Nothing
R/plot_spec.R
In reporter: Creates Statistical Reports
Defines functions
get_image_docx
get_plot_body_docx
create_plot_pages_docx
get_plot_body_pdf
create_plot_pages_pdf
get_plot_body_html
create_plot_pages_html
get_plot_body_rtf
create_plot_pages_rtf
get_plot_body
create_plot_pages_text
print.plot_spec
create_plot
Documented in
create_plot
print.plot_spec
# Create Plot Constructor ---------------------------------------------
#' @title Create plot content
#' @description Function to create a plot specification that can be
#' added as content to a report. The \code{create_plot} function can
#' be used to include charts, graphs, and figures on a statistical report.
#' The function supports plot objects returned by
#' \code{\link[ggplot2]{ggplot}} or \code{\link[survminer]{ggsurvplot}}.
#' It does not support the Base R
#' \code{plot} function.
#' @details
#' To add a plot to a report, use the \code{create_plot} function. The
#' function allows you to set a width and height for the plot. The
#' function will preserve any other geometries you apply to the plot. See
#' the \code{\link{add_content}} function to control page breaking and
#' blanks spaces above or below the plot.
#'
#' A plot specification accepts a \code{\link{page_by}} function. If a page by
#' is applied to the plot, the plot data will be subset by the page by
#' variable, and re-run for each subset.
#'
#' The plot specification also accepts titles and footnotes. See the
#' \code{\link{titles}} and \code{\link{footnotes}} functions for further
#' details.
#'
#' As of \strong{reporter} version 1.2.9, the \code{create_plot} function
#' also accepts a path to a JPEG stored on the file system instead of a
#' plot object. This
#' functionality was added to allow the user to create figures from other
#' plotting packages. If you pass an image path, the image will be inserted
#' into the report at the location specified.
#'
#' @param x The plot to create. Specifically, this parameter should be
#' set to an object returned from a call to \code{\link[ggplot2]{ggplot}}
#' or \code{\link[survminer]{ggsurvplot}}. This parameter also accepts
#' a path to a JPEG file. If a path is specified, the image will be appended
#' to the report at the point the content object is added.
#' @param height The height of the plot in the specified units of measure.
#' @param width The width of the plot in the specified units of measure.
#' @param borders Whether and where to place a border. Valid values are 'top',
#' 'bottom', 'left', 'right', 'all', 'none', and 'outside'.
#' Default is 'none'. The 'left', 'right', and 'outside'
#' border specifications only apply to RTF reports.
#' @return The plot specification.
#' @family plot
#' @seealso
#' \code{\link{titles}} to add a title block to the plot,
#' \code{\link{footnotes}} to add footnotes, and \code{\link{add_content}}
#' to add the plot object to a report.
#' @examples
#' library(reporter)
#' library(ggplot2)
#' library(magrittr)
#'
#' # Create temp file path
#' tmp <- file.path(tempdir(), "mtcars.rtf")
#'
#' # Create ggplot
#' p <- ggplot(mtcars, aes(x=cyl, y=mpg)) + geom_point()
#'
#' # Create plot object
#' plt <- create_plot(p, height = 4, width = 8)
#'
#' rpt <- create_report(tmp, output_type = "RTF") %>%
#' page_header("Client", "Study: XYZ") %>%
#' titles("Figure 1.0", "MTCARS Miles per Cylinder Plot") %>%
#' set_margins(top = 1, bottom = 1) %>%
#' add_content(plt) %>%
#' footnotes("* Motor Trend, 1974") %>%
#' page_footer("Time", "Confidential", "Page [pg] of [tpg]")
#'
#' # Write out report
#' write_report(rpt)
#'
#' # Uncomment to view RTF file
#' # shell.exec(tmp)
#' @export
create_plot <- function(x, height, width, borders = "none") {
if (!any(class(x) %in% c("gg", "ggplot", "ggcoxzph", "ggsurv", "character")))
stop("plot object must be of type 'ggplot', 'ggsurv', or a JPG file path.")
if (!all(borders %in% c("top", "bottom", "left", "right",
"all", "none", "outside")))
stop(paste("Borders parameter invalid. Valid values are",
"'top', 'bottom', 'left', 'right', 'all', ",
"'none', or 'outside'."))
ret <- structure(list(), class = c("plot_spec", "list"))
ret$plot <- x
ret$height <- height
ret$width <- width
ret$borders <- borders
return(ret)
}
# Utilities ---------------------------------------------------------------
#' @title Prints the plot spec
#' @description A function to print the plot spec.
#' The \strong{print} function will print the plot spec in summary
#' form. To view all parameters, set the \code{verbose} parameter to TRUE.
#' @param x The plot spec.
#' @param ... Additional parameters to pass to the underlying print function.
#' @param verbose Whether to print in verbose form. Default is FALSE.
#' @seealso
#' \code{\link{create_plot}} function to create a plot specification.
#' @return The plot spec, invisibly.
#' @family plot
#' @examples
#' txt <- create_text("Lorem ipsum dolor sit amet, consectetur...")
#' print(txt)
#'
#' # A text specification:
#' # - text: data.frame 'mtcars' 32 rows 11 cols
#' @import crayon
#' @export
print.plot_spec <- function(x, ..., verbose = FALSE){
if (verbose == TRUE) {
# If verbose mode is indicated, print values as a list
for (nm in names(x)) {
cat("$", nm, "\n", sep = "")
if (nm == "plot") {
print(unclass(x[[nm]]), ...)
}
else {
print(x[[nm]], ...)
}
cat("\n")
}
} else {
grey60 <- make_style(grey60 = "#999999")
cat(grey60("# A plot specification: \n"))
if (!is.null(x$plot)) {
if (typeof(x$plot) == "character") {
cat(paste0("- path: '", x$plot, "'\n"))
} else {
if ("ggplot" %in% class(x$plot) & !"patchwork" %in% class(x$plot)) {
if (!is.null(x$plot[["data"]])) {
dat <- x$plot[["data"]]
cat("- data: ")
cat(paste0(nrow(dat), " rows, ", ncol(dat), " cols\n"))
cat(paste0("- layers: ", length(x$plot[["layers"]]), "\n"))
}
}
}
}
cat(paste0("- height: ", x$height, "\n"))
cat(paste0("- width: ", x$width, "\n"))
if (!is.null(x$page_by)) {
cat(paste0("- page by: ", x$page_by$var, "\n"))
}
print_title_header(x$title_hdr)
print_titles(x$titles)
print_footnotes(x$footnotes)
}
invisible(x)
}
# Write Text Functions -------------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_text <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
ret <- list()
pgs <- get_plot_body(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
for (pg in pgs) {
ret <- c(ret, list(pg))
}
} else {
# Get data in case we need it for page by
raw <- p$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u)
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
# Can return multiple pages if it breaks across pages
# Not sure what that means for a plot, but that is the logic
pgs <- get_plot_body(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
# Within a content creation function, assumed that it will take
# care of filling out blanks for each page. Only the last page
# can have empty rows.
for (pg in pgs) {
ret <- c(ret, list(pg))
}
cntr <- cntr + 1
}
}
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body <- function(plt, plot_path, align, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Get titles and footnotes
w <- ceiling(plt$width / rs$char_width)
ttls <- get_titles(plt$titles, w, rs$line_size, rs$uchar, rs$char_width)
ttl_hdr <- get_title_header(plt$title_hdr, w, rs$line_size, rs$uchar,
rs$char_width)
pgbys <- get_page_by(pgby, w, pgval)
pltpth <- gsub("\\", "/", plot_path, fixed = TRUE)
s <- c(paste0("```", pltpth, "|", plt$height,
"|", plt$width, "|", align, "```"))
h <- ceiling(plt$height / rs$row_height) + 1 # adjustment needed? Appears so.
w <- ceiling(plt$width / rs$char_width)
fill <- rep("```fill```", h)
s <- c(s, fill)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- ""
# Add top border if requested
tbrdr <- NULL
if (any(plt$borders %in% c("top", "all")))
tbrdr <- paste0(rep(rs$uchar, w), collapse = "")
# Add bottom border if requested
bbrdr <- NULL
if (any(plt$borders %in% c("bottom", "all", "outside")))
bbrdr <- paste0(rep(rs$uchar, w), collapse = "")
# Add blank below content if requested
b <- NULL
if (content_blank_row %in% c("both", "below", "outside"))
b <- ""
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls, ttl_hdr, pgbys, tbrdr, s, bbrdr)
ftnts <- get_page_footnotes_text(rs, plt, w, lpg_rows, length(rws),
wrap_flag, content_blank_row)
rws <- c(rws, ftnts)
# Page list
ret <- list()
# Create tmp variable for 1 page of content
tmp <- c()
# Offset the first page with remaining rows from the
# last page of the previous content
offset <- lpg_rows
#print(paste("Offset:", offset))
# Assign content to pages
for (i in seq_along(rws)) {
if (length(tmp) < (rs$body_line_count - offset)) {
# Append to existing page
tmp[length(tmp) + 1] <- rws[i]
} else {
# Start a new page
ret[[length(ret) + 1]] <- pad_any(tmp, rs$line_size,
get_justify(align))
tmp <- rws[i]
# Set to zero on second page and leave it that way
offset <- 0
}
}
# Deal with last page
if (length(tmp) > 0 ) {
# If page is not empty
if (max(nchar(trimws(tmp))) > 0) {
# Add last page
ret[[length(ret) + 1]] <- pad_any(tmp, rs$line_size,
get_justify(align))
}
}
return(ret)
}
# Write RTF Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_rtf <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
fx <- ".jpg"
if (grepl(".emf", p, fixed = TRUE))
fx <- ".emf"
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = fx)
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_rtf(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
pgs[[length(pgs) + 1]] <- res$rtf
cnts[[length(cnts) + 1]] <- res$lines
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else if (any(class(p) %in% c("character"))) {
file.copy(p, tmp_nm, overwrite = TRUE)
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_rtf(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
pgs[[length(pgs) + 1]] <- res$rtf
cnts[[length(cnts) + 1]] <- res$lines
cntr <- cntr + 1
}
}
ret <- list(rtf = pgs,
lines = cnts)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_rtf <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_rtf(plt$titles, wth, rs, talign)
ttl_hdr <- get_title_header_rtf(plt$title_hdr, wth, rs, talign)
pgbys <- get_page_by_rtf(pgby, wth, pgval, rs, talign)
# Get image RTF codes
img <- get_image_rtf(plot_path, plt$width, plt$height, rs$units)
# Assign table alignment codes
if (talign == "left") {
talgn <- "\\trql"
} else if (talign == "right") {
talgn <- "\\trqr"
} else {
talgn <- "\\trqc"
}
algn <- "\\qc"
# Convert width to twips
w <- round(wth * rs$twip_conversion)
# Get border codes
b <- get_cell_borders(1, 1, 1, 1, plt$borders)
# Concat all header codes
hd <- paste0("\\sl0\\trowd\\trgaph0", talgn, b, "\\cellx", w, algn, " \n")
ft <- paste0("\\cell\\row\n\\ql", rs$font_rtf, rs$spacing_multiplier)
# Concat RTF codes for image
img <- paste0(hd, img, ft)
imght <- round((plt$height * rs$twip_conversion) / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- "\\par"
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_rtf(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign)
# On LibreOffice, have to protect the table from the title width or
# the table row will inherit the title row width. Terrible problem.
tpt <- "{\\pard\\fs1\\sl0\\par}"
if (any(plt$borders %in% c("all", "top", "outside"))) {
if (ttls$border_flag | rs$page_template$titles$border_flag |
rs$page_template$title_hdr$border_flag)
tpt <- ""
}
if (titles_aligned(plt$titles, plt$title_hdr))
tpt <- ""
# Prevent infection of widths on LibreOffice.
bpt <- "{\\pard\\fs1\\sl0\\par}"
if (any(plt$borders %in% c("all", "top", "outside"))) {
if (!is.null(ftnts)) {
if (ftnts$border_flag)
bpt <- ""
}
if (!is.null(rs$page_template$footnotes)) {
if (rs$page_template$footnotes$border_flag)
bpt <- ""
}
}
if (footnotes_aligned(plt$footnotes))
bpt <- ""
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$rtf, ttl_hdr$rtf, pgbys$rtf, tpt, img, bpt)
# Combine everything
rws <- c(rws, ftnts$rtf)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(rtf = rws,
lines = lns)
return(ret)
}
# Write HTML Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_html <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_html(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
pgs[[length(pgs) + 1]] <- res$html
cnts[[length(cnts) + 1]] <- res$lines
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_html(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
pgs[[length(pgs) + 1]] <- res$html
cnts[[length(cnts) + 1]] <- res$lines
cntr <- cntr + 1
}
}
ret <- list(html = pgs,
lines = cnts)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_html <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_html(plt$titles, wth, rs, talign)
ttl_hdr <- get_title_header_html(plt$title_hdr, wth, rs, talign)
exclude_top <- NULL
if (ttls$border_flag == TRUE | ttl_hdr$border_flag == TRUE) {
exclude_top <- "top"
pgbys <- get_page_by_html(pgby, wth, pgval, rs, talign, TRUE)
} else {
pgbys <- get_page_by_html(pgby, wth, pgval, rs, talign, FALSE)
}
if (is.null(exclude_top)) {
if (pgbys$border_flag)
exclude_top <- "top"
}
# Get image RTF codes
img <- get_image_html(plot_path, rs$modified_path, plt, rs$units)
# algn <- "\\qc"
u <- rs$units
if (u == "inches")
u <- "in"
# Convert width to twips
w <- paste0("width:", round(wth, 3), u, ";")
# Get border codes
b <- get_cell_borders_html(1, 1, 1, 1, plt$borders, exclude = exclude_top)
# Concat all header codes
hd <- paste0("<table style =\"", w, "\">\n",
"<tr><td style=\"", b, "\">\n")
ft <- "</td></tr></table>\n"
# Concat RTF codes for image
img <- paste0(hd, img, ft)
# ** Do something with this **
imght <- floor(plt$height / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- "<br>"
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
if ("bottom" %in% get_outer_borders(plt$borders))
extp <- TRUE
else
extp <- FALSE
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_html(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign, extp)
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$html, ttl_hdr$html, pgbys$html, img)
# Combine everything
rws <- c(rws, ftnts$html)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(html = rws,
lines = lns)
return(ret)
}
# Write PDF Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_pdf <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
pnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
ys <- sum(rs$page_template$titles$points, rs$page_template$title_hdr$points,
rs$page_template$page_header$points, (lpg_rows * rs$line_height))
# Get pdf page bodies
res <- get_plot_body_pdf(plt, tmp_nm, cntnt$align, rs, row_offset,
cntnt$blank_row, NULL, NULL,
FALSE, ystart = ys)
pgs[[length(pgs) + 1]] <- res$pdf
cnts[length(cnts) + 1] <- res$lines
pnts[length(pnts) + 1] <- res$lines * rs$line_height
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
row_offset <- lpg_rows
for (dat in dat_lst) {
if (cntr > 1)
row_offset <- 0
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
ys <- sum(rs$page_template$titles$points, rs$page_template$title_hdr$points,
rs$page_template$page_header$points, (row_offset * rs$line_height))
# Get pdf page bodies
res <- get_plot_body_pdf(plt, tmp_nm, cntnt$align, rs, row_offset,
cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst), ystart = ys)
pgs[[length(pgs) + 1]] <- res$pdf
cnts[length(cnts) + 1] <- res$lines
pnts[length(pnts) + 1] <- res$lines * rs$line_height
cntr <- cntr + 1
}
}
ret <- list(pdf = pgs,
lines = cnts,
points = pnts)
return(ret)
}
#' Create list of page_text or page_image objects for a single page
#' @noRd
get_plot_body_pdf <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval,
wrap_flag, ystart = 0) {
cnt <- 0
lh <- rs$line_height
conv <- rs$point_conversion
bh <- rs$border_height
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Add blank above content if requested
aln <- 0
if (content_blank_row %in% c("both", "above")) {
aln <- 1
ystart <- ystart + lh
}
# Get titles and footnotes
ttls <- get_titles_pdf(plt$titles, wth, rs, talign, ystart = ystart)
ttl_hdr <- get_title_header_pdf(plt$title_hdr, wth, rs,
talign, ystart = ystart)
if (ttls$border_flag | ttl_hdr$border_flag) {
pgbys <- get_page_by_pdf(pgby, wth, pgval, rs, talign,
ystart = sum(ystart, ttls$points, ttl_hdr$points) - 2)
} else {
pgbys <- get_page_by_pdf(pgby, wth, pgval, rs, talign,
ystart = sum(ystart, ttls$points, ttl_hdr$points))
}
# Get image PDF codes
#img <- get_image_pdf(plot_path, plt$width, plt$height, rs$units)
if (talign == "right") {
lb <- rs$content_size[["width"]] - wth
rb <- rs$content_size[["width"]]
} else if (talign %in% c("center", "centre")) {
lb <- (rs$content_size[["width"]] - wth) / 2
rb <- wth + lb
} else {
lb <- 0
rb <- wth
}
#
# algn <- "\\qc"
# Convert width to twips
w <- round(wth * rs$point_conversion)
if ((ttls$border_flag | ttl_hdr$border_flag) & pgbys$points > 0)
ypos <- sum(ystart, ttls$points, ttl_hdr$points, pgbys$points) - 2
else
ypos <- sum(ystart, ttls$points, ttl_hdr$points, pgbys$points)
lnstrt <- ceiling(ypos / rs$line_height)
imght <- round((plt$height * rs$point_conversion) / lh)
rws <- list()
rws[[length(rws) + 1]] <- page_image(plot_path,
height = plt$height,
width = plt$width,
align = talign,
line_start = lnstrt + aln)
yline <- ceiling(ypos + (plt$height * rs$point_conversion))
brdrs <- strip_borders(plt$borders)
ylpos <- ypos - lh + bh - 1
# Top border
if (any(brdrs %in% c("all", "outside", "top"))) {
rws[[length(rws) + 1]] <- page_hline(lb * conv,
ylpos,
(rb - lb) * conv)
}
# Bottom border
if (any(brdrs %in% c("all", "outside", "bottom"))) {
rws[[length(rws) + 1]] <- page_hline(lb * conv,
ylpos,
(rb - lb) * conv)
}
# Left border
if (any(brdrs %in% c("all", "outside", "left"))) {
rws[[length(rws) + 1]] <- page_vline(lb * conv,
ylpos,
yline - ypos)
}
# Right border
if (any(brdrs %in% c("all", "outside", "right"))) {
rws[[length(rws) + 1]] <- page_vline(rb * conv,
ylpos,
yline - ypos)
}
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_pdf(rs, plt, wth, lpg_rows, yline - bh - 1,
wrap_flag, content_blank_row, talign)
bln <- 0
if (content_blank_row %in% c("both", "below")) {
bln <- 1
}
# Add remaining page content.
# This needs to be done now so everything is on the page
# Different than all other output types.
if (ttls$lines > 0) {
rws<- append(rws, ttls$pdf)
}
if (ttl_hdr$lines > 0) {
rws <- append(rws, ttl_hdr$pdf)
}
if (pgbys$lines > 0) {
rws <- append(rws, pgbys$pdf)
}
if (ftnts$lines > 0) {
rws <- append(rws, ftnts$pdf)
}
# Get sum of all items to this point
lns <- sum(aln, ttls$lines, ttl_hdr$lines, pgbys$lines,
imght, ftnts$lines, bln)
# Page list
ret <- list(pdf = rws,
lines = lns,
points = ylpos - ystart)
return(ret)
}
# Write DOCX Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @param imgCnt The number of images in document.
#' @noRd
create_plot_pages_docx<- function(rs, cntnt, lpg_rows, tmp_dir, imgCnt) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
imgs <- list()
relIndex <- rs$relIndex + imgCnt
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_docx(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE, relIndex)
pgs[[length(pgs) + 1]] <- res$docx
cnts[[length(cnts) + 1]] <- res$lines
relID <- paste0("rId", relIndex)
imgs[[relID]] <- tmp_nm
relIndex <- relIndex + 1
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_docx(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst), relIndex)
pgs[[length(pgs) + 1]] <- res$docx
cnts[[length(cnts) + 1]] <- res$lines
relID <- paste0("rId", relIndex)
imgs[[relID]] <- tmp_nm
relIndex <- relIndex + 1
cntr <- cntr + 1
}
}
ret <- list(docx = pgs,
lines = cnts,
images = imgs)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_docx <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval,
wrap_flag, rID) {
conv <- rs$twip_conversion
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_docx(plt$titles, wth, rs, talign,
content_brdrs = plt$borders)
ttl_hdr <- get_title_header_docx(plt$title_hdr, wth, rs, talign)
exclude_top <- NULL
if (ttls$border_flag == TRUE | ttl_hdr$border_flag == TRUE) {
exclude_top <- "top"
pgbys <- get_page_by_docx(pgby, wth, pgval, rs, talign, TRUE)
} else {
pgbys <- get_page_by_docx(pgby, wth, pgval, rs, talign, FALSE)
}
if (is.null(exclude_top)) {
if (pgbys$border_flag)
exclude_top <- "top"
}
algn <- talign
if (talign == "centre")
algn <- "center"
# algn <- "\\qc"
# This height and width is for the image scaling.
u <- rs$units
iconv <- 914400 # Image unit conversion. Not even sure what units this is.
if (u == "inches") {
hgth <- (plt$height - .2) * iconv
wdth <- (plt$width - .2) * iconv
} else {
hgth <- (cin(plt$height) - .2) * iconv
wdth <- (cin(plt$width) - .2) * iconv
}
# Get image RTF codes
img <- get_image_docx(rID, algn, hgth, wdth)
# Get indent codes for alignment
ta <- get_indent_docx(talign, rs$line_size, round(wth * conv),
rs$base_indent, plt$borders, conv)
grd <- get_col_grid(c(img = round(wth * conv)), 1)
# Get border codes
tb <- get_table_borders_docx(plt$borders)
tcb <- paste('<w:tcBorders>',
ifelse(any(plt$borders %in% c("all", "outside", "top")),
'<w:top w:val="single" w:sz="4" w:space="0" w:color="auto"/>', ""),
ifelse(any(plt$borders %in% c("all", "outside", "bottom")),
'<w:bottom w:val="single" w:sz="4" w:space="0" w:color="auto"/>', ""),
'</w:tcBorders>')
# Concat all header codes
hd <- paste0("<w:tbl>", "<w:tblPr>",
'<w:tblStyle w:val="TableGrid"/>',
rs$cell_margin,
'<w:tblW w:w="', round(wth * conv),'"',
' w:type="dxa"/>', ta, tb,
"</w:tblPr>\n", grd,
"<w:tr><w:tc>\n",
'<w:tcPr><w:tcW w:w="', round(wth * conv),'"/>', tcb,'</w:tcPr>')
ft <- paste0("</w:tc></w:tr></w:tbl>\n")
# Concat RTF codes for image
img <- paste0(hd, img, ft)
# ** Do something with this **
imght <- floor(plt$height / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- rs$blank_row
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
if ("bottom" %in% get_outer_borders(plt$borders))
extp <- TRUE
else
extp <- FALSE
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_docx(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign, extp,
content_brdrs = plt$borders)
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$docx, ttl_hdr$docx, pgbys$docx, img)
# Combine everything
rws <- c(rws, ftnts$docx)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(docx = rws,
lines = lns)
return(ret)
}
get_image_docx <- function(id, algn, hgth, wdth) {
ret <- paste0('<w:p>',
'<w:pPr><w:jc w:val="', algn, '"/></w:pPr>',
'<w:r>
<w:rPr>
<w:noProof/>
</w:rPr>
<w:drawing>
<wp:inline distT="0" distB="0" distL="0" distR="0"
wp14:anchorId="53259B4E" wp14:editId="79F9BC2E">
<wp:extent cx="', wdth, '" cy="', hgth, '"/>
<wp:effectExtent l="0" t="0" r="0" b="0"/>
<wp:docPr id="', id, '" name="Picture ', id, '"/>
<wp:cNvGraphicFramePr>
<a:graphicFrameLocks
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" noChangeAspect="1"/>
</wp:cNvGraphicFramePr>
<a:graphic
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main">
<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture">
<pic:pic
xmlns:pic="http://schemas.openxmlformats.org/drawingml/2006/picture">
<pic:nvPicPr>
<pic:cNvPr id="', id, '" name="Picture ', id, '"/>
<pic:cNvPicPr/>
</pic:nvPicPr>
<pic:blipFill>
<a:blip r:embed="rId', id, '" cstate="print">
<a:extLst>
<a:ext uri="{28A0092B-C50C-407E-A947-70E740481C1C}">
<a14:useLocalDpi
xmlns:a14="http://schemas.microsoft.com/office/drawing/2010/main" val="0"/>
</a:ext>
</a:extLst>
</a:blip>
<a:stretch>
<a:fillRect/>
</a:stretch>
</pic:blipFill>
<pic:spPr>
<a:xfrm>
<a:off x="0" y="0"/>
<a:ext cx="', wdth, '" cy="', hgth, '"/>
</a:xfrm>
<a:prstGeom prst="rect">
<a:avLst/>
</a:prstGeom>
</pic:spPr>
</pic:pic>
</a:graphicData>
</a:graphic>
</wp:inline>
</w:drawing>
</w:r>
</w:p>')
#ret <- paste0('<w:p><w:r><w:t>Hello</w:t></w:r></w:p>')
return(ret)
}
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Defines functions get_image_docx get_plot_body_docx create_plot_pages_docx get_plot_body_pdf create_plot_pages_pdf get_plot_body_html create_plot_pages_html get_plot_body_rtf create_plot_pages_rtf get_plot_body create_plot_pages_text print.plot_spec create_plot
Documented in create_plot print.plot_spec
# Create Plot Constructor ---------------------------------------------
#' @title Create plot content
#' @description Function to create a plot specification that can be
#' added as content to a report. The \code{create_plot} function can
#' be used to include charts, graphs, and figures on a statistical report.
#' The function supports plot objects returned by
#' \code{\link[ggplot2]{ggplot}} or \code{\link[survminer]{ggsurvplot}}.
#' It does not support the Base R
#' \code{plot} function.
#' @details
#' To add a plot to a report, use the \code{create_plot} function. The
#' function allows you to set a width and height for the plot. The
#' function will preserve any other geometries you apply to the plot. See
#' the \code{\link{add_content}} function to control page breaking and
#' blanks spaces above or below the plot.
#'
#' A plot specification accepts a \code{\link{page_by}} function. If a page by
#' is applied to the plot, the plot data will be subset by the page by
#' variable, and re-run for each subset.
#'
#' The plot specification also accepts titles and footnotes. See the
#' \code{\link{titles}} and \code{\link{footnotes}} functions for further
#' details.
#'
#' As of \strong{reporter} version 1.2.9, the \code{create_plot} function
#' also accepts a path to a JPEG stored on the file system instead of a
#' plot object. This
#' functionality was added to allow the user to create figures from other
#' plotting packages. If you pass an image path, the image will be inserted
#' into the report at the location specified.
#'
#' @param x The plot to create. Specifically, this parameter should be
#' set to an object returned from a call to \code{\link[ggplot2]{ggplot}}
#' or \code{\link[survminer]{ggsurvplot}}. This parameter also accepts
#' a path to a JPEG file. If a path is specified, the image will be appended
#' to the report at the point the content object is added.
#' @param height The height of the plot in the specified units of measure.
#' @param width The width of the plot in the specified units of measure.
#' @param borders Whether and where to place a border. Valid values are 'top',
#' 'bottom', 'left', 'right', 'all', 'none', and 'outside'.
#' Default is 'none'. The 'left', 'right', and 'outside'
#' border specifications only apply to RTF reports.
#' @return The plot specification.
#' @family plot
#' @seealso
#' \code{\link{titles}} to add a title block to the plot,
#' \code{\link{footnotes}} to add footnotes, and \code{\link{add_content}}
#' to add the plot object to a report.
#' @examples
#' library(reporter)
#' library(ggplot2)
#' library(magrittr)
#'
#' # Create temp file path
#' tmp <- file.path(tempdir(), "mtcars.rtf")
#'
#' # Create ggplot
#' p <- ggplot(mtcars, aes(x=cyl, y=mpg)) + geom_point()
#'
#' # Create plot object
#' plt <- create_plot(p, height = 4, width = 8)
#'
#' rpt <- create_report(tmp, output_type = "RTF") %>%
#' page_header("Client", "Study: XYZ") %>%
#' titles("Figure 1.0", "MTCARS Miles per Cylinder Plot") %>%
#' set_margins(top = 1, bottom = 1) %>%
#' add_content(plt) %>%
#' footnotes("* Motor Trend, 1974") %>%
#' page_footer("Time", "Confidential", "Page [pg] of [tpg]")
#'
#' # Write out report
#' write_report(rpt)
#'
#' # Uncomment to view RTF file
#' # shell.exec(tmp)
#' @export
create_plot <- function(x, height, width, borders = "none") {
if (!any(class(x) %in% c("gg", "ggplot", "ggcoxzph", "ggsurv", "character")))
stop("plot object must be of type 'ggplot', 'ggsurv', or a JPG file path.")
if (!all(borders %in% c("top", "bottom", "left", "right",
"all", "none", "outside")))
stop(paste("Borders parameter invalid. Valid values are",
"'top', 'bottom', 'left', 'right', 'all', ",
"'none', or 'outside'."))
ret <- structure(list(), class = c("plot_spec", "list"))
ret$plot <- x
ret$height <- height
ret$width <- width
ret$borders <- borders
return(ret)
}
# Utilities ---------------------------------------------------------------
#' @title Prints the plot spec
#' @description A function to print the plot spec.
#' The \strong{print} function will print the plot spec in summary
#' form. To view all parameters, set the \code{verbose} parameter to TRUE.
#' @param x The plot spec.
#' @param ... Additional parameters to pass to the underlying print function.
#' @param verbose Whether to print in verbose form. Default is FALSE.
#' @seealso
#' \code{\link{create_plot}} function to create a plot specification.
#' @return The plot spec, invisibly.
#' @family plot
#' @examples
#' txt <- create_text("Lorem ipsum dolor sit amet, consectetur...")
#' print(txt)
#'
#' # A text specification:
#' # - text: data.frame 'mtcars' 32 rows 11 cols
#' @import crayon
#' @export
print.plot_spec <- function(x, ..., verbose = FALSE){
if (verbose == TRUE) {
# If verbose mode is indicated, print values as a list
for (nm in names(x)) {
cat("$", nm, "\n", sep = "")
if (nm == "plot") {
print(unclass(x[[nm]]), ...)
}
else {
print(x[[nm]], ...)
}
cat("\n")
}
} else {
grey60 <- make_style(grey60 = "#999999")
cat(grey60("# A plot specification: \n"))
if (!is.null(x$plot)) {
if (typeof(x$plot) == "character") {
cat(paste0("- path: '", x$plot, "'\n"))
} else {
if ("ggplot" %in% class(x$plot) & !"patchwork" %in% class(x$plot)) {
if (!is.null(x$plot[["data"]])) {
dat <- x$plot[["data"]]
cat("- data: ")
cat(paste0(nrow(dat), " rows, ", ncol(dat), " cols\n"))
cat(paste0("- layers: ", length(x$plot[["layers"]]), "\n"))
}
}
}
}
cat(paste0("- height: ", x$height, "\n"))
cat(paste0("- width: ", x$width, "\n"))
if (!is.null(x$page_by)) {
cat(paste0("- page by: ", x$page_by$var, "\n"))
}
print_title_header(x$title_hdr)
print_titles(x$titles)
print_footnotes(x$footnotes)
}
invisible(x)
}
# Write Text Functions -------------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_text <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
ret <- list()
pgs <- get_plot_body(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
for (pg in pgs) {
ret <- c(ret, list(pg))
}
} else {
# Get data in case we need it for page by
raw <- p$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u)
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
# Can return multiple pages if it breaks across pages
# Not sure what that means for a plot, but that is the logic
pgs <- get_plot_body(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
# Within a content creation function, assumed that it will take
# care of filling out blanks for each page. Only the last page
# can have empty rows.
for (pg in pgs) {
ret <- c(ret, list(pg))
}
cntr <- cntr + 1
}
}
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body <- function(plt, plot_path, align, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Get titles and footnotes
w <- ceiling(plt$width / rs$char_width)
ttls <- get_titles(plt$titles, w, rs$line_size, rs$uchar, rs$char_width)
ttl_hdr <- get_title_header(plt$title_hdr, w, rs$line_size, rs$uchar,
rs$char_width)
pgbys <- get_page_by(pgby, w, pgval)
pltpth <- gsub("\\", "/", plot_path, fixed = TRUE)
s <- c(paste0("```", pltpth, "|", plt$height,
"|", plt$width, "|", align, "```"))
h <- ceiling(plt$height / rs$row_height) + 1 # adjustment needed? Appears so.
w <- ceiling(plt$width / rs$char_width)
fill <- rep("```fill```", h)
s <- c(s, fill)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- ""
# Add top border if requested
tbrdr <- NULL
if (any(plt$borders %in% c("top", "all")))
tbrdr <- paste0(rep(rs$uchar, w), collapse = "")
# Add bottom border if requested
bbrdr <- NULL
if (any(plt$borders %in% c("bottom", "all", "outside")))
bbrdr <- paste0(rep(rs$uchar, w), collapse = "")
# Add blank below content if requested
b <- NULL
if (content_blank_row %in% c("both", "below", "outside"))
b <- ""
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls, ttl_hdr, pgbys, tbrdr, s, bbrdr)
ftnts <- get_page_footnotes_text(rs, plt, w, lpg_rows, length(rws),
wrap_flag, content_blank_row)
rws <- c(rws, ftnts)
# Page list
ret <- list()
# Create tmp variable for 1 page of content
tmp <- c()
# Offset the first page with remaining rows from the
# last page of the previous content
offset <- lpg_rows
#print(paste("Offset:", offset))
# Assign content to pages
for (i in seq_along(rws)) {
if (length(tmp) < (rs$body_line_count - offset)) {
# Append to existing page
tmp[length(tmp) + 1] <- rws[i]
} else {
# Start a new page
ret[[length(ret) + 1]] <- pad_any(tmp, rs$line_size,
get_justify(align))
tmp <- rws[i]
# Set to zero on second page and leave it that way
offset <- 0
}
}
# Deal with last page
if (length(tmp) > 0 ) {
# If page is not empty
if (max(nchar(trimws(tmp))) > 0) {
# Add last page
ret[[length(ret) + 1]] <- pad_any(tmp, rs$line_size,
get_justify(align))
}
}
return(ret)
}
# Write RTF Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_rtf <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
fx <- ".jpg"
if (grepl(".emf", p, fixed = TRUE))
fx <- ".emf"
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = fx)
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_rtf(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
pgs[[length(pgs) + 1]] <- res$rtf
cnts[[length(cnts) + 1]] <- res$lines
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else if (any(class(p) %in% c("character"))) {
file.copy(p, tmp_nm, overwrite = TRUE)
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_rtf(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
pgs[[length(pgs) + 1]] <- res$rtf
cnts[[length(cnts) + 1]] <- res$lines
cntr <- cntr + 1
}
}
ret <- list(rtf = pgs,
lines = cnts)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_rtf <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_rtf(plt$titles, wth, rs, talign)
ttl_hdr <- get_title_header_rtf(plt$title_hdr, wth, rs, talign)
pgbys <- get_page_by_rtf(pgby, wth, pgval, rs, talign)
# Get image RTF codes
img <- get_image_rtf(plot_path, plt$width, plt$height, rs$units)
# Assign table alignment codes
if (talign == "left") {
talgn <- "\\trql"
} else if (talign == "right") {
talgn <- "\\trqr"
} else {
talgn <- "\\trqc"
}
algn <- "\\qc"
# Convert width to twips
w <- round(wth * rs$twip_conversion)
# Get border codes
b <- get_cell_borders(1, 1, 1, 1, plt$borders)
# Concat all header codes
hd <- paste0("\\sl0\\trowd\\trgaph0", talgn, b, "\\cellx", w, algn, " \n")
ft <- paste0("\\cell\\row\n\\ql", rs$font_rtf, rs$spacing_multiplier)
# Concat RTF codes for image
img <- paste0(hd, img, ft)
imght <- round((plt$height * rs$twip_conversion) / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- "\\par"
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_rtf(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign)
# On LibreOffice, have to protect the table from the title width or
# the table row will inherit the title row width. Terrible problem.
tpt <- "{\\pard\\fs1\\sl0\\par}"
if (any(plt$borders %in% c("all", "top", "outside"))) {
if (ttls$border_flag | rs$page_template$titles$border_flag |
rs$page_template$title_hdr$border_flag)
tpt <- ""
}
if (titles_aligned(plt$titles, plt$title_hdr))
tpt <- ""
# Prevent infection of widths on LibreOffice.
bpt <- "{\\pard\\fs1\\sl0\\par}"
if (any(plt$borders %in% c("all", "top", "outside"))) {
if (!is.null(ftnts)) {
if (ftnts$border_flag)
bpt <- ""
}
if (!is.null(rs$page_template$footnotes)) {
if (rs$page_template$footnotes$border_flag)
bpt <- ""
}
}
if (footnotes_aligned(plt$footnotes))
bpt <- ""
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$rtf, ttl_hdr$rtf, pgbys$rtf, tpt, img, bpt)
# Combine everything
rws <- c(rws, ftnts$rtf)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(rtf = rws,
lines = lns)
return(ret)
}
# Write HTML Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_html <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_html(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE)
pgs[[length(pgs) + 1]] <- res$html
cnts[[length(cnts) + 1]] <- res$lines
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_html(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst))
pgs[[length(pgs) + 1]] <- res$html
cnts[[length(cnts) + 1]] <- res$lines
cntr <- cntr + 1
}
}
ret <- list(html = pgs,
lines = cnts)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_html <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval, wrap_flag) {
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_html(plt$titles, wth, rs, talign)
ttl_hdr <- get_title_header_html(plt$title_hdr, wth, rs, talign)
exclude_top <- NULL
if (ttls$border_flag == TRUE | ttl_hdr$border_flag == TRUE) {
exclude_top <- "top"
pgbys <- get_page_by_html(pgby, wth, pgval, rs, talign, TRUE)
} else {
pgbys <- get_page_by_html(pgby, wth, pgval, rs, talign, FALSE)
}
if (is.null(exclude_top)) {
if (pgbys$border_flag)
exclude_top <- "top"
}
# Get image RTF codes
img <- get_image_html(plot_path, rs$modified_path, plt, rs$units)
# algn <- "\\qc"
u <- rs$units
if (u == "inches")
u <- "in"
# Convert width to twips
w <- paste0("width:", round(wth, 3), u, ";")
# Get border codes
b <- get_cell_borders_html(1, 1, 1, 1, plt$borders, exclude = exclude_top)
# Concat all header codes
hd <- paste0("<table style =\"", w, "\">\n",
"<tr><td style=\"", b, "\">\n")
ft <- "</td></tr></table>\n"
# Concat RTF codes for image
img <- paste0(hd, img, ft)
# ** Do something with this **
imght <- floor(plt$height / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- "<br>"
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
if ("bottom" %in% get_outer_borders(plt$borders))
extp <- TRUE
else
extp <- FALSE
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_html(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign, extp)
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$html, ttl_hdr$html, pgbys$html, img)
# Combine everything
rws <- c(rws, ftnts$html)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(html = rws,
lines = lns)
return(ret)
}
# Write PDF Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @noRd
create_plot_pages_pdf <- function(rs, cntnt, lpg_rows, tmp_dir) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
pnts <- c()
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
ys <- sum(rs$page_template$titles$points, rs$page_template$title_hdr$points,
rs$page_template$page_header$points, (lpg_rows * rs$line_height))
# Get pdf page bodies
res <- get_plot_body_pdf(plt, tmp_nm, cntnt$align, rs, row_offset,
cntnt$blank_row, NULL, NULL,
FALSE, ystart = ys)
pgs[[length(pgs) + 1]] <- res$pdf
cnts[length(cnts) + 1] <- res$lines
pnts[length(pnts) + 1] <- res$lines * rs$line_height
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
row_offset <- lpg_rows
for (dat in dat_lst) {
if (cntr > 1)
row_offset <- 0
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
ys <- sum(rs$page_template$titles$points, rs$page_template$title_hdr$points,
rs$page_template$page_header$points, (row_offset * rs$line_height))
# Get pdf page bodies
res <- get_plot_body_pdf(plt, tmp_nm, cntnt$align, rs, row_offset,
cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst), ystart = ys)
pgs[[length(pgs) + 1]] <- res$pdf
cnts[length(cnts) + 1] <- res$lines
pnts[length(pnts) + 1] <- res$lines * rs$line_height
cntr <- cntr + 1
}
}
ret <- list(pdf = pgs,
lines = cnts,
points = pnts)
return(ret)
}
#' Create list of page_text or page_image objects for a single page
#' @noRd
get_plot_body_pdf <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval,
wrap_flag, ystart = 0) {
cnt <- 0
lh <- rs$line_height
conv <- rs$point_conversion
bh <- rs$border_height
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Add blank above content if requested
aln <- 0
if (content_blank_row %in% c("both", "above")) {
aln <- 1
ystart <- ystart + lh
}
# Get titles and footnotes
ttls <- get_titles_pdf(plt$titles, wth, rs, talign, ystart = ystart)
ttl_hdr <- get_title_header_pdf(plt$title_hdr, wth, rs,
talign, ystart = ystart)
if (ttls$border_flag | ttl_hdr$border_flag) {
pgbys <- get_page_by_pdf(pgby, wth, pgval, rs, talign,
ystart = sum(ystart, ttls$points, ttl_hdr$points) - 2)
} else {
pgbys <- get_page_by_pdf(pgby, wth, pgval, rs, talign,
ystart = sum(ystart, ttls$points, ttl_hdr$points))
}
# Get image PDF codes
#img <- get_image_pdf(plot_path, plt$width, plt$height, rs$units)
if (talign == "right") {
lb <- rs$content_size[["width"]] - wth
rb <- rs$content_size[["width"]]
} else if (talign %in% c("center", "centre")) {
lb <- (rs$content_size[["width"]] - wth) / 2
rb <- wth + lb
} else {
lb <- 0
rb <- wth
}
#
# algn <- "\\qc"
# Convert width to twips
w <- round(wth * rs$point_conversion)
if ((ttls$border_flag | ttl_hdr$border_flag) & pgbys$points > 0)
ypos <- sum(ystart, ttls$points, ttl_hdr$points, pgbys$points) - 2
else
ypos <- sum(ystart, ttls$points, ttl_hdr$points, pgbys$points)
lnstrt <- ceiling(ypos / rs$line_height)
imght <- round((plt$height * rs$point_conversion) / lh)
rws <- list()
rws[[length(rws) + 1]] <- page_image(plot_path,
height = plt$height,
width = plt$width,
align = talign,
line_start = lnstrt + aln)
yline <- ceiling(ypos + (plt$height * rs$point_conversion))
brdrs <- strip_borders(plt$borders)
ylpos <- ypos - lh + bh - 1
# Top border
if (any(brdrs %in% c("all", "outside", "top"))) {
rws[[length(rws) + 1]] <- page_hline(lb * conv,
ylpos,
(rb - lb) * conv)
}
# Bottom border
if (any(brdrs %in% c("all", "outside", "bottom"))) {
rws[[length(rws) + 1]] <- page_hline(lb * conv,
ylpos,
(rb - lb) * conv)
}
# Left border
if (any(brdrs %in% c("all", "outside", "left"))) {
rws[[length(rws) + 1]] <- page_vline(lb * conv,
ylpos,
yline - ypos)
}
# Right border
if (any(brdrs %in% c("all", "outside", "right"))) {
rws[[length(rws) + 1]] <- page_vline(rb * conv,
ylpos,
yline - ypos)
}
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_pdf(rs, plt, wth, lpg_rows, yline - bh - 1,
wrap_flag, content_blank_row, talign)
bln <- 0
if (content_blank_row %in% c("both", "below")) {
bln <- 1
}
# Add remaining page content.
# This needs to be done now so everything is on the page
# Different than all other output types.
if (ttls$lines > 0) {
rws<- append(rws, ttls$pdf)
}
if (ttl_hdr$lines > 0) {
rws <- append(rws, ttl_hdr$pdf)
}
if (pgbys$lines > 0) {
rws <- append(rws, pgbys$pdf)
}
if (ftnts$lines > 0) {
rws <- append(rws, ftnts$pdf)
}
# Get sum of all items to this point
lns <- sum(aln, ttls$lines, ttl_hdr$lines, pgbys$lines,
imght, ftnts$lines, bln)
# Page list
ret <- list(pdf = rws,
lines = lns,
points = ylpos - ystart)
return(ret)
}
# Write DOCX Functions -----------------------------------------------------
#' @description A function to output strings for plot content
#' @details Basic logic is to write the plot as a png file to a temporary
#' location, then put a token in the text that references the temp location.
#' Later code will pick up the image and insert it into the report. Blank
#' lines are generated to fill up the page based on a calculation using
#' the plot height and width.
#' @param rs The Report Spec
#' @param cntnt The text content to output
#' @param lpg_rows Last page rows.
#' @param imgCnt The number of images in document.
#' @noRd
create_plot_pages_docx<- function(rs, cntnt, lpg_rows, tmp_dir, imgCnt) {
if (!"report_spec" %in% class(rs))
stop("Report spec expected for parameter rs")
if (!"report_content" %in% class(cntnt))
stop("Report Content expected for parameter cntnt")
pgs <- list()
cnts <- c()
imgs <- list()
relIndex <- rs$relIndex + imgCnt
# Get plot spec
plt <- cntnt$object
p <- plt$plot
if (any(class(p) %in% c("character"))) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
file.copy(p, tmp_nm, overwrite = TRUE)
# Get rtf page bodies
res <- get_plot_body_docx(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, NULL, NULL,
FALSE, relIndex)
pgs[[length(pgs) + 1]] <- res$docx
cnts[[length(cnts) + 1]] <- res$lines
relID <- paste0("rId", relIndex)
imgs[[relID]] <- tmp_nm
relIndex <- relIndex + 1
} else {
# Get data in case we need it for page by
raw <- plt$plot$data
# Determine if there is a page by
pgby <- NULL
if (!is.null(rs$page_by))
pgby <- rs$page_by
if (!is.null(plt$page_by))
pgby <- plt$page_by
if (!is.null(pgby)) {
if (!pgby$var %in% names(raw))
stop("Page by variable not found in plot data.")
dat_lst <- split(raw, raw[[pgby$var]])
} else {
dat_lst <- list(raw)
}
u <- ifelse(rs$units == "inches", "in", rs$units)
p <- plt$plot
ret <- list()
cntr <- 1
for (dat in dat_lst) {
tmp_nm <- tempfile(tmpdir = tmp_dir, fileext = ".jpg")
p$data <- dat
pgval <- NULL
if (!is.null(pgby)) {
# print(pgby$var)
# print(dat)
pgval <- dat[1, c(pgby$var)]
if (!is.null(pgby$format)) {
pgval <- fapply(pgval, pgby$format)
}
}
# Save plot to temp file
if (any(class(p) %in% c("ggcoxzph", "ggsurv"))) {
# Deal with survival plots
ggplot2::ggsave(tmp_nm, gridExtra::arrangeGrob(grobs = p),
width = plt$width, height = plt$height,
dpi = 300, units = u )
} else {
# Any other type of plots
ggplot2::ggsave(tmp_nm, p, width = plt$width, height = plt$height,
dpi = 300, units = u)
}
# Get rtf page bodies
res <- get_plot_body_docx(plt, tmp_nm, cntnt$align, rs,
lpg_rows, cntnt$blank_row, pgby, pgval,
cntr < length(dat_lst), relIndex)
pgs[[length(pgs) + 1]] <- res$docx
cnts[[length(cnts) + 1]] <- res$lines
relID <- paste0("rId", relIndex)
imgs[[relID]] <- tmp_nm
relIndex <- relIndex + 1
cntr <- cntr + 1
}
}
ret <- list(docx = pgs,
lines = cnts,
images = imgs)
return(ret)
}
#' Create list of vectors of strings for each page
#' @noRd
get_plot_body_docx <- function(plt, plot_path, talign, rs,
lpg_rows, content_blank_row, pgby, pgval,
wrap_flag, rID) {
conv <- rs$twip_conversion
# Default to content width
wth <- rs$content_size[["width"]]
# If user supplies a width, override default
if (!is.null(plt$width))
wth <- plt$width
# Get titles and footnotes
ttls <- get_titles_docx(plt$titles, wth, rs, talign,
content_brdrs = plt$borders)
ttl_hdr <- get_title_header_docx(plt$title_hdr, wth, rs, talign)
exclude_top <- NULL
if (ttls$border_flag == TRUE | ttl_hdr$border_flag == TRUE) {
exclude_top <- "top"
pgbys <- get_page_by_docx(pgby, wth, pgval, rs, talign, TRUE)
} else {
pgbys <- get_page_by_docx(pgby, wth, pgval, rs, talign, FALSE)
}
if (is.null(exclude_top)) {
if (pgbys$border_flag)
exclude_top <- "top"
}
algn <- talign
if (talign == "centre")
algn <- "center"
# algn <- "\\qc"
# This height and width is for the image scaling.
u <- rs$units
iconv <- 914400 # Image unit conversion. Not even sure what units this is.
if (u == "inches") {
hgth <- (plt$height - .2) * iconv
wdth <- (plt$width - .2) * iconv
} else {
hgth <- (cin(plt$height) - .2) * iconv
wdth <- (cin(plt$width) - .2) * iconv
}
# Get image RTF codes
img <- get_image_docx(rID, algn, hgth, wdth)
# Get indent codes for alignment
ta <- get_indent_docx(talign, rs$line_size, round(wth * conv),
rs$base_indent, plt$borders, conv)
grd <- get_col_grid(c(img = round(wth * conv)), 1)
# Get border codes
tb <- get_table_borders_docx(plt$borders)
tcb <- paste('<w:tcBorders>',
ifelse(any(plt$borders %in% c("all", "outside", "top")),
'<w:top w:val="single" w:sz="4" w:space="0" w:color="auto"/>', ""),
ifelse(any(plt$borders %in% c("all", "outside", "bottom")),
'<w:bottom w:val="single" w:sz="4" w:space="0" w:color="auto"/>', ""),
'</w:tcBorders>')
# Concat all header codes
hd <- paste0("<w:tbl>", "<w:tblPr>",
'<w:tblStyle w:val="TableGrid"/>',
rs$cell_margin,
'<w:tblW w:w="', round(wth * conv),'"',
' w:type="dxa"/>', ta, tb,
"</w:tblPr>\n", grd,
"<w:tr><w:tc>\n",
'<w:tcPr><w:tcW w:w="', round(wth * conv),'"/>', tcb,'</w:tcPr>')
ft <- paste0("</w:tc></w:tr></w:tbl>\n")
# Concat RTF codes for image
img <- paste0(hd, img, ft)
# ** Do something with this **
imght <- floor(plt$height / rs$line_height)
# Add blank above content if requested
a <- NULL
if (content_blank_row %in% c("both", "above"))
a <- rs$blank_row
# Get sum of all items to this point
lns <- sum(length(a), ttls$lines, ttl_hdr$lines, pgbys$lines, imght)
if ("bottom" %in% get_outer_borders(plt$borders))
extp <- TRUE
else
extp <- FALSE
# Get footnotes, filler, and content blank line
ftnts <- get_page_footnotes_docx(rs, plt, wth, lpg_rows, lns,
wrap_flag, content_blank_row, talign, extp,
content_brdrs = plt$borders)
# Combine titles, blanks, body, and footnotes
rws <- c(a, ttls$docx, ttl_hdr$docx, pgbys$docx, img)
# Combine everything
rws <- c(rws, ftnts$docx)
lns <- sum(lns, ftnts$lines)
# Page list
ret <- list(docx = rws,
lines = lns)
return(ret)
}
get_image_docx <- function(id, algn, hgth, wdth) {
ret <- paste0('<w:p>',
'<w:pPr><w:jc w:val="', algn, '"/></w:pPr>',
'<w:r>
<w:rPr>
<w:noProof/>
</w:rPr>
<w:drawing>
<wp:inline distT="0" distB="0" distL="0" distR="0"
wp14:anchorId="53259B4E" wp14:editId="79F9BC2E">
<wp:extent cx="', wdth, '" cy="', hgth, '"/>
<wp:effectExtent l="0" t="0" r="0" b="0"/>
<wp:docPr id="', id, '" name="Picture ', id, '"/>
<wp:cNvGraphicFramePr>
<a:graphicFrameLocks
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" noChangeAspect="1"/>
</wp:cNvGraphicFramePr>
<a:graphic
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main">
<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture">
<pic:pic
xmlns:pic="http://schemas.openxmlformats.org/drawingml/2006/picture">
<pic:nvPicPr>
<pic:cNvPr id="', id, '" name="Picture ', id, '"/>
<pic:cNvPicPr/>
</pic:nvPicPr>
<pic:blipFill>
<a:blip r:embed="rId', id, '" cstate="print">
<a:extLst>
<a:ext uri="{28A0092B-C50C-407E-A947-70E740481C1C}">
<a14:useLocalDpi
xmlns:a14="http://schemas.microsoft.com/office/drawing/2010/main" val="0"/>
</a:ext>
</a:extLst>
</a:blip>
<a:stretch>
<a:fillRect/>
</a:stretch>
</pic:blipFill>
<pic:spPr>
<a:xfrm>
<a:off x="0" y="0"/>
<a:ext cx="', wdth, '" cy="', hgth, '"/>
</a:xfrm>
<a:prstGeom prst="rect">
<a:avLst/>
</a:prstGeom>
</pic:spPr>
</pic:pic>
</a:graphicData>
</a:graphic>
</wp:inline>
</w:drawing>
</w:r>
</w:p>')
#ret <- paste0('<w:p><w:r><w:t>Hello</w:t></w:r></w:p>')
return(ret)
}
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