This vignette introduces how to format columns in flextable.
knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = rmarkdown::pandoc_available("2.7.2") && ("dplyr" %in% rownames(installed.packages())) )
library(flextable) library(ftExtra)
The flextable package is an excellent package that allows fine controls on styling tables, and export it to variety of formats (HTML, MS Word, PDF). Especially, when output format is MS Word, this package is the best solution in R.
On the other hand, styling texts with the flextable package often require large efforts. The following example subscripts numeric values in chemical formulas.
df <- data.frame(Oxide = c("SiO2", "Al2O3"), stringsAsFactors = FALSE) ft <- flextable::flextable(df) ft %>% flextable::compose( i = 1, j = "Oxide", value = flextable::as_paragraph( "SiO", as_sub("2") ) ) %>% flextable::compose( i = 2, j = "Oxide", value = flextable::as_paragraph( "Al", as_sub("2"), "O", as_sub("3") ) )
The above example has two problems:
compose
for each cells one by one.compose
, as_paragraph
, and as_sub
in the above exampleThe first point can be solved by using a for
loop, however, the code becomes quite complex.
df <- data.frame(Oxide = c("SiO2", "Fe2O3"), stringsAsFactors = FALSE) ft <- flextable::flextable(df) for (i in seq_len(nrow(df))) { ft <- flextable::compose( ft, i = i, j = "Oxide", value = flextable::as_paragraph( list_values = df$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
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.
flextable
function or flextable
function.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()
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.
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()
The table header can also be formatted by specifying part = "header"
or "all"
to colformat_md()
Supported syntax are
code
[foo]{.underline})
[foo]{color=red}
[foo]{shading.color=gray}
[foo]{font.family=Roboto}
Notes:
.sep
argument (default: "\n\n"
).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)
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)
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()
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)
Some notes:
colformat_md()
should be applied separately to the header and the body. In other words, part = "all"
is not recommended. That may order footnotes unexpectedly.footnote_options(ref)
should not be shared among the header and the body.r
# DO NOT SHARE fopts among header and body
fopts <- footnote_options(ref)
... %>%
colformat_md(part = "header", .footnote_options = fopts) %>%
colformat_md(part = "body", .footnote_options = fopts)
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()
The R logo is distributed by The R Foundation with the CC-BY-SA 4.0 license.
By default, soft line breaks becomes spaces.
data.frame(linebreak = c("a\nb"), stringsAsFactors = FALSE) %>% flextable() %>% colformat_md()
Pandoc's markdown supports hard line breaks by adding a backslash or double spaces at the end of a line.
data.frame(linebreak = c("a\\\nb"), stringsAsFactors = FALSE) %>% flextable() %>% colformat_md()
It is also possible to make \n
as a hard line break by extending Pandoc's Markdown.
data.frame(linebreak = c("a\nb"), stringsAsFactors = FALSE) %>% flextable() %>% colformat_md(md_extensions = "+hard_line_breaks")
Markdown treats continuous linebreaks as a separator of blocks such as paragraphs.
However, flextable package lacks the support for multiple paragraphs in a cell.
To workaround, colformat_md
collapses them to a single paragraph with a separator given to .sep
(default: \n\n
).
data.frame(linebreak = c("a\n\nb"), stringsAsFactors = FALSE) %>% flextable() %>% colformat_md(.sep = "\n\n")
Citations is experimentally supported. Note that there are no citation lists. It is expected to be produced by using R Markdown.
First, create a ftExtra.bib
file like below.
knitr::write_bib("ftExtra")
Second, specify it, and optionally a CSL file, within the YAML front matter.
--- bibliography: ftExtra.bib # csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl ---
Finally, cite the references within tables.
data.frame( Cite = c("@R-ftExtra", "[@R-ftExtra]", "[-@R-ftExtra]"), stringsAsFactors = FALSE ) %>% flextable() %>% colformat_md() %>% flextable::autofit(add_w = 0.2)
tf <- tempfile(fileext = ".bib") knitr::write_bib("ftExtra", tf) data.frame( Cite = c("@R-ftExtra", "[@R-ftExtra]", "[-@R-ftExtra]"), stringsAsFactors = FALSE ) %>% flextable() %>% colformat_md(pandoc_args = c("--bibliography", tf)) %>% flextable::autofit(add_w = 0.2)
If citation style such as Vancouver requires citations be numbered sequentially and consistently with the body,
manually offset the number for example by colformat_md(.cite_offset = 5)
.
The rendering of math is also possible.
data.frame( math = "$e^{i\\theta} = \\cos \\theta + i \\sin \\theta$", stringsAsFactors = FALSE ) %>% flextable() %>% colformat_md() %>% flextable::autofit(add_w = 0.2)
Note that results can be insufficient. This feature relies on Pandoc's HTML writer, which
render TeX math as far as possible using Unicode characters \ https://pandoc.org/MANUAL.html#math-rendering-in-html
Pandoc's markdown provides an extension, emoji
.
To use it with colformat_md()
, specify md_extensions="+emoji"
.
data.frame(emoji = c(":+1:"), stringsAsFactors = FALSE) %>% flextable() %>% colformat_md(md_extensions = "+emoji")
colformat_md
supports variety of formats.
They can even be HTML despite the name of the function.
data.frame( x = "H<sub>2</sub>O", stringsAsFactors = FALSE ) %>% flextable() %>% colformat_md(.from = "html")
Note that multiple paragraphs are not supported if .from
is not "markdown"
.
Below is an example with commonmark.
data.frame( x = "foo\n\nbar", stringsAsFactors = FALSE ) %>% flextable() %>% colformat_md(.from = "commonmark")
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