An R package for generating advanced tables
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README.md

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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)
# 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

As of version 1.0.2 you no longer need to specify results='asis' for each knitr chunk.

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)
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:

htmlTable(mx, 
          css.rgroup = "",
          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

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")
Table 5: A table caption above
1st hdr 2nd hdr
1st row 1:1 1:2
2nd row 2:1 2:2
htmlTable(mx[1:2,1:2], 
          pos.caption = "bottom",
          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")
Table 1: A table caption with a numbering
1st hdr 2nd hdr
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

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

Putting it all together

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

htmlTable(mx, 
          align="r",
          rgroup = paste("Group", LETTERS[1:3]),
          n.rgroup = c(2,4,nrow(mx) - 6),
          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,
          col.columns = c(rep("none", 2),
                          rep("#F5FBFF", 4)),
          col.rgroup = c("none", "#F7F7F7"),
          css.cell = "padding-left: .5em; padding-right: .2em;")
Table 2: A table with column spanners, row groups, and zebra striping
  Column spanners
  Cgroup 1  Cgroup 2†
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
† A table footer comment