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, line, scatter and pointrange plots. 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 breaks The `break` option in `hist`. Default is "Sturges" but you can
 #' also provide a vector to manually specify break points.
 #' @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. Can be character (e.g., `"pdf"`)
 #'   or a graphics device function (`grDevices::pdf`). This defaults
 #'   to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
 #' 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()) "pdf" else svglite::svglite,
                       ...) {
   if (is.list(x)) {
     if (same_lim & is.null(lim)) {
       lim <- base::range(unlist(x), na.rm=TRUE)
     }

     dots <- listify_args(x, width, height, res, breaks,
                          lim, xaxt, yaxt, ann, col, border,
                          dir, file, file_type,
                          lengths = c(1, length(x)))
     return(do.call(Map, c(list(f = spec_hist), dots)))
   }

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

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

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

   file_ext <- dev_chr(file_type)
   if (is.null(file)) {
     file <- normalizePath(
       tempfile(pattern = "hist_", tmpdir = dir, fileext = paste0(".", file_ext)),
       winslash = "/", mustWork = FALSE)
   }

   graphics_dev(filename = file, dev = file_type,
                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, 0.2, 0), lwd=0.5)
   graphics::hist(x, breaks = breaks, xlim = lim, border = border,
                  xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, ...)

   grDevices::dev.off(curdev)

   out <- make_inline_plot(
     file, file_ext, file_type,
     width, height, res,
     del = TRUE)
   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, line, scatter and pointrange plots. 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 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 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. Can be character (e.g., `"pdf"`)
 #'   or a graphics device function (`grDevices::pdf`). This defaults
 #'   to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
 #' @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()) "pdf" else svglite::svglite,
                          ...) {
   if (is.list(x)) {
     if (same_lim & is.null(lim)) {
       lim <- base::range(unlist(x), na.rm=TRUE)
     }

     dots <- listify_args(x, width, height, res,
                          add_label, label_digits,
                          lim, xaxt, yaxt, ann, col, border,
                          dir, file, file_type,
                          lengths = c(1, length(x)))
     return(do.call(Map, c(list(f = spec_boxplot), dots)))
   }

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

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

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

   file_ext <- dev_chr(file_type)
   if (is.null(file)) {
     file <- normalizePath(
       tempfile(pattern = "boxplot_", tmpdir = dir, fileext = paste0(".", file_ext)),
       winslash = "/", mustWork = FALSE)
   }

   graphics_dev(filename = file, dev = file_type,
                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))

   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(curdev)

   out <- make_inline_plot(
     file, file_ext, file_type,
     width, height, res,
     del = TRUE)
   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, line, scatter, pointrange, barplot plots. 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 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 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. Can be character (e.g., `"pdf"`)
 #'   or a graphics device function (`grDevices::pdf`). This defaults
 #'   to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
 #' @param ... extraparameters passing to boxplot
 #'
 #' @export
 spec_barplot <- function(x, devwidth = 200, devheight = 40, res = 300,
                       beside = F,
                       horiz = F,
                       same_lim = TRUE, lim = NULL,
                       xaxt = 'n', yaxt = 'n', ann = FALSE,
                       col = NULL, border = NA,
                       dir = if (is_latex()) rmd_files_dir() else tempdir(),
                       file = NULL,
                       file_type = if (is_latex()) "pdf" else svglite::svglite,
                       ...) {
   if (is.list(x)) {
     if (same_lim & is.null(lim)) {
       lim <- base::range(unlist(x), na.rm=TRUE)
     }

     dots <- listify_args(x, devwidth, devheight, res, beside,horiz,
                          lim, xaxt, yaxt, ann, col, border,
                          dir, file, file_type,
                          lengths = c(1, length(x)))
     return(do.call(Map, c(list(f = spec_barplot), dots)))
   }

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

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

   if (!dir.exists(dir)) {
     dir.create(dir)
   }
   height<-matrix(x)
   height<-cbind(height,0)
   file_ext <- dev_chr(file_type)
   if (is.null(file)) {
     file <- normalizePath(
       tempfile(pattern = "barplot_", tmpdir = dir, fileext = paste0(".", file_ext)),
       winslash = "/", mustWork = FALSE)
   }

   graphics_dev(filename = file, dev = file_type,
                width = devwidth, height = devheight, 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=0.5)
   graphics::barplot(height=height, beside = beside,horiz = horiz, col = col, border = border,xaxt = xaxt, yaxt = yaxt, ann = ann)#,xlim = lim, ann = ann, ...)

   grDevices::dev.off(curdev)

   out <- make_inline_plot(
     file, file_ext, file_type,
     devwidth, devheight, res,
     del = TRUE)
   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, line, scatter and pointrange plots. 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. Can be character (e.g., `"pdf"`)
 #'   or a graphics device function (`grDevices::pdf`). This defaults
 #'   to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
 #' @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()) "pdf" else svglite::svglite,
                       ...) {
   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")
     }

     dots <- listify_args(x, y = y, width, height, res,
                          xlim, ylim, xaxt, yaxt, ann, col, border, frame.plot,
                          lwd, pch, cex, type, polymin, minmax, min, max,
                          dir, file, file_type,
                          lengths = c(1, lenx))

     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

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

   file_ext <- dev_chr(file_type)
   if (is.null(file)) {
     file <- normalizePath(
       tempfile(pattern = "plot_", tmpdir = dir, fileext = paste0(".", file_ext)),
       winslash = "/", mustWork = FALSE)
   }

   graphics_dev(filename = file, dev = file_type,
                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$lty else graphics::par("lty")
     graphics::polygon(c(x[1], x, x[length(x)]), c(polymin, y, polymin),
             border = NA, col = col, angle = angle, lty = lty,
             xpd = if ("xpd" %in% names(dots)) dots$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)

   out <- make_inline_plot(
     file, file_ext, file_type,
     width, height, res,
     del = TRUE)
   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, line, scatter and pointrange plots. 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,xmin,xmax A scalar value or List of scalar values for dot, left
 #' and right errorbar.
 #' @param vline A scalar value for where to draw a vertical line.
 #' @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 mean dot.
 #' @param line_col Color for the line and the error bar.
 #' @param cex size of the mean dot and error bar size.
 #' @param frame.plot T/F for whether to plot the plot frames.
 #' @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. Can be character (e.g., `"pdf"`)
 #'   or a graphics device function (`grDevices::pdf`). This defaults
 #'   to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
 #' for HTML output
 #' @param ... extra parameters sending to `hist()`
 #'
 #' @export
 spec_pointrange <- function(
   x, xmin, xmax, vline = NULL,
   width = 200, height = 50, res = 300,
   same_lim = TRUE, lim = NULL,
   xaxt = 'n', yaxt = 'n', ann = FALSE,
   col = "red", line_col = "black", cex = 0.3, frame.plot = FALSE,
   dir = if (is_latex()) rmd_files_dir() else tempdir(),
   file = NULL,
   file_type = if (is_latex()) "pdf" else svglite::svglite, ...) {
   if (length(x) > 1) {
     if (same_lim & is.null(lim)) {
       all_range <- c(unlist(xmin), unlist(xmax))
       lim <- base::range(all_range, na.rm=TRUE)
       lim <- lim + c(-0.04 * diff(lim), 0.04 * diff(lim))
     }

     dots <- listify_args(
       x = as.list(x), xmin = as.list(xmin), xmax = as.list(xmax), vline,
       width, height, res,
       lim, xaxt, yaxt, ann, col, line_col, cex, frame.plot,
       dir, file, file_type,
       lengths = c(1, length(x)),
       passthru = c("x", "xmin", "xmax"))
     return(do.call(Map, c(list(f = spec_pointrange), dots)))
   }

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

   if (is.null(lim)) {
     one_range <- unlist(c(xmin, xmax))
     lim <- base::range(one_range, na.rm=TRUE)
     lim <- lim + c(-0.04 * diff(lim), 0.04 * diff(lim))
   }

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

   file_ext <- dev_chr(file_type)
   if (is.null(file)) {
     file <- normalizePath(
       tempfile(pattern = "pointrange_", tmpdir = dir, fileext = paste0(".", file_ext)),
       winslash = "/", mustWork = FALSE)
   }

   graphics_dev(filename = file, dev = file_type,
                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, 0.2, 0), lwd=1,
                 ann = ann, xaxt = xaxt, yaxt = yaxt)

   graphics::plot(x, 0, type = "p", pch = ".",
                  xlim = lim, frame.plot = frame.plot)
   graphics::arrows(xmin, 0, xmax, 0, cex / 15, angle = 90, code = 3,
                    col = line_col)
   graphics::points(x, 0, col = col, type = "p", pch = 15, cex = cex)
   if (!is.null(vline)) {
     graphics::abline(v = vline, lty = 3)
   }

   grDevices::dev.off(curdev)

   out <- make_inline_plot(
     file, file_ext, file_type,
     width, height, res,
     del = TRUE)
   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, line, scatter and pointrange plots. 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 breaks The `break` option in `hist`. Default is "Sturges" but you can
	#' also provide a vector to manually specify break points.
	#' @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. Can be character (e.g., `"pdf"`)
	#' or a graphics device function (`grDevices::pdf`). This defaults
	#' to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
	#' 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()) "pdf" else svglite::svglite,
	...) {
	if (is.list(x)) {
	if (same_lim & is.null(lim)) {
	lim <- base::range(unlist(x), na.rm=TRUE)
	}

	dots <- listify_args(x, width, height, res, breaks,
	lim, xaxt, yaxt, ann, col, border,
	dir, file, file_type,
	lengths = c(1, length(x)))
	return(do.call(Map, c(list(f = spec_hist), dots)))
	}

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

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

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

	file_ext <- dev_chr(file_type)
	if (is.null(file)) {
	file <- normalizePath(
	tempfile(pattern = "hist_", tmpdir = dir, fileext = paste0(".", file_ext)),
	winslash = "/", mustWork = FALSE)
	}

	graphics_dev(filename = file, dev = file_type,
	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, 0.2, 0), lwd=0.5)
	graphics::hist(x, breaks = breaks, xlim = lim, border = border,
	xaxt = xaxt, yaxt = yaxt, ann = ann, col = col, ...)

	grDevices::dev.off(curdev)

	out <- make_inline_plot(
	file, file_ext, file_type,
	width, height, res,
	del = TRUE)
	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, line, scatter and pointrange plots. 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 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 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. Can be character (e.g., `"pdf"`)
	#' or a graphics device function (`grDevices::pdf`). This defaults
	#' to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
	#' @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()) "pdf" else svglite::svglite,
	...) {
	if (is.list(x)) {
	if (same_lim & is.null(lim)) {
	lim <- base::range(unlist(x), na.rm=TRUE)
	}

	dots <- listify_args(x, width, height, res,
	add_label, label_digits,
	lim, xaxt, yaxt, ann, col, border,
	dir, file, file_type,
	lengths = c(1, length(x)))
	return(do.call(Map, c(list(f = spec_boxplot), dots)))
	}

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

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

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

	file_ext <- dev_chr(file_type)
	if (is.null(file)) {
	file <- normalizePath(
	tempfile(pattern = "boxplot_", tmpdir = dir, fileext = paste0(".", file_ext)),
	winslash = "/", mustWork = FALSE)
	}

	graphics_dev(filename = file, dev = file_type,
	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))

	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(curdev)

	out <- make_inline_plot(
	file, file_ext, file_type,
	width, height, res,
	del = TRUE)
	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, line, scatter, pointrange, barplot plots. 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 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 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. Can be character (e.g., `"pdf"`)
	#' or a graphics device function (`grDevices::pdf`). This defaults
	#' to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
	#' @param ... extraparameters passing to boxplot
	#'
	#' @export
	spec_barplot <- function(x, devwidth = 200, devheight = 40, res = 300,
	beside = F,
	horiz = F,
	same_lim = TRUE, lim = NULL,
	xaxt = 'n', yaxt = 'n', ann = FALSE,
	col = NULL, border = NA,
	dir = if (is_latex()) rmd_files_dir() else tempdir(),
	file = NULL,
	file_type = if (is_latex()) "pdf" else svglite::svglite,
	...) {
	if (is.list(x)) {
	if (same_lim & is.null(lim)) {
	lim <- base::range(unlist(x), na.rm=TRUE)
	}

	dots <- listify_args(x, devwidth, devheight, res, beside,horiz,
	lim, xaxt, yaxt, ann, col, border,
	dir, file, file_type,
	lengths = c(1, length(x)))
	return(do.call(Map, c(list(f = spec_barplot), dots)))
	}

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

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

	if (!dir.exists(dir)) {
	dir.create(dir)
	}
	height<-matrix(x)
	height<-cbind(height,0)
	file_ext <- dev_chr(file_type)
	if (is.null(file)) {
	file <- normalizePath(
	tempfile(pattern = "barplot_", tmpdir = dir, fileext = paste0(".", file_ext)),
	winslash = "/", mustWork = FALSE)
	}

	graphics_dev(filename = file, dev = file_type,
	width = devwidth, height = devheight, 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=0.5)
	graphics::barplot(height=height, beside = beside,horiz = horiz, col = col, border = border,xaxt = xaxt, yaxt = yaxt, ann = ann)#,xlim = lim, ann = ann, ...)

	grDevices::dev.off(curdev)

	out <- make_inline_plot(
	file, file_ext, file_type,
	devwidth, devheight, res,
	del = TRUE)
	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, line, scatter and pointrange plots. 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. Can be character (e.g., `"pdf"`)
	#' or a graphics device function (`grDevices::pdf`). This defaults
	#' to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
	#' @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()) "pdf" else svglite::svglite,
	...) {
	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")
	}

	dots <- listify_args(x, y = y, width, height, res,
	xlim, ylim, xaxt, yaxt, ann, col, border, frame.plot,
	lwd, pch, cex, type, polymin, minmax, min, max,
	dir, file, file_type,
	lengths = c(1, lenx))

	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

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

	file_ext <- dev_chr(file_type)
	if (is.null(file)) {
	file <- normalizePath(
	tempfile(pattern = "plot_", tmpdir = dir, fileext = paste0(".", file_ext)),
	winslash = "/", mustWork = FALSE)
	}

	graphics_dev(filename = file, dev = file_type,
	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$lty else graphics::par("lty")
	graphics::polygon(c(x[1], x, x[length(x)]), c(polymin, y, polymin),
	border = NA, col = col, angle = angle, lty = lty,
	xpd = if ("xpd" %in% names(dots)) dots$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)

	out <- make_inline_plot(
	file, file_ext, file_type,
	width, height, res,
	del = TRUE)
	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, line, scatter and pointrange plots. 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,xmin,xmax A scalar value or List of scalar values for dot, left
	#' and right errorbar.
	#' @param vline A scalar value for where to draw a vertical line.
	#' @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 mean dot.
	#' @param line_col Color for the line and the error bar.
	#' @param cex size of the mean dot and error bar size.
	#' @param frame.plot T/F for whether to plot the plot frames.
	#' @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. Can be character (e.g., `"pdf"`)
	#' or a graphics device function (`grDevices::pdf`). This defaults
	#' to `"pdf"` if the rendering is in LaTeX and `"svg"` otherwise.
	#' for HTML output
	#' @param ... extra parameters sending to `hist()`
	#'
	#' @export
	spec_pointrange <- function(
	x, xmin, xmax, vline = NULL,
	width = 200, height = 50, res = 300,
	same_lim = TRUE, lim = NULL,
	xaxt = 'n', yaxt = 'n', ann = FALSE,
	col = "red", line_col = "black", cex = 0.3, frame.plot = FALSE,
	dir = if (is_latex()) rmd_files_dir() else tempdir(),
	file = NULL,
	file_type = if (is_latex()) "pdf" else svglite::svglite, ...) {
	if (length(x) > 1) {
	if (same_lim & is.null(lim)) {
	all_range <- c(unlist(xmin), unlist(xmax))
	lim <- base::range(all_range, na.rm=TRUE)
	lim <- lim + c(-0.04 * diff(lim), 0.04 * diff(lim))
	}

	dots <- listify_args(
	x = as.list(x), xmin = as.list(xmin), xmax = as.list(xmax), vline,
	width, height, res,
	lim, xaxt, yaxt, ann, col, line_col, cex, frame.plot,
	dir, file, file_type,
	lengths = c(1, length(x)),
	passthru = c("x", "xmin", "xmax"))
	return(do.call(Map, c(list(f = spec_pointrange), dots)))
	}

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

	if (is.null(lim)) {
	one_range <- unlist(c(xmin, xmax))
	lim <- base::range(one_range, na.rm=TRUE)
	lim <- lim + c(-0.04 * diff(lim), 0.04 * diff(lim))
	}

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

	file_ext <- dev_chr(file_type)
	if (is.null(file)) {
	file <- normalizePath(
	tempfile(pattern = "pointrange_", tmpdir = dir, fileext = paste0(".", file_ext)),
	winslash = "/", mustWork = FALSE)
	}

	graphics_dev(filename = file, dev = file_type,
	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, 0.2, 0), lwd=1,
	ann = ann, xaxt = xaxt, yaxt = yaxt)

	graphics::plot(x, 0, type = "p", pch = ".",
	xlim = lim, frame.plot = frame.plot)
	graphics::arrows(xmin, 0, xmax, 0, cex / 15, angle = 90, code = 3,
	col = line_col)
	graphics::points(x, 0, col = col, type = "p", pch = 15, cex = cex)
	if (!is.null(vline)) {
	graphics::abline(v = vline, lty = 3)
	}

	grDevices::dev.off(curdev)

	out <- make_inline_plot(
	file, file_ext, file_type,
	width, height, res,
	del = TRUE)
	return(out)
	}