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

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

The function is also aware of the dimnames:

# A simple output
matrix(1:4,
       ncol = 2,
       dimnames = list(rows = c("Row 1", "Row 2"),
                       cols = c("Column 1", "Column 2"))) %>% 
  htmlTable

	cols
	Column 1	Column 2
rows
Row 1	1	3
Row 2	2	4

This can be convenient when working with the base::table function:

data("mtcars")
with(mtcars,
     table(cyl, gear)) %>% 
  addmargins %>%
  htmlTable

	gear
	3	4	5	Sum
cyl
4	1	8	2	11
6	2	4	1	7
8	12	0	2	14
Sum	15	12	5	32

As of version 1.1 you no longer need to specify results='asis' for each knitr chunk.

Tip: If you are working a lot with dplyr and the tidyverse approach to exploring data you can make your life much easier using the tidyHtmlTable() function included in this package that automatically calculates the rgroup, cgroup and other parameters that make htmlTable so useful.

Table caption

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

output <- matrix(1:4,
                 ncol = 2,
                 dimnames = list(c("Row 1", "Row 2"),
                                 c("Column 1", "Column 2")))
htmlTable(output,
          ctable = c("solid", "double"),
          caption = "A table caption above and ctable borders")

	Column 1	Column 2
Row 1	1	3
Row 2	2	4
A table caption above and ctable borders

The caption defaults to above but by setting the pos.caption argument to “bottom” it appears below the table.

output %>%
  addHtmlTableStyle(pos.caption = "bottom") %>% 
  htmlTable(caption = "A table caption below")

	Column 1	Column 2
Row 1	1	3
Row 2	2	4
A table caption below

Cell alignment

Cell alignment is specified through the align, align.header, align.cgroup arguments. For aligning the cell values just use align. The argument can accept either a vector or a string, although supplying it with a string is the simplest option as in the example below:

1:3 %>% 
  addHtmlTableStyle(align = "lcr") %>% 
  htmlTable(rnames = "Row 1",
            header = c("'l' = left", "'c' = center", "'r' = right"),
            caption = "The alignment is set through the align options. Available alternatives are l, r, c as designated by the below table.")

	‘l’ = left	‘c’ = center	‘r’ = right
Row 1	1	2	3
The alignment is set through the align options. Available alternatives are l, r, c as designated by the below table.

Note that you can specify a string shorter than the number of columns. This can be useful if you have plenty of columns and you simply want all remaining columns to keep the alignment of the last column. To align the row name you can just add another letter to the string while the header is aligned through the align.header argument:

1:3 %>% 
  addHtmlTableStyle(align = "clcr",
                    align.header = "lcr") %>% 
  htmlTable(rnames = "Row 1",
            header = c("'l' = left", "'c' = center", "'r' = right"),
            caption = "The alignment is set through the align options. Available alternatives are l, r, c as designated by the below table.")

	‘l’ = left	‘c’ = center	‘r’ = right
Row 1	1	2	3
The alignment is set through the align options. Available alternatives are l, r, c as designated by the below table.

Advanced

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

row groups
column spanners
table spanners
total row
table footer
zebra coloring (also known 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 also looks nice in the final document not only in the browser. The htmlTable-function is written for all these purposes.

For demonstration purposes we will setup a basic matrix:

mx <- matrix(ncol = 6, nrow = 8)
rownames(mx) <- paste(c("1st", "2nd",
                        "3rd",
                        paste0(4:8, "th")),
                      "row")
colnames(mx) <- 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:

mx %>% 
  addHtmlTableStyle(css.rgroup = "") %>% 
  htmlTable(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

The rgroup is most commonly a single row without any additional cells but sometimes you may want to have a p-value or similar at the end of the row. This can be achieved by setting the ‘add’ attribute to the rgroup:

rgroup <- c(paste("Group", LETTERS[1:2]), "")
attr(rgroup, "add") <- list(`2` = "More")
htmlTable(mx, 
          rgroup = rgroup,
          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						More
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

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 and you can also provide a list with elements that allows you to skip the NA at the end of the matrix:

htmlTable(mx,
          cgroup = list(c("Super column spanner", ""),
                        c("", "Another cgroup"),
                        c("", "Cgroup 1", "Cgroup 2")),
          n.cgroup = list(c(5,1),
                          c(1,2),
                          c(2,2,2)))

	Super column spanner
			Another cgroup
			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

Note that you actually don’t need the last n.tspanner, i.e. you can simplify the above to:

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

	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

Similarly you can use the number rgroups included in each tspanner instead of actual rows. This is convenient as the tspannners must align with underlying rgroups.

Total row

Many financial tables use the concept of a total row at the end that sums the above elements:

htmlTable(mx[1:3,], total = TRUE)

	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

This can also be combined with table spanners:

mx %>% 
  addHtmlTableStyle(css.total = c("border-top: 1px dashed grey;",
                                  "border-top: 1px dashed grey;",
                                  "border-top: 1px solid grey; font-weight: 900")) %>% 
  htmlTable(total = "tspanner",
            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 numbering

The htmlTable has built-in numbering, initialized by:

options(table_counter = TRUE)

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

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

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

tblNoLast()

## [1] 1

tblNoNext()

## [1] 2

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

	1st hdr	2nd hdr
1st row	1:1	1:2
2nd row	2:1	2:2
Table 2: Another table with numbering

If you want to start the counter at 2 you can instead of setting table_counter to TRUE set it to 1. Note that you need to set the value to one less as each time the table is called the counter is incremented by one. You can also turn off the feature by:

options(table_counter = FALSE)

Table footer

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

Zebra coloring (or banded colors)

Zebra coloring is also know as an alternating color pattern or row shading. It is most commonly applied to rows:

mx %>% 
  addHtmlTableStyle(col.rgroup = c("none", "#F7F7F7")) %>% 
  htmlTable

	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

The zebra coloring in htmlTable is unique in that it follows the rgroups. The zebra striping is centered around the rgroup although rows with no set rgroup, i.e. “” will have alternating colors event though they programatically are within the same group:

mx %>% 
  addHtmlTableStyle(col.rgroup = c("none", "#F7F7F7")) %>% 
  htmlTable(rgroup = c(paste("Group", LETTERS[1:2]), ""),
            n.rgroup = c(2,2,nrow(mx) - 4))

	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

We can also color the columns:

mx %>% 
  addHtmlTableStyle(col.columns = c("none", "#F7F7F7")) %>% 
  htmlTable

	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

Or do both (note that the colors blend at the intersections):

mx %>% 
  addHtmlTableStyle(col.rgroup = c("none", "#F9FAF0"),
                    col.columns = c("none", "#F1F0FA")) %>% 
  htmlTable

	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

Putting it all together

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

rgroup = paste("Group", LETTERS[1:3])
attr(rgroup, "add") <- list(`3` = "Group p-value < 0.001")

mx %>% 
  addHtmlTableStyle(align = "rr|r",
                    align.header = "cc|c",
                    spacer.celltype = "double_cell",
                    col.columns = c(rep("none", 2),
                                    rep("#F5FBFF", 4)),
                    col.rgroup = c("none", "#F7F7F7"),
                    css.cell = "padding-left: .5em; padding-right: .2em;",
                    css.header = "font-weight: normal") %>% 
  htmlTable(rgroup = rgroup,
            n.rgroup = c(2,4),
            tspanner = paste("Spanner", LETTERS[1:2]),
            n.tspanner = c(1),
            cgroup = list(c("", "Column spanners"),
                          c("", "Cgroup 1", "Cgroup 2&dagger;")),
            n.cgroup = list(c(1,5),
                            c(2,2,2)),
            caption = "A table with column spanners, row groups, and zebra striping",
            tfoot = "&dagger; A table footer commment",
            cspan.rgroup = 2)

		Column spanners
			Cgroup 1		Cgroup 2†
	1st hdr	2nd hdr	3rd hdr	4th hdr	5th hdr	6th hdr
Spanner A
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
Spanner B
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						Group p-value < 0.001
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
A table with column spanners, row groups, and zebra striping
† A table footer commment

How-to use htmlTable

Max Gordon

2023-10-29