Basics

The htmlTable package is intended for generating tables using HTML formatting. This format is compatible with Markdown when used for HTML-output. The most basic table can easily be created by just passing a matrix or a data.frame to the htmlTable-function:

library(magrittr)
library(htmlTable)
# A simple output
output <- matrix(1:4,
                 ncol=2,
                 dimnames = list(list("Row 1", "Row 2"),
                                 list("Column 1", "Column 2")))
htmlTable(output)

	Column 1	Column 2
Row 1	1	3
Row 2	2	4

If you are using dplyr and tidyverse a convenient wrapper is the tidyHtmlTable function (check out vignette("tidyHtmlTable")). A simple example of the tidyHtmlTable would look something like this:

library(tidyverse)
library(glue)
mtcars |>
  as_tibble(rownames = "rnames") |>
  filter(cyl == 6 & qsec < 18) |>
  pivot_longer(names_to = "per_metric",
               cols = c(hp, mpg, qsec)) |>
  arrange(gear, rnames) |>
  mutate(gear = glue("{gear} gears")) |>
  addHtmlTableStyle(align = "r") |>
  tidyHtmlTable(header = per_metric, rnames = rnames, rgroup = gear,
                caption = "A simple <code>tidyHtmlTable</code> example using <code>mtcars</code>")

	hp	mpg	qsec
A simple `tidyHtmlTable` example using `mtcars`
4 gears
Mazda RX4	110	21	16.46
Mazda RX4 Wag	110	21	17.02
5 gears
Ferrari Dino	175	19.7	15.5

Advanced

While it may be sufficient for basic tables a more advanced layout is often needed in medical publications with elements such as:

row groups
column spanners
table spanners
caption
table footer
zebra coloring (also know as banding):
- rows
- columns

As many journals require that a MS Word-document is submitted it is furthermore also important that the table imports correctly to a word processor, i.e. that the table doesn’t only look nice in a web browser but also in the final document. The htmlTable-function is written for all these purposes.

Note: Due to GitHub CSS-styles the rows get automatically zebra-striped (in a bad way), borders get overridden and I haven’t been able to figure out how to change this. See the vignette for a correct example: vignette("general", package = "htmlTable")

For demonstration purposes we will setup a basic matrix:

mx <-
  matrix(ncol=6, nrow=8) |>
  set_rownames(paste(c("1st", "2nd", "3rd",
                       paste0(4:8, "th")),
                     "row")) |>
  set_colnames(paste(c("1st", "2nd", "3rd",
                       paste0(4:6, "th")),
                     "hdr"))

for (nr in 1:nrow(mx)){
  for (nc in 1:ncol(mx)){
    mx[nr, nc] <-
      paste0(nr, ":", nc)
  }
}

Row groups

The purpose of the row groups is to group variables that belong to the same group, e.g. a factored variable with more than two levels often benefit from grouping variables together.

htmlTable(mx,
          rgroup = paste("Group", LETTERS[1:3]),
          n.rgroup = c(2,4,nrow(mx) - 6))

	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
Group A
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
Group B
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
Group C
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

We can easily mix row groups with regular variables by having an empty row group name "":

htmlTable(mx,
          rgroup = c(paste("Group", LETTERS[1:2]), ""),
          n.rgroup = c(2,4,nrow(mx) - 6))

	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
Group A
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
Group B
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

When mixing row groups with variables without row groups we may want to omit the bold formatting of the row group label. As of htmlTable version 2.0 you can separate the css styling using addHtmlTableStyle:

mx |>
  addHtmlTableStyle(css.rgroup = "") |>
  htmlTable(rgroup = c(paste("Group", LETTERS[1:2]), ""),
            n.rgroup = c(2,4,nrow(mx) - 6))

Row highlighting

If you want to highlight an entire row based on a condition, use highlightRow() before htmlTable(). The condition is evaluated against the table columns, and you can also use .rowname:

df <- data.frame(
  Name = c("Max", "Eva", "Nils"),
  Score = c(10, 20, 30),
  stringsAsFactors = FALSE
)

df |>
  highlightRow(Name == "Max", style = "warning") |>
  highlightRow(.rowname == "3", style = "background-color: #d1ecf1; color: #0c5460;") |>
  htmlTable(rnames = FALSE)

Name	Score
Max	10
Eva	20
Nils	30

Column spanners

A column spanner spans 2 or more columns:

htmlTable(mx,
          cgroup = c("Cgroup 1", "Cgroup 2"),
          n.cgroup = c(2,4))

	Cgroup 1		Cgroup 2
	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

It can sometimes be convenient to have column spanners in multiple levels:

htmlTable(mx,
          cgroup = rbind(c("", "Column spanners", NA),
                         c("", "Cgroup 1", "Cgroup 2")),
          n.cgroup = rbind(c(1,2,NA),
                           c(2,2,2)))

			Column spanners
			Cgroup 1		Cgroup 2
	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

Above example allows the column spanner to be a sum of the underlying cgroups (see n.cgroup), this is not required by the function:

htmlTable(mx,
          cgroup = rbind(c("", "Column spanners", NA),
                         c("", "Cgroup 1", "Cgroup 2")),
          n.cgroup = rbind(c(1,5,NA),
                           c(2,1,3)))

		Column spanners
			Cgroup 1	Cgroup 2
	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

Table spanners

A table spanner is similar to rgroup but has the primary purpose of combining 2 or more tables with the same columns into one:

htmlTable(mx,
          tspanner = paste("Spanner", LETTERS[1:3]),
          n.tspanner = c(2,4,nrow(mx) - 6))

	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
Spanner A
1st row	1:1	1:2	1:3	1:4	1:5	1:6
2nd row	2:1	2:2	2:3	2:4	2:5	2:6
Spanner B
3rd row	3:1	3:2	3:3	3:4	3:5	3:6
4th row	4:1	4:2	4:3	4:4	4:5	4:6
5th row	5:1	5:2	5:3	5:4	5:5	5:6
6th row	6:1	6:2	6:3	6:4	6:5	6:6
Spanner C
7th row	7:1	7:2	7:3	7:4	7:5	7:6
8th row	8:1	8:2	8:3	8:4	8:5	8:6

Table caption

The table caption is simply the table description and can be either located above or below the table:

htmlTable(mx[1:2,1:2],
          caption="A table caption above")

	1st hdr	2nd hdr
Table 5: A table caption above
1st row	1:1	1:2
2nd row	2:1	2:2

mx[1:2,1:2] |>
  addHtmlTableStyle(pos.caption = "bottom") |>
  htmlTable(caption="A table caption below")

	1st hdr	2nd hdr
1st row	1:1	1:2
2nd row	2:1	2:2
Table 6: A table caption below

A more interesting detail that the function allows for is table numbering, initialized by:

options(table_counter = TRUE)

htmlTable(mx[1:2,1:2],
          caption="A table caption with a numbering")

	1st hdr	2nd hdr
Table 1: A table caption with a numbering
1st row	1:1	1:2
2nd row	2:1	2:2

As we often want to reference the table number in the text there are two associated functions:

tblNoLast()

## [1] 1

tblNoNext()

## [1] 2

The footer usually contains specifics regarding variables and is always located at the foot of the table:

htmlTable(mx[1:2,1:2],
          tfoot="A table footer")

	1st hdr	2nd hdr
1st row	1:1	1:2
2nd row	2:1	2:2
A table footer

Putting it all together

Now if we want to do everything in one table it may look like this:

mx |>
  addHtmlTableStyle(col.columns = c(rep("none", 2), rep("#F5FBFF", 4)),
                    col.rgroup = c("none", "#F7F7F7"),
                    css.cell = "padding-left: .5em; padding-right: .2em;",
                    align="r") |>
  htmlTable(rgroup = paste("Group", LETTERS[1:3]),
            n.rgroup = c(2, 4),
            cgroup = rbind(c("", "Column spanners", NA),
                           c("", "Cgroup 1", "Cgroup 2&dagger;")),
            n.cgroup = rbind(c(1, 2, NA), c(2, 2, 2)),
            caption="A table with column spanners, row groups, and zebra striping",
            tfoot="&dagger; A table footer commment",
            cspan.rgroup = 2)

    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right;'></td>
    <td style='font-weight: 900;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='font-weight: 900; background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td></tr>
<tr>
    <td style='text-align: left;'>&nbsp;&nbsp;1st row</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>1:1</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>1:2</td>
    <td style='' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>1:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>1:4</td>
    <td style='background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>1:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>1:6</td>
</tr>
<tr>
    <td style='text-align: left;'>&nbsp;&nbsp;2nd row</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>2:1</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>2:2</td>
    <td style='' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>2:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>2:4</td>
    <td style='background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>2:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>2:6</td>
</tr>
<tr><td colspan='2' style='font-weight: 900; background-color: #f7f7f7;'>Group B</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; background-color: #f7f7f7; text-align: right;'></td>
    <td style='font-weight: 900; background-color: #f7f7f7;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #F6F9FB;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #F6F9FB;'></td>
    <td style='font-weight: 900; background-color: #F6F9FB;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #F6F9FB;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #F6F9FB;'></td></tr>
<tr style='background-color: #f7f7f7;'>
    <td style='background-color: #f7f7f7; text-align: left;'>&nbsp;&nbsp;3rd row</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>3:1</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>3:2</td>
    <td style='background-color: #f7f7f7;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>3:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>3:4</td>
    <td style='background-color: #F6F9FB;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>3:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>3:6</td>
</tr>
<tr style='background-color: #f7f7f7;'>
    <td style='background-color: #f7f7f7; text-align: left;'>&nbsp;&nbsp;4th row</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>4:1</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>4:2</td>
    <td style='background-color: #f7f7f7;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>4:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>4:4</td>
    <td style='background-color: #F6F9FB;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>4:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>4:6</td>
</tr>
<tr style='background-color: #f7f7f7;'>
    <td style='background-color: #f7f7f7; text-align: left;'>&nbsp;&nbsp;5th row</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>5:1</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>5:2</td>
    <td style='background-color: #f7f7f7;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>5:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>5:4</td>
    <td style='background-color: #F6F9FB;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>5:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>5:6</td>
</tr>
<tr style='background-color: #f7f7f7;'>
    <td style='background-color: #f7f7f7; text-align: left;'>&nbsp;&nbsp;6th row</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>6:1</td>
    <td style='padding-left: .5em; padding-right: .2em; background-color: #f7f7f7; text-align: right;'>6:2</td>
    <td style='background-color: #f7f7f7;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>6:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>6:4</td>
    <td style='background-color: #F6F9FB;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>6:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #F6F9FB;'>6:6</td>
</tr>
<tr><td colspan='2' style='font-weight: 900;'>Group C</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right;'></td>
    <td style='font-weight: 900;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='font-weight: 900; background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td>
    <td style='padding-left: .5em; padding-right: .2em; font-weight: 900; text-align: right; background-color: #f5fbff;'></td></tr>
<tr>
    <td style='text-align: left;'>&nbsp;&nbsp;7th row</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>7:1</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right;'>7:2</td>
    <td style='' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>7:3</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>7:4</td>
    <td style='background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>7:5</td>
    <td style='padding-left: .5em; padding-right: .2em; text-align: right; background-color: #f5fbff;'>7:6</td>
</tr>
<tr>
    <td style='border-bottom: 2px solid grey; text-align: left;'>&nbsp;&nbsp;8th row</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right;'>8:1</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right;'>8:2</td>
    <td style='border-bottom: 2px solid grey;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right; background-color: #f5fbff;'>8:3</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right; background-color: #f5fbff;'>8:4</td>
    <td style='border-bottom: 2px solid grey; background-color: #f5fbff;' colspan='1'>&nbsp;</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right; background-color: #f5fbff;'>8:5</td>
    <td style='padding-left: .5em; padding-right: .2em; border-bottom: 2px solid grey; text-align: right; background-color: #f5fbff;'>8:6</td>
</tr>
</tbody>
<tfoot><tr><td colspan='9'>
&dagger; A table footer comment</td></tr></tfoot>

			Column spanners
Table 2: A table with column spanners, row groups, and zebra striping
			Cgroup 1		Cgroup 2†
	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
Group A