Format Data Set as Flextable

Format a data.frame as flextable() with Certe style, bold headers and Dutch number formats. This function can also transform existing flextable and gtsummary objects to allow the formatting provided in this tbl_flextable() function.

tbl_flextable(
  x,
  row.names = rownames(x),
  row.names.bold = TRUE,
  rows.italic = NULL,
  rows.bold = NULL,
  rows.height = NULL,
  rows.fill = NULL,
  rows.zebra = TRUE,
  row.total = FALSE,
  row.total.name = "Totaal",
  row.total.function = sum,
  row.total.widths = NULL,
  row.total.bold = TRUE,
  row.extra.header = list(values = NULL, widths = 1),
  row.extra.footer = list(values = NULL, widths = 1),
  column.names = colnames(x),
  column.names.bold = TRUE,
  columns.width = NULL,
  columns.percent = NULL,
  columns.italic = NULL,
  columns.bold = NULL,
  columns.fill = NULL,
  columns.zebra = FALSE,
  column.total = FALSE,
  column.total.name = "Totaal",
  column.total.function = sum,
  column.total.bold = TRUE,
  align = "c",
  align.part = "all",
  caption = "",
  na = "",
  logicals = c("X", ""),
  round.numbers = 2,
  round.percent = 1,
  format.dates = "d mmm yyyy",
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  font.family = "Calibri",
  font.size = 9,
  font.size.header = font.size + 1,
  values.colour = NULL,
  values.fill = NULL,
  values.bold = NULL,
  values.italic = NULL,
  autofit = is.null(columns.width) & is.null(rows.height),
  autofit.fullpage = TRUE,
  autofit.fullpage.width = 16,
  vline = NULL,
  vline.part = c("body", "footer"),
  theme = current_markdown_colour(),
  colours = list(rows.fill.even = paste0(theme, "6"), rows.fill.odd = paste0(theme, "5"),
    columns.fill = paste0(theme, "5"), values.fill = paste0(theme, "3"), values.colour =
    theme, vline.colour = theme, hline.colour = theme, header.fill = theme, header.colour
    = "white", vline.header.colour = "white"),
  split.across.pages = NROW(x) > 37,
  print = !interactive(),
  ...
)

# S3 method for certetoolbox_flextable
print(x, use_knitr = !is_latex_output(), ...)

Arguments

x: a data.frame or a flextable object or a gtsummary object
row.names: row names to be displayed. Will be 1:nrow(x) if set to TRUE, but can be a vector of values.
row.names.bold: display row names in bold
rows.italic: column indexes of rows in italics
rows.bold: column indexes of rows in bold
rows.height: height of the rows in centimetres
rows.fill: the column indices of rows to be shaded
rows.zebra: banded rows in the body - equivalent to rows.fill = seq(2, nrow(x), 2)
row.total: add a row total (at the bottom of the table)
row.total.name: name of the row total
row.total.function: function used to calculate all numeric values per column (non-numeric columns are skipped)
row.total.widths: cell width in row total
row.total.bold: bold formatting of row total
row.extra.header: an extra header to be displayed above the table
row.extra.footer: an extra footer to show below the table
column.names: column names to be displayed. Can also be a named vector where the names are existing columns, or indices of columns. When this vector is smaller than ncol(x), only the first length(column.names) are replaced. When this vector is longer than ncol(x), all column names are replaced
column.names.bold: display column names in bold
columns.width: width of columns. For autofit.fullpage = TRUE, these are proportions to autofit.fullpage.width. For autofit.fullpage = FALSE, these are centimeters
columns.percent: display the column indices as percentages using format2() - example: columns.percent = c(2, 3)
columns.italic: column indices of columns to be displayed in italics
columns.bold: column indices of columns in bold
columns.fill: the column indices of rows to be shaded
columns.zebra: banded columns - equivalent to columns.fill = seq(2, ncol(x), 2)
column.total: adding a column total (to the right of the table)
column.total.name: name of the column total
column.total.function: function used to calculate all numeric values per row
column.total.bold: bold formatting of column total
align: default is "c", which aligns everything centrally. Use "r", "l", "c" and "j"/"u" (justify/align) to change alignment. Can be a vector or a character (like "lrrrcc")
align.part: part of the table where the alignment should take place ("all", "header", "body", "footer")
caption: table caption
na: text for missing values
logicals: vector with two values that replace TRUE and FALSE
round.numbers: number of decimal places to round up for numbers
round.percent: number of decimal places to round to when using columns.percent
format.dates: see format2()
decimal.mark: decimal separator, defaults to dec_mark()
big.mark: thousands separator, defaults to big_mark()
font.family: table font family
font.size: table font size
font.size.header: font size of header
values.colour, values.fill, values.bold, values.italic: values to be formatted
autofit: format table in width automatically. This will apply autofit().
autofit.fullpage: display table across width of page
autofit.fullpage.width: set number of centimetres to width of table
vline: indices of columns to have a vertical line to their right
vline.part: part of the table where the vertical lines should be placed ("all", "header", "body", "footer")
theme: a Certe colour theme, defaults to current_markdown_colour() which determines the Certe colour based on a markdown YAML header and defaults to "certeblauw". Can also be "certeroze", "certegroen", etc. This will set the list in colours and will be ignored if colours is set manually. Can be set to "white" for a clean look.
colours: a list with the following named character values: rows.fill.even, rows.fill.odd, columns.fill, values.fill, and values.colour. All values will be evaluated with colourpicker().
split.across.pages: a logical whether tables are allowed to split across page. This argument only has effect for PDF output.
print: forced printing (required in a for loop), default is TRUE in non-interactive sessions
...: not used
use_knitr: use the knitr package for printing. Ignored when in an interactive session. If FALSE, an internal certetoolbox function will be used to convert the LaTeX longtable that would print across multiple PDF pages. If in a non-interactive session where the output is non-LaTeX, the knitr package will always be used.

Value

flextable object

Details

Run tbl_markdown() on a flextable object to transform it into markdown for use in Quarto or R Markdown reports. If print = TRUE in non-interactive sessions (Quarto or R Markdown), the flextable object will also be printed in markdown.

The value for theme is dependent on whether a colour is set in the markdown YAML header. Otherwise, use theme to set a Certe colour theme, defaults to "certeblauw":

# from the example below
tbl_flextable(df)

tbl_flextable(df, theme = "certeroze")

tbl_flextable(df, theme = "certegeel")

tbl_flextable(df, theme = "certegroen", vline = c(2:3))

tbl_flextable(
  df,
  theme = "certelila",
  row.total = TRUE,
  row.total.function = median,
  round.numbers = 4,
  row.extra.header = list(values = LETTERS[1:5])
)

Examples

if (FALSE) {

# generate a data.frame
df <- data.frame(text = LETTERS[1:10],
                 `decimal numbers` = runif(10, 0, 10),
                 `whole numbers` = as.integer(runif(10, 0, 10)),
                 `logical values` = as.logical(round(runif(10, 0, 1))),
                 dates = today() - runif(10, 200, 2000),
                 stringsAsFactors = FALSE)

# default
tbl_flextable(df)      # dataset has no row names
tbl_flextable(mtcars)  # dataset has row names

# print in markdown
df |> 
  tbl_flextable() |> 
  tbl_markdown()
  
# transform a gtsummary to a flextable
iris |>
  tbl_gtsummary(Species, add_p = TRUE) |>
  tbl_flextable()
  
# extra formatting
tbl_flextable(df,
              logicals = c("X", "-"),     # replaces TRUE en FALSE
              values.colour = "X",
              values.fill = "X",
              row.names = "S. aureus",
              columns.italic = 1,
              format.dates = "ddd dd-mm-yy",
              round.numbers = 3)

# row totals
tbl_flextable(df,
              row.total = TRUE,           # add row total
              row.total.function = max,   # instead of sum()
              row.total.name = "Maximum", # also works with dates
              columns.percent = 2,        # 2nd column as percentages
              round.percent = 0)          # rounding percentages

# column names
tbl_flextable(df,
              column.names = c("1" = "Column 1",
                               "2" = "Column 2",
                               dates = "DATES!"))
tbl_flextable(df,
              column.names = LETTERS)

# vertical lines, alignment and row names
tbl_flextable(df,
              align = "lrrcc", # also works: c("l", "r", "r", "c", "c")
              font.size = 12,
              vline = c(2, 4),
              vline.part = "all",
              row.names = paste("Experiment", 1:10))

# width of cells and table
tbl_flextable(data.frame(test1 = "A", test2 = "B"),
              vline = 1,
              autofit.fullpage.width = 16, # default values in cm
              columns.width = c(1, 3))     # ratio; cells become 4 and 12 cm

tbl_flextable(data.frame(test1 = "A", test2 = "B"),
              vline = 1,
              autofit.fullpage = FALSE,    # no fullpage autofit
              columns.width = c(1, 3))     # cells become 1 and 3 cm
              
# adding extra header or footer
tbl_flextable(data.frame(test1 = "A", test2 = "B"),
              row.extra.header = list(values = c("Header", "Header"),
                                      widths = c(1, 1)),
              row.extra.footer = list(values = c("Footer", "Footer"),
                                      widths = c(1, 1)))
}

Arguments

Value

Details

See also

Examples