to `points` to highlight minimum
 #' and maximum values in `spec_plot`. If `min` or `max` are `NULL`, they
 #' default to the value of `minmax`. Set to an empty `list()` to disable.
 #' @param dir Directory of where the images will be saved.
 #' @param file File name. If not provided, a random name will be used
 #' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
 #' for HTML output.
 #' @param ... extra parameters passing to `plot`
 #'
 #' @export
 spec_plot <- function(x, y = NULL, width = 200, height = 50, res = 300,
                       same_lim = TRUE, xlim = NULL, ylim = NULL,
                       xaxt = 'n', yaxt = 'n', ann = FALSE,
                       col = "lightgray", border = NULL,
                       frame.plot = FALSE, lwd = 2,
                       pch = ".", cex = 2, type = "l", polymin = NA,
                       minmax = list(pch = ".", cex = cex, col = "red"),
                       min = minmax, max = minmax,
                       dir = if (is_latex()) rmd_files_dir() else tempdir(),
                       file = NULL, file_type = if (is_latex()) "png" else "svg", ...) {
   if (is.list(x)) {
     lenx <- length(x)

     if (same_lim) {
       if (is.null(xlim)) {
         xlim <- base::range(unlist(x), na.rm = TRUE)
       }
       if (is.null(ylim) && !is.null(y)) {
         ylim <- base::range(c(unlist(y), polymin), na.rm = TRUE)
       }
     }

     if (is.null(y)) {
       y <- list(y)
     } else if (length(y) != lenx) {
       stop("'x' and 'y' are not the same length")
     }

     # any of the arguments can be per-plot controlling, but an arg
     # that is normally not length-1 may be recycled (incorrectly) by
     # Map, so we have to listify them if not already lists;
     # enforce a restriction of recycling only length 1 or lenx

     # first, start with the literals (x,y)
     # (same_lim is not a factor anymore)
     dots <- list(x = x, y = y)

     # second, we know these args are likely to be vectors (length > 1)
     # or lists, so we have to handle them carefully and double-list if
     # present
     notlen1vec <- list(xlim = xlim, ylim = ylim)
     dots <- c(dots, Map(
       function(L, nm) {
         if (is.null(L)) return(list(NULL))
         if (!is.list(L)) return(list(L))
         if (length(L) == lenx) return(L)
         stop("length of '", nm, "' must be 1 or the same length as 'x'")
       }, notlen1vec, names(notlen1vec)))

     # these are special ... they are lists which may need to be
     # nested, and we can't pass NULL since that may default to the
     # actual values instead of the intended
     notlen1lst <- list(minmax = minmax, min = min, max = max)
     dots <- c(dots, Map(
       function(L, nm) {
         if (is.null(L)) return(list(NULL))
         if (!length(L)) return(list(list()))
         if (!is.list(L[[1]])) return (list(L))
         if (length(L) == lenx) return(L)
         stop("length of '", nm, "' must be 1 or the same length as 'x'")
       }, notlen1lst, names(notlen1lst)))

     # last, all remaining arguments that we don't already know about
     # are length-1, so can be easily listified; using 'formals()'
     # allows us to not hard-code all params
     len1args <- mget(setdiff(names(formals()),
                              c(names(dots), "same_lim", "x", "y", "...")))
     dots <- c(dots, Map(
       function(V, nm) {
         if (is.null(V)) return(list(NULL))
         if (!length(V) %in% c(1L, lenx)) {
           stop("length of '", nm, "' must be 1 or the same length as 'x'")
         }
         V
       }, len1args, names(len1args)))

     return(do.call(Map, c(list(f = spec_plot), dots)))

   }

   if (is.null(x)) return(NULL)

   if (is.null(y) || !length(y)) {
     y <- x
     x <- seq_along(y)
     if (!is.null(xlim) && is.null(ylim)) {
       ylim <- range(c(xlim, polymin), na.rm = TRUE)
       xlim <- range(x)
     }
   }

   if (is.null(xlim)) {
     xlim <- base::range(x, na.rm = TRUE)
   }

   if (is.null(ylim) && !is.null(y)) {
     ylim <- base::range(c(y, polymin), na.rm = TRUE)
   }

   if (is.null(min)) min <- minmax
   if (is.null(max)) max <- minmax

   expand <- c(
     if (!is.null(min) && length(min)) -0.04 else 0,
     if (!is.null(max) && length(max)) +0.04 else 0)
   xlim <- xlim + diff(xlim) * expand
   ylim <- ylim + diff(ylim) * expand

   file_type <- match.arg(file_type, c("svg", "png"))

   if (!dir.exists(dir)) {
     dir.create(dir)
   }

   if (is.null(file)) {
     file <- file.path(dir, paste0(
       "hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
   }

   if (file_type == "svg") {
     grDevices::svg(filename = file, width = width / res, height = height / res,
                    bg = 'transparent')
   } else {
     grDevices::png(filename = file, width = width, height = height, res = res,
                    bg = 'transparent')
   }
   curdev <- grDevices::dev.cur()
   on.exit(grDevices::dev.off(curdev), add = TRUE)

   graphics::par(mar = c(0, 0, 0, 0), lwd = lwd)

   dots <- list(...)
   if (!is.na(polymin) && "angle" %in% names(dots)) {
     angle <- dots$angle
     dots$angle <- NULL
   } else angle <- 45

   do.call(graphics::plot,
           c(list(x, y, type = if (is.na(polymin)) type else "n",
                  xlim = xlim, ylim = ylim,
                  xaxt = xaxt, yaxt = yaxt, ann = ann, col = col,
                  frame.plot = frame.plot, cex = cex, pch = pch),
             dots))

   if (!is.na(polymin)) {
     lty <- if ("lty" %in% names(dots)) dots$lty else graphics::par("lty")
     polygon(c(x[1], x, x[length(x)]), c(polymin, y, polymin),
             border = NA, col = col, angle = angle, lty = lty,
             xpd = if ("xpd" %in% names(dots)) dots$xpd else NA)
   }

   if (!is.null(min) && length(min)) {
     if (!"xpd" %in% names(min)) min$xpd <- NA
     ind <- which.min(y)
     do.call(graphics::points, c(list(x[ind], y[ind]), min))
   }

   if (!is.null(max) && length(max)) {
     if (!"xpd" %in% names(max)) max$xpd <- NA
     ind <- which.max(y)
     do.call(graphics::points, c(list(x[ind], y[ind]), max))
   }

   grDevices::dev.off(curdev)

   if (file_type == "svg") {
     svg_xml <- xml2::read_xml(file)
     svg_text <- as.character(svg_xml)
     unlink(file)
   } else {
     svg_text <- NULL
   }
   out <- list(path = file, dev = file_type, type = "line",
               width = width, height = height, res = res,
               svg_text = svg_text)

   class(out) <- "kableExtraInlinePlots"
   return(out)
 }
	#' Helper functions to generate inline sparklines
	#'
	#' @description These functions helps you quickly generate sets of sparkline
	#' style plots using base R plotting system. Currently, we support histogram,
	#' boxplot, and line. You can use them together with `column_spec` to
	#' generate inline plot in tables. By default, this function will save images
	#' in a folder called "kableExtra" and return the address of the file.
	#'
	#' @param x Vector of values or List of vectors of values.
	#' @param width The width of the plot in pixel
	#' @param height The height of the plot in pixel
	#' @param res The resolution of the plot. Default is 300.
	#' @param same_lim T/F. If x is a list of vectors, should all the plots be
	#' plotted in the same range? Default is True.
	#' @param lim Manually specify plotting range in the form of
	#' `c(0, 10)`.
	#' @param xaxt On/Off for xaxis text
	#' @param yaxt On/Off for yaxis text
	#' @param ann On/Off for annotations (titles and axis titles)
	#' @param col Color for the fill of the histogram bar/boxplot box.
	#' @param border Color for the border.
	#' @param dir Directory of where the images will be saved.
	#' @param file File name. If not provided, a random name will be used
	#' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
	#' for HTML output
	#' @param ... extra parameters sending to `hist()`
	#'
	#' @export
	spec_hist <- function(x, width = 200, height = 50, res = 300,
	breaks = "Sturges",
	same_lim = TRUE, lim = NULL,
	xaxt = 'n', yaxt = 'n', ann = FALSE,
	col = "lightgray", border = NULL,
	dir = if (is_latex()) rmd_files_dir() else tempdir(),
	file = NULL,
	file_type = if (is_latex()) "png" else "svg", ...) {
	if (is.list(x)) {
	if (same_lim & is.null(lim)) {
	lim <- base::range(unlist(x))
	}
	return(lapply(x, function(x_) {spec_hist(
	x = x_, width = width, height = height,
	breaks = breaks, same_lim = same_lim, lim = lim,
	xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, border = border,
	dir = dir, file = file, file_type = file_type, ...
	)}))
	}

	if (is.null(x)) return(NULL)

	if (is.null(lim)) {
	lim <- base::range(x)
	}

	file_type <- match.arg(file_type, c("svg", "png"))

	if (!dir.exists(dir)) {
	dir.create(dir)
	}

	if (is.null(file)) {
	file <- file.path(dir, paste0(
	"hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
	}

	if (file_type == "svg") {
	grDevices::svg(filename = file, width = width / res, height = height / res,
	bg = 'transparent')
	} else {
	grDevices::png(filename = file, width = width, height = height, res = res,
	bg = 'transparent')
	}

	graphics::par(mar = c(0, 0, 0.2, 0), lwd=0.5)
	graphics::hist(x, breaks = breaks, xlim = lim, border = border,
	xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, ...)
	grDevices::dev.off()

	if (file_type == "svg") {
	svg_xml <- xml2::read_xml(file)
	svg_text <- as.character(svg_xml)
	unlink(file)
	} else {
	svg_text <- NULL
	}
	out <- list(path = file, dev = file_type, type = "hist",
	width = width, height = height, res = res,
	svg_text = svg_text)

	class(out) <- "kableExtraInlinePlots"
	return(out)
	}

	#' Helper functions to generate inline sparklines
	#'
	#' @description These functions helps you quickly generate sets of sparkline
	#' style plots using base R plotting system. Currently, we support histogram,
	#' boxplot, and line. You can use them together with `column_spec` to
	#' generate inline plot in tables. By default, this function will save images
	#' in a folder called "kableExtra" and return the address of the file.
	#'
	#' @param x Vector of values or List of vectors of values.
	#' @param width The width of the plot in pixel
	#' @param height The height of the plot in pixel
	#' @param res The resolution of the plot. Default is 300.
	#' @param add_label For boxplot. T/F to add labels for min, mean and max.
	#' @param label_digits If T for add_label, rounding digits for the label.
	#' Default is 2.
	#' @param same_lim T/F. If x is a list of vectors, should all the plots be
	#' plotted in the same range? Default is True.
	#' @param lim,xlim,ylim Manually specify plotting range in the form of
	#' `c(0, 10)`. `lim` is used in `spec_hist` and `spec_boxplot`; `xlim`
	#' and `ylim` are used in `spec_plot`.
	#' @param xaxt On/Off for xaxis text
	#' @param yaxt On/Off for yaxis text
	#' @param ann On/Off for annotations (titles and axis titles)
	#' @param col Color for the fill of the histogram bar/boxplot box.
	#' @param border Color for the border.
	#' @param boxlty Boxplot - box boarder type
	#' @param medcol Boxplot - median line color
	#' @param medlwd Boxplot - median line width
	#' @param dir Directory of where the images will be saved.
	#' @param file File name. If not provided, a random name will be used
	#' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
	#' for HTML output
	#' @param ... extraparameters passing to boxplot
	#'
	#' @export
	spec_boxplot <- function(x, width = 200, height = 50, res = 300,
	add_label = FALSE, label_digits = 2,
	same_lim = TRUE, lim = NULL,
	xaxt = 'n', yaxt = 'n', ann = FALSE,
	col = "lightgray", border = NULL,
	boxlty = 0, medcol = "red", medlwd = 1,
	dir = if (is_latex()) rmd_files_dir() else tempdir(),
	file = NULL,
	file_type = if (is_latex()) "png" else "svg", ...) {
	if (is.list(x)) {
	if (same_lim & is.null(lim)) {
	lim <- base::range(unlist(x))
	}
	return(lapply(x, function(x_) {spec_boxplot(
	x = x_, width = width, height = height,
	add_label = add_label, same_lim = same_lim, lim = lim,
	xaxt = xaxt, yaxt = yaxt, ann = ann,
	col = col, border = border,
	boxlty = boxlty, medcol = medcol, medlwd = medlwd,
	dir = dir, file = file, file_type = file_type, ...
	)}))
	}

	if (is.null(x)) return(NULL)

	if (is.null(lim)) {
	lim <- base::range(x)
	lim[1] <- lim[1] - (lim[2] - lim[1]) / 10
	lim[2] <- (lim[2] - lim[1]) / 10 + lim[2]
	}

	file_type <- match.arg(file_type, c("svg", "png"))

	if (!dir.exists(dir)) {
	dir.create(dir)
	}

	if (is.null(file)) {
	file <- file.path(dir, paste0(
	"hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
	}

	if (file_type == "svg") {
	grDevices::svg(filename = file, width = width / res, height = height / res,
	bg = 'transparent')
	} else {
	grDevices::png(filename = file, width = width, height = height, res = res,
	bg = 'transparent')
	}

	graphics::par(mar = c(0, 0, 0, 0))

	graphics::boxplot(x, horizontal = TRUE, ann = ann, frame = FALSE, bty = 'n', ylim = lim,
	col = col, border = border,
	boxlty = boxlty, medcol = medcol, medlwd = medlwd,
	axes = FALSE, outcex = 0.2, whisklty = 1,
	...)
	if (add_label) {
	x_median <- round(median(x, na.rm = T), label_digits)
	x_min <- round(min(x, na.rm = T), label_digits)
	x_max <- round(max(x, na.rm = T), label_digits)
	graphics::text(x_median, y = 1.4, labels = x_median, cex = 0.5)
	graphics::text(x_min, y = 0.6, labels = x_min, cex = 0.5)
	graphics::text(x_max, y = 0.6, labels = x_max, cex = 0.5)
	}
	grDevices::dev.off()

	if (file_type == "svg") {
	svg_xml <- xml2::read_xml(file)
	svg_text <- as.character(svg_xml)
	unlink(file)
	} else {
	svg_text <- NULL
	}
	out <- list(path = file, dev = file_type, type = "boxplot",
	width = width, height = height, res = res,
	svg_text = svg_text)
	class(out) <- "kableExtraInlinePlots"
	return(out)
	}

	is_latex <- knitr::is_latex_output

	rmd_files_dir <- function(create = TRUE) {
	curr_file_name <- sub("\\.[^\\.]*$", "", knitr::current_input())
	dir_name <- paste0(curr_file_name, "_files")
	if (!dir.exists(dir_name) & create) dir.create(dir_name)
	fig_dir_name <- file.path(dir_name, "figure-latex/")
	if (!dir.exists(fig_dir_name) & create) dir.create(fig_dir_name)
	return(fig_dir_name)
	}

	#' Helper functions to generate inline sparklines
	#'
	#' @description These functions helps you quickly generate sets of sparkline
	#' style plots using base R plotting system. Currently, we support histogram,
	#' boxplot, and line. You can use them together with `column_spec` to
	#' generate inline plot in tables. By default, this function will save images
	#' in a folder called "kableExtra" and return the address of the file.
	#'
	#' @param x,y Vector of values or List of vectors of values. y is optional.
	#' @param width The width of the plot in pixel
	#' @param height The height of the plot in pixel
	#' @param res The resolution of the plot. Default is 300.
	#' @param same_lim T/F. If x is a list of vectors, should all the plots be
	#' plotted in the same range? Default is True.
	#' @param xlim,ylim Manually specify plotting range in the form of
	#' `c(0, 10)`.
	#' @param xaxt On/Off for xaxis text
	#' @param yaxt On/Off for yaxis text
	#' @param ann On/Off for annotations (titles and axis titles)
	#' @param col Color for the fill of the histogram bar/boxplot box.
	#' @param border Color for the border.
	#' @param frame.plot On/Off for surrounding box (`spec_plot` only). Default
	#' is False.
	#' @param lwd Line width for `spec_plot`; within `spec_plot`, the `minmax`
	#' argument defaults to use this value for `cex` for points. Default is 2.
	#' @param pch,cex Shape and size for points (if type is other than "l").
	#' @param type Passed to `plot`, often one of "l", "p", or "b", see
	#' [graphics::plot.default()] for more details. Ignored when 'polymin' is
	#' not 'NA'.
	#' @param polymin Special argument that converts a "line" to a polygon,
	#' where the flat portion is this value, and the other side of the polygon
	#' is the 'y' value ('x' if no 'y' provided). If 'NA' (the default), then
	#' this is ignored; otherwise if this is numeric then a polygon is
	#' created (and 'type' is ignored). Note that if 'polymin' is in the middle
	#' of the 'y' values, it will generate up/down polygons around this value.
	#' @param minmax,min,max Arguments passed to `points` to highlight minimum
	#' and maximum values in `spec_plot`. If `min` or `max` are `NULL`, they
	#' default to the value of `minmax`. Set to an empty `list()` to disable.
	#' @param dir Directory of where the images will be saved.
	#' @param file File name. If not provided, a random name will be used
	#' @param file_type Graphic device. Support `png` or `svg`. SVG is recommended
	#' for HTML output.
	#' @param ... extra parameters passing to `plot`
	#'
	#' @export
	spec_plot <- function(x, y = NULL, width = 200, height = 50, res = 300,
	same_lim = TRUE, xlim = NULL, ylim = NULL,
	xaxt = 'n', yaxt = 'n', ann = FALSE,
	col = "lightgray", border = NULL,
	frame.plot = FALSE, lwd = 2,
	pch = ".", cex = 2, type = "l", polymin = NA,
	minmax = list(pch = ".", cex = cex, col = "red"),
	min = minmax, max = minmax,
	dir = if (is_latex()) rmd_files_dir() else tempdir(),
	file = NULL, file_type = if (is_latex()) "png" else "svg", ...) {
	if (is.list(x)) {
	lenx <- length(x)

	if (same_lim) {
	if (is.null(xlim)) {
	xlim <- base::range(unlist(x), na.rm = TRUE)
	}
	if (is.null(ylim) && !is.null(y)) {
	ylim <- base::range(c(unlist(y), polymin), na.rm = TRUE)
	}
	}

	if (is.null(y)) {
	y <- list(y)
	} else if (length(y) != lenx) {
	stop("'x' and 'y' are not the same length")
	}

	# any of the arguments can be per-plot controlling, but an arg
	# that is normally not length-1 may be recycled (incorrectly) by
	# Map, so we have to listify them if not already lists;
	# enforce a restriction of recycling only length 1 or lenx

	# first, start with the literals (x,y)
	# (same_lim is not a factor anymore)
	dots <- list(x = x, y = y)

	# second, we know these args are likely to be vectors (length > 1)
	# or lists, so we have to handle them carefully and double-list if
	# present
	notlen1vec <- list(xlim = xlim, ylim = ylim)
	dots <- c(dots, Map(
	function(L, nm) {
	if (is.null(L)) return(list(NULL))
	if (!is.list(L)) return(list(L))
	if (length(L) == lenx) return(L)
	stop("length of '", nm, "' must be 1 or the same length as 'x'")
	}, notlen1vec, names(notlen1vec)))

	# these are special ... they are lists which may need to be
	# nested, and we can't pass NULL since that may default to the
	# actual values instead of the intended
	notlen1lst <- list(minmax = minmax, min = min, max = max)
	dots <- c(dots, Map(
	function(L, nm) {
	if (is.null(L)) return(list(NULL))
	if (!length(L)) return(list(list()))
	if (!is.list(L[[1]])) return (list(L))
	if (length(L) == lenx) return(L)
	stop("length of '", nm, "' must be 1 or the same length as 'x'")
	}, notlen1lst, names(notlen1lst)))

	# last, all remaining arguments that we don't already know about
	# are length-1, so can be easily listified; using 'formals()'
	# allows us to not hard-code all params
	len1args <- mget(setdiff(names(formals()),
	c(names(dots), "same_lim", "x", "y", "...")))
	dots <- c(dots, Map(
	function(V, nm) {
	if (is.null(V)) return(list(NULL))
	if (!length(V) %in% c(1L, lenx)) {
	stop("length of '", nm, "' must be 1 or the same length as 'x'")
	}
	V
	}, len1args, names(len1args)))

	return(do.call(Map, c(list(f = spec_plot), dots)))

	}

	if (is.null(x)) return(NULL)

	if (is.null(y) \|\| !length(y)) {
	y <- x
	x <- seq_along(y)
	if (!is.null(xlim) && is.null(ylim)) {
	ylim <- range(c(xlim, polymin), na.rm = TRUE)
	xlim <- range(x)
	}
	}

	if (is.null(xlim)) {
	xlim <- base::range(x, na.rm = TRUE)
	}

	if (is.null(ylim) && !is.null(y)) {
	ylim <- base::range(c(y, polymin), na.rm = TRUE)
	}

	if (is.null(min)) min <- minmax
	if (is.null(max)) max <- minmax

	expand <- c(
	if (!is.null(min) && length(min)) -0.04 else 0,
	if (!is.null(max) && length(max)) +0.04 else 0)
	xlim <- xlim + diff(xlim) * expand
	ylim <- ylim + diff(ylim) * expand

	file_type <- match.arg(file_type, c("svg", "png"))

	if (!dir.exists(dir)) {
	dir.create(dir)
	}

	if (is.null(file)) {
	file <- file.path(dir, paste0(
	"hist_", round(as.numeric(Sys.time()) * 1000), ".", file_type))
	}

	if (file_type == "svg") {
	grDevices::svg(filename = file, width = width / res, height = height / res,
	bg = 'transparent')
	} else {
	grDevices::png(filename = file, width = width, height = height, res = res,
	bg = 'transparent')
	}
	curdev <- grDevices::dev.cur()
	on.exit(grDevices::dev.off(curdev), add = TRUE)

	graphics::par(mar = c(0, 0, 0, 0), lwd = lwd)

	dots <- list(...)
	if (!is.na(polymin) && "angle" %in% names(dots)) {
	angle <- dots$angle
	dots$angle <- NULL
	} else angle <- 45

	do.call(graphics::plot,
	c(list(x, y, type = if (is.na(polymin)) type else "n",
	xlim = xlim, ylim = ylim,
	xaxt = xaxt, yaxt = yaxt, ann = ann, col = col,
	frame.plot = frame.plot, cex = cex, pch = pch),
	dots))

	if (!is.na(polymin)) {
	lty <- if ("lty" %in% names(dots)) dots$lty else graphics::par("lty")
	polygon(c(x[1], x, x[length(x)]), c(polymin, y, polymin),
	border = NA, col = col, angle = angle, lty = lty,
	xpd = if ("xpd" %in% names(dots)) dots$xpd else NA)
	}

	if (!is.null(min) && length(min)) {
	if (!"xpd" %in% names(min)) min$xpd <- NA
	ind <- which.min(y)
	do.call(graphics::points, c(list(x[ind], y[ind]), min))
	}

	if (!is.null(max) && length(max)) {
	if (!"xpd" %in% names(max)) max$xpd <- NA
	ind <- which.max(y)
	do.call(graphics::points, c(list(x[ind], y[ind]), max))
	}

	grDevices::dev.off(curdev)

	if (file_type == "svg") {
	svg_xml <- xml2::read_xml(file)
	svg_text <- as.character(svg_xml)
	unlink(file)
	} else {
	svg_text <- NULL
	}
	out <- list(path = file, dev = file_type, type = "line",
	width = width, height = height, res = res,
	svg_text = svg_text)

	class(out) <- "kableExtraInlinePlots"
	return(out)
	}