| #' 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. 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 "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") |
| } |
| |
| 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") |
| 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) |
| } |