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flextable.R
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flextable.R
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#' Turns a `crosstable` object into a formatted `flextable`
#'
#' @param x the result of [crosstable()].
#' @param keep_id whether to keep the `.id` column.
#' @param by_header a string to override the header if `x` has only one `by` stratum.
#' @param autofit whether to automatically adjust the table. Can also be a function.
#' @param compact whether to compact the table. If `TRUE`, see [ct_compact.crosstable()] to see how to use `keep_id`.
#' @param show_test_name in the `test` column, show the test name.
#' @param fontsizes font sizes as a list of keys. Default to `list(body=11, subheaders=11, header=11)`. If set through arguments instead of options, all 3 names should be specified.
#' @param padding_v vertical padding (body).
#' @param remove_header_keys if `TRUE` and `x` has several `by` strata, header will only display values.
#' @param header_show_n numeric vector telling on which depth the group size should be indicated in the header. You can control the pattern using option `crosstable_options`. See [crosstable_options()] for details about it. See example for use case.
#' @param header_show_n_pattern glue pattern used when `header_show_n==TRUE`. `.col` is the name of the column and `.n` the size of the group. Default to `{.col} (N={.n})`; you can also use `{.col_key}` and `{.col_val}` when `by` has multiple stratum. To control the "Total" column, enter this as a `list` with names "cell" and "total".
#' @param generic_labels names of the crosstable default columns. Useful for translation for instance.
#' @param ... unused.
#'
#' @return a flextable.
#'
#' @author Dan Chaltiel
#' @aliases ctf cross_to_flextable to_flextable
#' @describeIn as_flextable Turns a `crosstable` object into a formatted `flextable`.
#' @seealso [crosstable()], [flextable::flextable()], [as_gt.crosstable()]
#'
#' @importFrom checkmate assert_class vname
#' @importFrom cli cli_warn
#' @importFrom dplyr across all_of any_of filter group_by intersect lead mutate pull recode select starts_with sym ungroup
#' @importFrom flextable align autofit bold border border_inner_h fix_border_issues flextable fontsize hline hline_bottom hline_top merge_h merge_v padding set_header_df set_header_labels set_table_properties vline_left vline_right
#' @importFrom glue glue
#' @importFrom officer fp_border
#' @importFrom purrr map
#' @importFrom rlang set_names
#' @importFrom stringr str_remove str_replace str_split str_sub
#' @importFrom tibble lst tibble
#' @importFrom tidyr replace_na separate_wider_delim
#' @importFrom utils modifyList
#' @export
#'
#' @examples
#' crosstable_options(crosstable_fontsize_header=14,
#' crosstable_fontsize_subheaders=10,
#' crosstable_fontsize_body=8)
#' crosstable(iris) %>% as_flextable()
#' crosstable(mtcars2, -model, by=c(am, vs)) %>% as_flextable(header_show_n=1)
#' crosstable(mtcars2, cols=c(mpg, cyl), by=am, effect=TRUE) %>%
#' as_flextable(keep_id=TRUE, autofit=FALSE)
#' crosstable(mtcars2, cols=c(mpg, cyl), by=am, effect=TRUE, total=TRUE) %>%
#' as_flextable(compact=TRUE, header_show_n=TRUE,
#' header_show_n_pattern=list(cell="{.col} (N={.n})", total="Total\n(N={.n})"))
#'
#' #Renaming (because why not?)
#' crosstable(mtcars2, am, by=vs, total="both", test=TRUE, effect=TRUE) %>%
#' dplyr::rename(ID=.id, math=variable, Tot=Total, lab=label, pval=test, fx=effect) %>%
#' as_flextable(by_header = "Engine shape",
#' generic_labels=list(id = "ID", variable = "math", total="Tot",
#' label = "lab", test = "pval", effect="fx"))
as_flextable.crosstable = function(x, keep_id=FALSE, by_header=NULL,
autofit=TRUE, compact=FALSE,
show_test_name=TRUE,
fontsizes=list(body=11, subheaders=11, header=11),
padding_v=NULL, remove_header_keys=TRUE,
header_show_n=FALSE, header_show_n_pattern="{.col} (N={.n})",
generic_labels=list(id=".id", variable="variable", value="value",
total="Total", label="label", test="test",
effect="effect"),
...) {
assert_class(x, "crosstable", .var.name=vname(x))
if(any(dim(x)==0)){
cli_abort("{.fun as_flextable} cannot apply to an empty crosstable.",
class="crosstable_af_empty_error")
}
if(missing(keep_id)) keep_id = getOption("crosstable_keep_id", keep_id)
if(missing(by_header)) by_header = getOption("crosstable_by_header", by_header)
if(missing(autofit)) autofit = getOption("crosstable_autofit", autofit)
if(missing(compact)) compact = getOption("crosstable_compact", compact)
if(missing(show_test_name)) show_test_name = getOption("crosstable_show_test_name", show_test_name)
if(missing(padding_v)) padding_v = getOption("crosstable_padding_v", padding_v)
if(missing(remove_header_keys)) remove_header_keys = getOption("crosstable_remove_header_keys",
remove_header_keys)
if(missing(header_show_n)) header_show_n = getOption("crosstable_header_show_n", header_show_n)
if(missing(header_show_n_pattern)) header_show_n_pattern = getOption("crosstable_header_show_n_pattern",
header_show_n_pattern)
header_show_n_pattern = get_show_n_pattern(header_show_n_pattern)
if(missing(generic_labels)) generic_labels = getOption("crosstable_generic_labels", generic_labels)
if(missing(fontsizes)) fontsizes = list(
body=getOption("crosstable_fontsize_body", fontsizes$body),
subheaders=getOption("crosstable_fontsize_subheaders", fontsizes$subheaders),
header=getOption("crosstable_fontsize_header", fontsizes$header)
)
border1 = fp_border(color = "black", style = "solid", width = 1)
border2 = fp_border(color = "black", style = "solid", width = 1.5)
xattr = attributes(x)
has_test = attr(x, "has_test")
has_effect = attr(x, "has_effect")
has_total = attr(x, "has_total")
has_label = attr(x, "has_label")
by_label = attr(x, "by_label")
by_table = attr(x, "by_table")
showNA = attr(x, "showNA")
by_levels = attr(x, "by_levels") %>% map(~{
if(showNA=="always") .x=unique(c(.x, NA))
replace_na(.x, replace="NA")
})
n_levels = length(by_levels)
by = attr(x, "by")
has_by = !is.null(by)
if(has_by && is.null(by_label)) by_label=by
if(isTRUE(by_header)) by_header=NULL
if(!is.null(by_header) && all(is.na(by_header) | by_header=="", na.rm=TRUE)) by_header=FALSE
inner_labels = attr(x, "inner_labels")
if(!is.null(inner_labels)){
generic_labels = modifyList(generic_labels, inner_labels)
}
generic_labels = get_generic_labels(generic_labels)
test=generic_labels$test
id=generic_labels$id
label=generic_labels$label
if (has_test && !is.null(x[[test]]) && !show_test_name) {
x[[test]] = str_remove(x[[test]], "\\n\\(.*\\)")
}
if (compact && !inherits(x, "compacted_crosstable")) {
x = ct_compact.crosstable(x, keep_id=keep_id)
}
rtn = replace(x, is.na(x), "NA")
if(inherits(x, "compacted_crosstable")) {
rows = attr(x, "title_rows")
title_rows = which(rows)+(0:(sum(rows)-1))
padded_rows = 1:nrow(rtn)
padded_rows = padded_rows[!padded_rows %in% title_rows]
header_labels = names(rtn) %>% recode(!!generic_labels$variable:="")
hl = set_names("", generic_labels$variable)
rtn = rtn %>%
flextable() %>%
set_header_labels(values=hl) %>%
fontsize(size=fontsizes$body) %>%
fontsize(i=title_rows, size=fontsizes$subheaders) %>%
border(title_rows, border.top = fp_border()) %>%
bold(title_rows, j=1:2) %>%
align(title_rows, align="left") %>%
padding(i=padded_rows, j=1, padding.left=getOption("crosstable_compact_padding", 25))
} else {
sep.rows = which(rtn[[id]] != lead(rtn[[id]]))
body_merge = intersect(names(rtn), generic_labels[c("label", "test", "effect", "id")]) %>%
unlist()
cols = names(rtn)
if(!keep_id) {
cols = rtn %>% select(-any_of(id)) %>% names()
body_merge = body_merge[body_merge!=id]
}
rtn = rtn %>%
mutate(
!!id:=str_wrap2(.data[[id]], width = getOption("crosstable_wrap_id", 70))
) %>%
flextable(col_keys=cols) %>%
fontsize(size=fontsizes$body) %>%
hline(i=sep.rows, border=border1) %>%
merge_v(j=id, target=body_merge, part="body")
}
if(n_levels==0) {
if(!isFALSE(header_show_n)){
if(is.null(by_header)) by_header = generic_labels$value
by_header = glue(header_show_n_pattern$cell, .col=by_header, .n=attr(x,"N"))
}
if(!is.null(by_header)){
rtn = rtn %>%
set_header_labels(values=lst(!!generic_labels$value := by_header))
}
} else if(n_levels==1) {
by_levels2 = unlist(by_levels)
byname = if(has_label) by_label else by
header_mapping = tibble(
col_keys = names(x),
.col_2 = ifelse(names(x) %in% by_levels2, byname, names(x)),
.col_1 = col_keys
)
if(inherits(x, "compacted_crosstable")) {
header_mapping[header_mapping$col_keys==generic_labels$variable, -1] = ""
}
if(!isFALSE(header_show_n)){
header_mapping = header_mapping %>%
mutate(
.n = by_table[col_keys],
.col_1 = ifelse(!is.na(.n), glue(header_show_n_pattern$cell, .col=.col_1), .col_1)
) %>%
select(-.n)
if(!is.null(header_show_n_pattern$total)){
tmp = glue(header_show_n_pattern$total, .n={attr(x,"N")})
header_mapping[header_mapping$col_keys=="Total", ".col_2"] = tmp
header_mapping[header_mapping$col_keys=="Total", ".col_1"] = tmp
}
}
if(!isFALSE(by_header)){
if(!is.null(by_header)){
header_mapping = header_mapping %>%
mutate(.col_2=str_replace(.col_2, byname, by_header))
}
} else {
header_mapping = header_mapping %>% select(-.col_2)
}
rtn = rtn %>%
set_header_df(header_mapping, key = "col_keys") %>%
merge_h(part = "head")
} else if(n_levels>1) {
if(!is.null(by_header)){
cli_warn("by_header is ignored if the crosstable has several `by` stratum.",
class="crosstable_af_byheader_multi")
}
header_mapping = tibble(col_keys = names(x)) %>%
separate_wider_delim(col_keys, names=paste0(".col_", seq(n_levels)),
delim=" & ", cols_remove=FALSE, too_few="align_start") %>%
mutate(across(starts_with(".col_"), ~ifelse(is.na(.x), col_keys, .x))) %>%
select(col_keys, rev(everything()))
if(!isFALSE(header_show_n)){
if(isTRUE(header_show_n)) header_show_n = seq(n_levels)
header_show_n = as.numeric(header_show_n)
.cols = paste0(".col_", seq(n_levels))
header_show_n2 = .cols[as.numeric(header_show_n)]
for(i in seq_along(.cols)){
.c = .cols[i:length(.cols)]
header_mapping = header_mapping %>%
group_by(across(all_of(.c))) %>%
mutate(!!.c[1] := {
.col = !!sym(.c[1])
.col2 = str_split(.col, "=")[[1]]
.col_key = .col2[1]
.col_val = .col2[2]
.n = sum(by_table[col_keys])
ifelse(!is.na(.n) & .c[1] %in% header_show_n2,
glue(header_show_n_pattern$cell), .col)
}) %>%
ungroup()
if(!is.null(header_show_n_pattern$total)){
tmp = glue(header_show_n_pattern$total, .n={attr(x,"N")})
header_mapping[header_mapping$col_keys=="Total", ".col_2"] = tmp
header_mapping[header_mapping$col_keys=="Total", ".col_1"] = tmp
}
}
}
if(remove_header_keys){
a = unlist(generic_labels[c("label", "variable")])
header_mapping =
header_mapping %>%
mutate(across(-col_keys, ~str_remove(.x, "^.*?="))) %>%
mutate(across(-col_keys, ~{
i=as.numeric(str_sub(cur_column(), -1))
ifelse(col_keys %in% a, by_label[i], .x)
}))
}
border_left_first = sum(rtn$header$col_keys %in% generic_labels[c("label", "variable", "id")])
border_separations = header_mapping %>%
filter(col_keys %in% rtn$header$col_keys) %>%
pull(-2) %>% {which(!. %in% generic_labels & .!=lead(.))}
borders_j = c(border_left_first+1, border_separations+1)
rtn = rtn %>%
set_header_df(header_mapping, key = "col_keys") %>%
merge_h(i=seq.int(n_levels), part = "head") %>%
border(j=borders_j, border.left=border1, part="all") %>%
vline_left(border=border1) %>%
vline_right(border=border1)
}
merge_cols = names(rtn$header$dataset) %>% .[. %in% generic_labels]
rtn = rtn %>%
merge_v(part = "head", j=merge_cols) %>%
bold(part = "head") %>%
align(align = "left", part = "all") %>%
align(align="center", part="head") %>%
fontsize(part="head", size=fontsizes$header) %>%
hline_top(border = border2, part = "head") %>%
hline_bottom(border = border2, part = "head") %>%
border_inner_h(border = border1, part = "head") %>%
fix_border_issues()
if(length(padding_v)!=0)
rtn = padding(rtn, padding.top=padding_v, padding.bottom=padding_v, part="body")
if(isTRUE(autofit)){
rtn = set_table_properties(rtn, layout="autofit")
} else if(is.function(autofit)){
rtn = autofit(rtn)
}
return(rtn)
}
#' @usage NULL
#' @export
#' @rdname as_flextable
to_flextable = as_flextable.crosstable
#' @usage NULL
#' @export
#' @importFrom lifecycle deprecate_warn
#' @rdname as_flextable
cross_to_flextable = function(...){
deprecate_warn("0.1.0", "cross_to_flextable()", "as_flextable()")# nocov
as_flextable.crosstable(...)# nocov
}
#' @usage NULL
#' @export
#' @rdname as_flextable
ctf = cross_to_flextable
#' @name as_flextable
#' @rdname as_flextable
#' @export
#' @importFrom flextable as_flextable
flextable::as_flextable
#' @usage NULL
#' @export
#' @rdname as_flextable
af = as_flextable.crosstable
#' Open a `crosstable` in a temporary document
#'
#' This eases copy-pasting
#'
#' @param x a crosstable
#' @param docx if true, peek as a `docx`, else, peek as `xlsx`
#' @param ... passed on to `as_flextable.crosstable()` or to `as_workbook()`
#'
#' @return Nothing, called for its side effects
#'
#' @author Dan Chaltiel
#' @export
#' @importFrom checkmate assert_class
#' @importFrom flextable as_flextable flextable
#' @importFrom utils browseURL
peek = function(x, docx=getOption("crosstable_peek_docx", TRUE), ...) {
if(has_method(x, "as_flextable")){
x = as_flextable(x, ...)
} else if(!inherits(x, "flextable")){
x = flextable(x)
}
assert_class(x, "flextable")
if(docx){
print(x, preview="docx")
} else {
x=as_workbook(x, ...)
filename = tempfile(fileext=".xlsx")
openxlsx::saveWorkbook(x, file=filename)
if(interactive()) browseURL(normalizePath(filename))
}
invisible()
}
# utils ---------------------------------------------------------------------------------------
#' @keywords internal
#' @noRd
#' @examples
#' get_show_n_pattern()
#' get_show_n_pattern("a")
#' get_show_n_pattern(list(cell="a"))
#' get_show_n_pattern(list(total="b"))
#' get_show_n_pattern(list(cell="a", total="b"))
#' @importFrom cli cli_abort
#' @importFrom purrr map_lgl
#' @importFrom rlang is_scalar_character names2
get_show_n_pattern = function(x=NULL){
rtn = list(cell="{.col} (N={.n})", total=NULL)
if(is.null(x)){
return(rtn)
} else if(!is.list(x)){
if(!is_scalar_character(x))
cli_abort("{.arg x} should be either a list or a character vector of length 1.",
class="get_show_n_pattern_class")
rtn$cell=x
} else {
if(any(!names2(x) %in% c("cell", "total")))
cli_abort("When {.arg x} is a list, its names should be {.val cell} and {.val total}.",
class="get_show_n_pattern_names")
if(!all(map_lgl(x, is_scalar_character)))
cli_abort("When {.arg x} is a list, all its values should be character vectors of length 1.",
class="get_show_n_pattern_length")
rtn[names(x)] = x
}
rtn
}
#' TODO validate_generic_labels
#' @keywords internal
#' @noRd
validate_generic_labels = function(x, generic_labels){
}