Format columns as markdown

This vignette introduces how to format columns in flextable.

library(flextable)
library(ftExtra)
#> Registered S3 method overwritten by 'ftExtra':
#>   method                  from     
#>   as_flextable.data.frame flextable
#> 
#> Attaching package: 'ftExtra'
#> The following object is masked from 'package:flextable':
#> 
#>     separate_header

Why markdown?

The flextable package is an excellent package that allows fine controls on styling tables, and export it to variety of formats (HTML, MS Word, PDF). Especially, when output format is MS Word, this package is the best solution in R.

On the other hand, styling texts with the flextable package often require large efforts. The following example subscripts numeric values in chemical formulas.

df <- data.frame(Oxide = c("SiO2", "Al2O3"), stringsAsFactors = FALSE)
ft <- flextable::flextable(df)

ft %>%
  flextable::compose(
    i = 1, j = "Oxide",
    value = flextable::as_paragraph(
      "SiO", as_sub("2")
    )
  ) %>%
  flextable::compose(
    i = 2, j = "Oxide",
    value = flextable::as_paragraph(
      "Al", as_sub("2"), "O", as_sub("3")
    )
  )

Oxide

SiO2

Al2O3

The above example has two problems:

  1. This is just a manual re-writing of the table.
    • Basically, users will explicitly input which characters to subscript.
    • For fine formatting, users have to apply compose for each cells one by one.
  2. Users have to learn a lot of functions from the flextable package
    • compose, as_paragraph, and as_sub in the above example

The first point can be solved by using a for loop, however, the code becomes quite complex.

df <- data.frame(Oxide = c("SiO2", "Fe2O3"), stringsAsFactors = FALSE)
ft <- flextable::flextable(df)

for (i in seq_len(nrow(df))) {
  ft <- flextable::compose(
    ft,
    i = i,
    j = "Oxide",
    value = flextable::as_paragraph(
      list_values = df$Oxide[i] %>%
        stringr::str_replace_all("([2-9]+)", " \\1 ") %>%
        stringr::str_split(" ", simplify = TRUE) %>%
        purrr::map_if(
          function(x) stringr::str_detect(x, "[2-9]+"),
          flextable::as_sub
        )
    )
  )
}
ft

Oxide

SiO2

Fe2O3

The ftExtra package provides easy solution by introducing markdown. As markdown texts self-explain their formats by plain texts, what users have to do is manipulations of character columns with their favorite tools such as the famous dplyr and stringr packages.

  1. Preprocess a data frame to decorate texts with markdown syntax.
  2. Convert the data frame into a flextable object with the flextable function or flextable function.
  3. Format markdown columns with colformat_md

The following example elegantly simplifies the prior example.

df <- data.frame(Oxide = c("SiO2", "Fe2O3"), stringsAsFactors = FALSE)

df %>%
  dplyr::mutate(
    Oxide = stringr::str_replace_all(Oxide, "([2-9]+)", "~\\1~")
  ) %>%
  flextable::flextable() %>%
  ftExtra::colformat_md()

Oxide

SiO2

Fe2O3

The colformat_md function is smart enough to detect character columns, so users can start without learning its arguments. Of course, it is possible to chose columns.

Another workflow is to read a markdown-formatted table from a external file. Again, markdown is by design a plain text, and can easily be embed in any formats such as CSV and Excel. So users can do something like

readr::read_csv("example.csv") %>%
  flextable::flextable() %>%
  ftExtra::colformat_md()

By default, the ftExtra package employs Pandoc’s markdown, which is also employed by R Markdown. This enables consistent user experience when using the ftExtra package in R Markdown.

Basic examples

The example below shows that colformat_md() function parses markdown texts in the flextable object.

data.frame(
  a = c("**bold**", "*italic*"),
  b = c("^superscript^", "~subscript~"),
  c = c("`code`", "[underline]{.underline}"),
  d = c(
    "*[**~ft~^Extra^**](https://ftextra.atusy.net/) is*",
    "[Cool]{.underline shading.color='skyblue'}"
  ),
  stringsAsFactors = FALSE
) %>%
  flextable() %>%
  colformat_md()

a

b

c

d

bold

superscript

code

ftExtra is

italic

subscript

underline

Cool

The table header can also be formatted by specifying part = "header" or "all" to colformat_md()

Supported syntax are

Notes:

Footnotes

An easy way to add a footnote is inline footnote.

data.frame(
  package = "ftExtra",
  description = "Extensions for 'Flextable'^[Supports of footnotes]",
  stringsAsFactors = FALSE
) %>%
  flextable() %>%
  colformat_md() %>%
  flextable::autofit(add_w = 0.5)

package

description

ftExtra

Extensions for Flextable1

1Supports of footnotes

Reference symbols can be configured by footnote_options(). Of course, markdown can be used inside footnotes as well.

data.frame(
  package = "ftExtra^[Short of *flextable extra*]",
  description = "Extensions for 'Flextable'^[Supports of footnotes]",
  stringsAsFactors = FALSE
) %>%
  flextable() %>%
  colformat_md(
    .footnote_options = footnote_options(
      ref = "i",
      prefix = "[",
      suffix = "]",
      start = 2,
      inline = TRUE,
      sep = "; "
    )
  ) %>%
  flextable::autofit(add_w = 0.5)

package

description

ftExtra[ii]

Extensions for Flextable[iii]

[ii]Short of flextable extra; [iii]Supports of footnotes;

In order to add multiple footnotes to a cell, use normal footnotes syntax.

data.frame(
  x =
    "foo[^a]^,^ [^b]

[^a]: aaa

[^b]: bbb",
  stringsAsFactors = FALSE
) %>%
  flextable() %>%
  colformat_md()

x

foo1, 2

1aaa

2bbb

Experimentally, reference symbols can be formatted by an user-defined function.

#' Custom formatter of reference symbols
#'
#' @param n n-th reference symbol (integer)
#' @param part where footnote exists: "body" or "header"
#' @param footer whether to format symbols in the footer: `TRUE` or `FALSE`
#'
#' @return a character vector which will further be processed as markdown texts
ref <- function(n, part, footer) {
  # Header uses letters and body uses integers for the symbols
  s <- if (part == "header") {
    letters[n]
  } else {
    as.character(n)
  }

  # Suffix symbols with ": " (a colon and a space) in the footer
  if (footer) {
    return(paste0(s, ":\\ "))
  }

  # Use superscript in the header and the body
  return(paste0("^", s, "^"))
}

# Apply custom function to format a table with footnotes
tibble::tibble(
  "header1^[note a]" = c("x^[note 1]", "y"),
  "header2" = c("a", "b^[note 2]")
) %>%
  flextable() %>%
  # process header first
  colformat_md(
    part = "header", .footnote_options = footnote_options(ref = ref)
  ) %>%
  # process body next
  colformat_md(
    part = "body", .footnote_options = footnote_options(ref = ref)
  ) %>%
  # tweak width for visibility
  flextable::autofit(add_w = 0.2)

header1a

header2

x1

a

y

b2

a: note a

1: note 1

2: note 2

Some notes:

Images

Images can be inserted optionally with width and/or height attributes. Specifying one of them changes the other while keeping the aspect ratio.

data.frame(
  R = sprintf("![](%s)", file.path(R.home("doc"), "html", "logo.jpg")),
  stringsAsFactors = FALSE
) %>%
  flextable() %>%
  colformat_md() %>%
  flextable::autofit()

R