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knitr format

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dr. M.S. (Matthijs) Berends
2023-02-23 16:27:40 +01:00
parent a84101db08
commit e70f2cd32c
10 changed files with 236 additions and 257 deletions
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83
R/antibiogram.R
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@ -45,7 +45,7 @@
#' @param sep a separating character for antibiotic columns in combination antibiograms
#' @param info a [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode
#' @param object an [antibiogram()] object
#' @param ... when used in [print()]: arguments passed on to [knitr::kable()] (otherwise, has no use)
#' @param ... when used in [R Markdown or Quarto][knitr::kable()]: arguments passed on to [knitr::kable()] (otherwise, has no use)
#' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
#'
#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
@ -103,7 +103,7 @@
#' "Study Group", "Control Group"))
#' ```
#'
#' All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]) or printed into R Markdown / Quarto formats for reports using `print()`. Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`.
#' All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]) or directly used into R Markdown / Quarto formats for reports (in the last case, [knitr::kable()] will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`.
#'
#' Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the `only_all_tested` argument (default is `FALSE`). See this example for two antibiotics, Drug A and Drug B, about how [antibiogram()] works to calculate the %SI:
#'
@ -215,8 +215,11 @@
#' antibiotics = ureidopenicillins(),
#' ab_transform = "name")
#'
#' # in an Rmd file, you would just need print(ureido), but to be explicit:
#' print(ureido, as_kable = TRUE, format = "markdown", italicise = TRUE)
#' # in an Rmd file, you would just need to return `ureido` in a chunk,
#' # but to be explicit here:
#' if (requireNamespace("knitr")) {
#' knitr::knit_print(ureido)
#' }
#'
#'
#' # Generate plots with ggplot2 or base R --------------------------------
@ -489,7 +492,7 @@ antibiogram <- function(x,
}
if (NCOL(new_df) == edit_col + 1) {
# only 1 antibiotic
new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", unlist(lapply(strsplit(count_group, "-"), function(x) x[1])), ")")
new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", unlist(lapply(strsplit(x = count_group, split = "-", fixed = TRUE), function(x) x[1])), ")")
colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N)")
} else {
# more than 1 antibiotic
@ -574,48 +577,40 @@ autoplot.antibiogram <- function(object, ...) {
)
}
#' @export
#' @param as_kable a [logical] to indicate whether the printing should be done using [knitr::kable()] (which is the default in non-interactive sessions)
#' @param italicise (only when `as_kable = TRUE`) a [logical] to indicate whether the microorganism names in the output table should be made italic, using [italicise_taxonomy()]. This only works when the output format is markdown, such as in HTML output.
#' @param na (only when `as_kable = TRUE`) character to use for showing `NA` values
#' @details Printing the antibiogram in non-interactive sessions will be done by [knitr::kable()], with support for [all their implemented formats][knitr::kable()], such as "markdown". The knitr format will be automatically determined if printed inside a knitr document (LaTeX, HTML, etc.).
# will be exported in zzz.R
#' @param italicise a [logical] to indicate whether the microorganism names in the [knitr][knitr::kable()] table should be made italic, using [italicise_taxonomy()]. This only works when the output format is markdown, such as in HTML output.
#' @param na character to use for showing `NA` values
#' @rdname antibiogram
print.antibiogram <- function(x, as_kable = !interactive(), italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
meet_criteria(as_kable, allow_class = "logical", has_length = 1)
knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
stop_ifnot_installed("knitr")
meet_criteria(italicise, allow_class = "logical", has_length = 1)
meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE)
if (isTRUE(as_kable) &&
pkg_is_available("knitr") &&
# be sure not to run kable in pkgdown for our website generation
!(missing(as_kable) && identical(Sys.getenv("IN_PKGDOWN"), "true"))) {
old_option <- getOption("knitr.kable.NA")
options(knitr.kable.NA = na)
on.exit(options(knitr.kable.NA = old_option))
out <- knitr::kable(x, ...)
format <- attributes(out)$format
if (!is.null(format) && format %in% c("markdown", "pipe")) {
# try to italicise the output
rows_with_txt <- which(out %like% "[a-z]")
rows_without_txt <- setdiff(seq_len(length(out)), rows_with_txt)
out[rows_with_txt] <- gsub("^[|]", "| ", out[rows_with_txt])
# put hyphen directly after second character
out[rows_without_txt] <- gsub("^[|](.)", "|\\1-", out[rows_without_txt])
out_ita <- italicise_taxonomy(as.character(out), type = "markdown")
if (length(unique(nchar(out_ita))) != 1) {
# so there has been alterations done by italicise_taxonomy()
to_fill <- which(nchar(out_ita) < max(nchar(out_ita)))
out_ita[intersect(to_fill, rows_with_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1 \\2\\3", out_ita[intersect(to_fill, rows_with_txt)], perl = TRUE)
out_ita[intersect(to_fill, rows_without_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1--\\2\\3", out_ita[intersect(to_fill, rows_without_txt)], perl = TRUE)
}
attributes(out_ita) <- attributes(out)
out <- out_ita
old_option <- getOption("knitr.kable.NA")
options(knitr.kable.NA = na)
on.exit(options(knitr.kable.NA = old_option))
out <- knitr::kable(x, ..., output = FALSE)
format <- attributes(out)$format
if (isTRUE(italicise) &&
!is.null(format) &&
format %in% c("markdown", "pipe")) {
# try to italicise the output
rows_with_txt <- which(out %like% "[a-z]")
rows_without_txt <- setdiff(seq_len(length(out)), rows_with_txt)
out[rows_with_txt] <- gsub("^[|]", "| ", out[rows_with_txt])
# put hyphen directly after second character
out[rows_without_txt] <- gsub("^[|](.)", "|\\1-", out[rows_without_txt])
out_ita <- italicise_taxonomy(as.character(out), type = "markdown")
if (length(unique(nchar(out_ita))) != 1) {
# so there has been alterations done by italicise_taxonomy()
to_fill <- which(nchar(out_ita) < max(nchar(out_ita)))
out_ita[intersect(to_fill, rows_with_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1 \\2\\3", out_ita[intersect(to_fill, rows_with_txt)], perl = TRUE)
out_ita[intersect(to_fill, rows_without_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1--\\2\\3", out_ita[intersect(to_fill, rows_without_txt)], perl = TRUE)
}
out
} else {
# remove 'antibiogram' class and print with default method
class(x) <- class(x)[class(x) != "antibiogram"]
print(x, ...)
attributes(out_ita) <- attributes(out)
out <- out_ita
}
res <- paste(c("", "", out), collapse = "\n")
knitr::asis_output(res)
}