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# Basics

The **htmlTable** package is intended for generating tables using [HTML](https://en.wikipedia.org/wiki/HTML) formatting. This format is compatible with [Markdown](https://rmarkdown.rstudio.com/) 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:

```r
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:

```r
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>")
```


	 	  A simple tidyHtmlTable example using mtcars

		 hp
		 mpg
		 qsec

	 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:

```r
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.

```r
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 `""`:

```r
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`:

```r
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`:

```r
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:

```r
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:

```r
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:

```r
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:

```r
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:

```r
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

```r
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:

```r
options(table_counter = TRUE)
```

```r
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:

```r
tblNoLast()
```

```
## [1] 1
```

```r
tblNoNext()
```

```
## [1] 2
```

## Table footer

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

```r
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:

```r
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)
```


	 	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

