htmlTable: Output an HTML table

Description

Generates advanced HTML tables with column and row groups for a dense representation of complex data. Designed for maximum compatibility with copy-paste into word processors. For styling, see addHtmlTableStyle() and setHtmlTableTheme(). Note: If you are using tidyverse and dplyr you may want to check out tidyHtmlTable() that automates many of the arguments that htmlTable requires.

Usage

htmlTable(
  x,
  header = NULL,
  rnames = NULL,
  rowlabel = NULL,
  caption = NULL,
  tfoot = NULL,
  label = NULL,
  rgroup = NULL,
  n.rgroup = NULL,
  cgroup = NULL,
  n.cgroup = NULL,
  tspanner = NULL,
  n.tspanner = NULL,
  total = NULL,
  ctable = TRUE,
  compatibility = getOption("htmlTableCompat", "LibreOffice"),
  cspan.rgroup = "all",
  escape.html = FALSE,
  ...
)
# S3 method for default
htmlTable(
  x,
  header = NULL,
  rnames = NULL,
  rowlabel = NULL,
  caption = NULL,
  tfoot = NULL,
  label = NULL,
  rgroup = NULL,
  n.rgroup = NULL,
  cgroup = NULL,
  n.cgroup = NULL,
  tspanner = NULL,
  n.tspanner = NULL,
  total = NULL,
  ctable = TRUE,
  compatibility = getOption("htmlTableCompat", "LibreOffice"),
  cspan.rgroup = "all",
  escape.html = FALSE,
  ...
)
# S3 method for htmlTable
knit_print(x, ...)
# S3 method for htmlTable
print(x, useViewer, ...)

Value

Returns a formatted string representing an HTML table of class htmlTable.

Arguments

x: The matrix/data.frame with the data. For the print and knit_print it takes a string of the class htmlTable as x argument.
header: A vector of character strings specifying column header, defaulting to colnames(x)
rnames: Default row names are generated from rownames(x). If you provide FALSE then it will skip the row names. Note: For data.frames if you do rownames(my_dataframe) <- NULL it still has row names. Thus you need to use FALSE if you want to supress row names for data.frames.
rowlabel: If the table has row names or rnames, rowlabel is a character string containing the column heading for the rnames.
caption: Adds a table caption.
tfoot: Adds a table footer (uses the <tfoot> HTML element). The output is run through txtMergeLines() simplifying the generation of multiple lines.
label: A text string representing a symbolic label for the table for referencing as an anchor. All you need to do is to reference the table, for instance <a href="#anchor_name">see table 2</a>. This is known as the element's id attribute, i.e. table id, in HTML linguo, and should be unique id for an HTML element in contrast to the css.class element attribute.
rgroup: A vector of character strings containing headings for row groups. n.rgroup must be present when rgroup is given. See detailed description in section below.
n.rgroup: An integer vector giving the number of rows in each grouping. If rgroup is not specified, n.rgroup is just used to divide off blocks of rows by horizontal lines. If rgroup is given but n.rgroup is omitted, n.rgroup will default so that each row group contains the same number of rows. If you want additional rgroup column elements to the cells you can sett the "add" attribute to rgroup through attr(rgroup, "add"), see below explaining section.
cgroup: A vector, matrix or list of character strings defining major column header. The default is to have none. These elements are also known as column spanners. If you want a column not to have a spanner then put that column as "". If you pass cgroup and n.crgroup as matrices you can have column spanners for several rows. See cgroup section below for details.
n.cgroup: An integer vector, matrix or list containing the number of columns for which each element in cgroup is a heading. For example, specify cgroup=c("Major_1","Major_2"), n.cgroup=c(3,3) if "Major_1" is to span columns 1-3 and "Major_2" is to span columns 4-6. rowlabel does not count in the column numbers. You can omit n.cgroup if all groups have the same number of columns. If the n.cgroup is one less than the number of columns in the matrix/data.frame then it automatically adds those.
tspanner: The table spanner is somewhat of a table header that you can use when you want to join different tables with the same columns.
n.tspanner: An integer vector with the number of rows or rgroups in the original matrix that the table spanner should span. If you have provided one fewer n.tspanner elements the last will be imputed from the number of rgroups (if you have provided rgroup and sum(n.tspanner) < length(rgroup)) or the number of rows in the table.
total: The last row is sometimes a row total with a border on top and bold fonts. Set this to TRUE if you are interested in such a row. If you want a total row at the end of each table spanner you can set this to "tspanner".
ctable: If the table should have a double top border or a single a' la LaTeX ctable style
compatibility: Is default set to LibreOffice as some settings need to be in old HTML format as Libre Office can't handle some commands such as the css caption-alignment. Note: this option is not yet fully implemented for all details, in the future I aim to generate a HTML-correct table and one that is aimed at Libre Office compatibility. Word-compatibility is difficult as Word ignores most settings and destroys all layout attempts (at least that is how my 2010 version behaves). You can additinally use the options(htmlTableCompat = "html") if you want a change to apply to the entire document. MS Excel sometimes misinterprets certain cell data when opening HTML-tables (eg. 1/2 becomes 1. February). To avoid this please specify the correct Microsoft Office format for each cell in the table using the css.cell-argument. To make MS Excel interpret everything as text use "mso-number-format:\"\@\"".
cspan.rgroup: The number of columns that an rgroup should span. It spans by default all columns but you may want to limit this if you have column colors that you want to retain.
escape.html: logical: should HTML characters be escaped? Defaults to FALSE.
...: Passed on to print.htmlTable function and any argument except the useViewer will be passed on to the base::cat() functions arguments. Note: as of version 2.0.0 styling options are still allowed but it is recommended to instead preprocess your object with addHtmlTableStyle().
useViewer: If you are using RStudio there is a viewer thar can render the table within that is envoced if in base::interactive() mode. Set this to FALSE if you want to remove that functionality. You can also force the function to call a specific viewer by setting this to a viewer function, e.g. useViewer = utils::browseURL if you want to override the default RStudio viewer. Another option that does the same is to set the options(viewer=utils::browseURL) and it will default to that particular viewer (this is how RStudio decides on a viewer). Note: If you want to force all output to go through the base::cat() the set [options][base::options](htmlTable.cat = TRUE).

Multiple rows of column spanners <code>cgroup</code>

If you want to have a column spanner in multiple levels (rows) you can set the cgroup and n.cgroup arguments to a matrix or list.

For different level elements, set absent ones to NA in a matrix. For example, cgroup = rbind(c("first", "second", NA), c("a", "b", "c")). And the corresponding n.cgroup would be n.cgroup = rbind(c(1, 2, NA), c(2, 1, 2)). for a table consisting of 5 columns. The "first" spans the first two columns, the "second" spans the last three columns, "a" spans the first two, "b" the middle column, and "c" the last two columns.

Using a list is recommended to avoid handling NAs.

For an empty cgroup, use "".

The <code>rgroup</code> argument

The rgroup groups rows seamlessly. Each row in a group is indented by two spaces (unless the rgroup is "") and grouped by its rgroup element. The sum(n.rgroup) should be zr3ywKOjLZACY4j7TuGXu4v6I8wVWuKy-\(\leq\) matrix rows. If fewer, remaining rows are padded with an empty rgroup (""). If rgroup has one more element than n.rgroup, the last n.rgroup is computed as nrow(x) - sum(n.rgroup) for a smoother table generation.

The add attribute to <code>rgroup</code>

To add an extra element at the rgroup level/row, use attr(rgroup, 'add'). The value can either be a vector, a list, or a matrix. See vignette("general", package = "htmlTable") for examples.

A vector of either equal number of rgroups to the number of rgroups that aren't empty, i.e. rgroup[rgroup != ""]. Or a named vector where the name must correspond to either an rgroup or to an rgroup number.
A list that has exactly the same requirements as the vector. In addition to the previous we can also have a list with column numbers within as names within the list.
A matrix with the dimension nrow(x) x ncol(x) or nrow(x) x 1 where the latter is equivalent to a named vector. If you have rownames these will resolve similarly to the names to the list/vector arguments. The same thing applies to colnames.

Important <span class="pkg">knitr</span>-note

This function will only work with knitr outputting HTML, i.e. markdown mode. As the function returns raw HTML-code the compatibility with non-HTML formatting is limited, even with pandoc.

Thanks to the the knitr::knit_print() and the knitr::asis_output() the results='asis' is no longer needed except within for-loops. If you have a knitr-chunk with a for loop and use print() to produce raw HTML you must set the chunk option results='asis'. Note: the print-function relies on the base::interactive() function for determining if the output should be sent to a browser or to the terminal. In vignettes and other directly knitted documents you may need to either set useViewer = FALSE alternatively set options(htmlTable.cat = TRUE).

RStudio's notebook

RStudio has an interactive notebook that allows output directly into the document. In order for the output to be properly formatted it needs to have the class of html. The htmlTable tries to identify if the environment is a notebook document (uses the rstudioapi and identifies if its a file with and Rmd file ending or if there is an element with html_notebook). If you don't want this behavior you can remove it using the options(htmlTable.skip_notebook = TRUE).

Table counter

If you set the option table_counter you will get a Table 1,2,3 etc before each table, just set options(table_counter=TRUE). If you set it to a number then that number will correspond to the start of the table_counter. The table_counter option will also contain the number of the last table, this can be useful when referencing it in text. By setting the option options(table_counter_str = "<b>Table %s:</b> ") you can manipulate the counter table text that is added prior to the actual caption. Note, you should use the sprintf() %s instead of %d as the software converts all numbers to characters for compatibility reasons. If you set options(table_counter_roman = TRUE) then the table counter will use Roman numerals instead of Arabic.

Empty data frames

An empty data frame will result in a warning and output an empty table, provided that rgroup and n.rgroup are not specified. All other row layout options will be ignored.

Options

There are multiple options that can be set, here is a set of the perhaps most used

table_counter - logical - activates a counter for each table
table_counter_roman - logical - if true the counter is in Roman numbers, i.e. I, II, III, IV...
table_counter_str - string - the string used for generating the table counter text
useViewer - logical - if viewer should be used fro printing the table
htmlTable.cat - logical - if the output should be directly sent to cat()
htmlTable.skip_notebook - logical - skips the logic for detecting notebook
htmlTable.pretty_indentation - logical - there was some issues in previous Pandoc versions where HTML indentation caused everything to be interpreted as code. This seems to be fixed and if you want to look at the raw HTML code it is nice to have this set to TRUE so that the tags and elements are properly indented.
htmlTableCompat - string - see parameter description

Other

Copy-pasting: As you copy-paste results into Word you need to keep the original formatting. Either right click and choose that paste option or click on the icon appearing after a paste. Currently the following compatibilities have been tested with MS Word 2016:

Internet Explorer (v. 11.20.10586.0) Works perfectly when copy-pasting into Word
RStudio (v. 0.99.448) Works perfectly when copy-pasting into Word. Note: can have issues with multi-line cgroups - see bug
Chrome (v. 47.0.2526.106) Works perfectly when copy-pasting into Word. Note: can have issues with multi-line cgroups - see bug
Firefox (v. 43.0.3) Works poorly - looses font-styling, lines and general feel
Edge (v. 25.10586.0.0) Works poorly - looses lines and general feel

Direct word processor opening: Opening directly in Libre Office or Word is no longer recommended. You get much prettier results using the cut-and-paste option.

Google docs: Copy-paste directly into a Google docs document is handled rather well. This seems to work especially well when the paste comes directly from a Chrome browser.

Note that when using complex cgroup alignments with multiple levels not every browser is able to handle this. For instance the RStudio webkit browser seems to have issues with this and a bug has been filed.

As the table uses HTML for rendering you need to be aware of that headers, row names, and cell values should try respect this for optimal display. Browsers try to compensate and frequently the tables still turn out fine but it is not advised. Most importantly you should try to use < instead of < and > instead of >. You can find a complete list of HTML characters here.

Lastly, I want to mention that function was inspired by the Hmisc::latex() that can be an excellent alternative if you wish to switch to PDF-output. For the sibling function tidyHtmlTable() you can directly switch between the two using the table_fn argument.

Examples

Run this code

library(magrittr)

# Basic example
output <- matrix(1:4,
                 ncol = 2,
                 dimnames = list(list("Row 1", "Row 2"),
                                 list("Column 1", "Column 2")))
htmlTable(output)
invisible(readline(prompt = "Press [enter] to continue"))

# An advanced output
output <- matrix(ncol = 6, nrow = 8)

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

output %>% addHtmlTableStyle(align = "r",
                             col.columns = c(rep("none", 2),
                                             rep("#F5FBFF", 4)),
                             col.rgroup = c("none", "#F7F7F7"),
                             css.cell = "padding-left: .5em; padding-right: .2em;") %>%
  htmlTable(header =  paste(c("1st", "2nd",
                              "3rd", "4th",
                              "5th", "6th"),
                            "hdr"),
            rnames = paste(c("1st", "2nd",
                             "3rd",
                             paste0(4:8, "th")),
                           "row"),
            rgroup = paste("Group", LETTERS[1:3]),
            n.rgroup = c(2,4,nrow(output) - 6),
            cgroup = rbind(c("", "Column spanners", NA),
                           c("", "Cgroup 1", "Cgroup 2†")),
            n.cgroup = rbind(c(1,2,NA),
                             c(2,2,2)),
            caption = "Basic table with both column spanners (groups) and row groups",
            tfoot = "† A table footer commment",
            cspan.rgroup = 2)
invisible(readline(prompt = "Press [enter] to continue"))

# An advanced empty table
suppressWarnings({
  matrix(ncol = 6,
         nrow = 0) %>%
    addHtmlTableStyle(col.columns = c(rep("none", 2),
                                      rep("#F5FBFF", 4)),
                      col.rgroup = c("none", "#F7F7F7"),
                      css.cell = "padding-left: .5em; padding-right: .2em;") %>%
    htmlTable(align = "r",
              header =  paste(c("1st", "2nd",
                                "3rd", "4th",
                                "5th", "6th"),
                              "hdr"),
              cgroup = rbind(c("", "Column spanners", NA),
                             c("", "Cgroup 1", "Cgroup 2†")),
              n.cgroup = rbind(c(1,2,NA),
                               c(2,2,2)),
              caption = "Basic empty table with column spanners (groups) and ignored row colors",
              tfoot = "† A table footer commment",
              cspan.rgroup = 2)
})
invisible(readline(prompt = "Press [enter] to continue"))

# An example of how to use the css.cell for header styling
simple_output <- matrix(1:4, ncol = 2)

simple_output %>%
  addHtmlTableStyle(css.cell = rbind(rep("background: lightgrey; font-size: 2em;",
                                         times = ncol(simple_output)),
                                     matrix("",
                                            ncol = ncol(simple_output),
                                            nrow = nrow(simple_output)))) %>%
  htmlTable(header = LETTERS[1:2])
invisible(readline(prompt = "Press [enter] to continue"))

# See vignette("tables", package = "htmlTable")
# for more examples, also check out tidyHtmlTable() that manages
# the group arguments for you through tidy-select syntax

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