docs/awesome_table_in_html.Rmd

---
title: "Create Awesome HTML Table with knitr::kable and kableExtra"
author: "Hao Zhu"
date: "`r Sys.Date()`"
output: 
  html_document:
    theme: simplex
    toc: true
    toc_depth: 2
    toc_float: true
vignette: >
  %\VignetteIndexEntry{Create Awesome HTML Table with knitr::kable and kableExtra}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

> Please see the package [documentation site](http://haozhu233.github.io/kableExtra/) for how to use this package in LaTeX.

# Overview
The goal of `kableExtra` is to help you build common complex tables and manipulate table styles. It imports the pipe `%>%` symbol from `magrittr` and verbalize all the functions, so basically you can add "layers" to a kable output in a way that is similar with `ggplot2` and `plotly`. 

To learn how to generate complex tables in LaTeX, please visit [http://haozhu233.github.io/kableExtra/awesome_table_in_pdf.pdf](http://haozhu233.github.io/kableExtra/awesome_table_in_pdf.pdf)

# Installation
```r
install.packages("kableExtra")

# For dev version
# install.packages("devtools")
devtools::install_github("haozhu233/kableExtra")
```
# Getting Started
Here we are using the first few columns and rows from dataset `mtcars`
```{r}
library(knitr)
library(kableExtra)
dt <- mtcars[1:5, 1:6]
```

When you are using `kable()`, if you don't specify `format`, by default it will generate a markdown table and let pandoc handle the conversion from markdown to HTML/PDF. This is the most favorable approach to render most simple tables as it is format independent. If you switch from HTML to pdf, you basically don't need to change anything in your code. However, markdown doesn't support complex table. For example, if you want to have a double-row header table, markdown just cannot provide you the functionality you need. As a result, when you have such a need, you should **define `format` in `kable()`** as either "html" or "latex". *You can also define a global option at the beginning using `options(knitr.table.format = "html")` so you don't repeat the step everytime.* **In this tutorial, I'll still put `format="html"` in the function in case users just want to quickly replicate the results.** 

```{r}
options(knitr.table.format = "html") 
## If you don't define format here, you'll need put `format = "html"` in every kable function.
```

## Basic HTML table
Basic HTML output of `kable` looks very crude. To the end, it's just a plain HTML table without any love from css.
```{r}
kable(dt, "html")
```

## Bootstrap theme
When used on a HTML table, `kable_styling()` will automatically apply twitter bootstrap theme to the table. Now it should looks the same as the original pandoc output (the one when you don't specify `format` in `kable()`) but this time, you are controlling it.
```{r}
dt %>%
  kable("html") %>%
  kable_styling()
```

# Table Styles
`kable_styling` offers a few other ways to customize the look of a HTML table. 

## Bootstrap table classes
If you are familiar with twitter bootstrap, you probably have already known its predefined classes, including `striped`, `bordered`, `hover`, `condensed` and `responsive`. If you are not familiar, no worries, you can take a look at their [documentation site](http://getbootstrap.com/css/#tables) to get a sense of how they look like. All of these options are available here. 

For example, to add striped lines (alternative row colors) to your table and you want to highlight the hovered row, you can simply type:
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = c("striped", "hover"))
```

The option `condensed` can also be handy in many cases when you don't want your table to be too large. It has slightly shorter row height.
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed"))
```

Tables with option `responsive` looks the same with others on a large screen. However, on a small screen like phone, they are horizontally scrollable. Please resize your window to see the result.
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
```

## Full width?
By default, a bootstrap table takes 100% of the width. It is supposed to use together with its grid system to scale the table properly. However, when you are writing a rmarkdown document, you probably don't want to write your own css/or grid. For some small tables with only few columns, a page wide table looks awful. To make it easier, you can specify whether you want the table to have  `full_width` or not in `kable_styling`. By default, `full_width` is set to be `TRUE` for HTML tables (note that for LaTeX, the default is `FALSE` since I don't want to change the "common" looks unless you specified it.)
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = "striped", full_width = F)
```

## Position
Table Position only matters when the table doesn't have `full_width`. You can choose to align the table to `center`, `left` or `right` side of the page
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left")
```

Becides these three common options, you can also wrap text around the table using the `float-left` or `float-right` options. 
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "float_right")
```
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras sit amet mauris in ex ultricies elementum vel rutrum dolor. Phasellus tempor convallis dui, in hendrerit mauris placerat scelerisque. Maecenas a accumsan enim, a maximus velit. Pellentesque in risus eget est faucibus convallis nec at nulla. Phasellus nec lacinia justo. Morbi fermentum, orci id varius accumsan, nibh neque porttitor ipsum, consectetur luctus risus arcu ac ex. Aenean a luctus augue. Suspendisse et auctor nisl. Suspendisse cursus ultrices quam non vulputate. Phasellus et pharetra neque, vel feugiat erat. Sed feugiat elit at mauris commodo consequat. Sed congue lectus id mattis hendrerit. Mauris turpis nisl, congue eget velit sed, imperdiet convallis magna. Nam accumsan urna risus, non feugiat odio vehicula eget.

## Font size
If one of your tables is huge and you want to use a smaller font size for that specific table, you can use the `font_size` option. 
```{r}
kable(dt, "html") %>%
  kable_styling(bootstrap_options = "striped", font_size = 7)
```

# Column / Row Specification
## Column spec
When you have a table with lots of explanatory texts, you may want to specified the column width for different column, since the auto adjust in HTML may not work in its best way while basic LaTeX table is really bad at handling text wrapping. Also, sometimes, you may want to highlight a column (e.g. a "Total" column) by making it bold. In these scenario, you can use `column_spec()`. You can find an example below. 

Warning: If you have a super long table, you should be cautious when you use `column_spec` as the xml node modification takes time.

```{r}
text_tbl <- data.frame(
  Items = c("Item 1", "Item 2", "Item 3"),
  Features = c(
    "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin vehicula tempor ex. Morbi malesuada sagittis turpis, at venenatis nisl luctus a. ",
    "In eu urna at magna luctus rhoncus quis in nisl. Fusce in velit varius, posuere risus et, cursus augue. Duis eleifend aliquam ante, a aliquet ex tincidunt in. ", 
    "Vivamus venenatis egestas eros ut tempus. Vivamus id est nisi. Aliquam molestie erat et sollicitudin venenatis. In ac lacus at velit scelerisque mattis. "
  )
)

kable(text_tbl, "html") %>%
  kable_styling(full_width = F) %>%
  column_spec(1, bold = T, border_right = T) %>%
  column_spec(2, width = "30em", background = "yellow")
```


## Row spec
Similar with `column_spec`, you can define specifications for rows. Currently, you can either bold or italiciz an entire row. Note that, similar with other row-related functions in `kableExtra`, for the position of the target row, you don't need to count in header rows or the group labelling rows.

```{r}
kable(dt, "html") %>%
  kable_styling("striped", full_width = F) %>%
  column_spec(5:7, bold = T) %>%
  row_spec(3:5, bold = T, color = "white", background = "#D7261E")
```

# Cell Specification
`cell_spec` is different from the rest. You should use it before you pipe the table into the `kable` function. It is designed in such a way that you can easily use it inside a `dplyr::mutate()` together with conditional logic like `ifelse`. Since everything happens before `kable`, you have to tell this function which format you want to go to, `html` or `latex`. To reduce unnecessary finger typing, I linked the `format` argument here with `knitr::kable`'s global format option `knitr.table.format`. If you have defined this option to be `html` at the beginning of your document (as suggested earlier), it is not necessary for you to define format again for every `cell_spec`. 

```{r, message=FALSE}
library(dplyr)
mtcars[1:5, 1:3] %>%
  mutate(
    car = row.names(.),
    mpg = ifelse(mpg > 20, 
                 cell_spec(mpg, "html", font_size = 18), mpg),
    cyl = cell_spec(cyl, "html", angle = (1:5)*60, hover_message = mpg,
                    background = "red", color = "white", align = "center"),
    disp = ifelse(disp > 200,
                  cell_spec(disp, "html", color = "red", bold = T),
                  cell_spec(disp, "html", color = "green", italic = T)),
    fancy = c(12, 14, 16, 18, 20),
    fancy = cell_spec(fancy, "html", font_size = fancy, 
                      color = viridisLite::inferno(length(fancy), end = 0.8)),
    car = cell_spec(car, "html", bold = T,
                    color = viridisLite::inferno(length(fancy), end = 0.8))
  ) %>%
  select(car, everything()) %>%
  kable("html", escape = F) %>%
  kable_styling("hover", full_width = F) %>%
  add_header_above(c(" ", "Hello" = 2, "World" = 2)) 
```

## 

# Grouped Columns / Rows
## Add header rows to group columns
Tables with multi-row headers can be very useful to demonstrate grouped data. To do that, you can pipe your kable object into `add_header_above()`. The header variable is supposed to be a named character with the names as new column names and values as column span. For your convenience, if column span equals to 1, you can ignore the `=1` part so the function below can be written as `add_header_above(c(" ", "Group 1" = 2, "Group 2" = 2, "Group 3" = 2)).
```{r}
kable(dt, "html") %>%
  kable_styling("striped") %>%
  add_header_above(c(" " = 1, "Group 1" = 2, "Group 2" = 2, "Group 3" = 2))
```

In fact, if you want to add another row of header on top, please feel free to do so.
```{r}
kable(dt, "html") %>%
  kable_styling(c("striped", "bordered")) %>%
  add_header_above(c(" ", "Group 1" = 2, "Group 2" = 2, "Group 3" = 2)) %>%
  add_header_above(c(" ", "Group 4" = 4, "Group 5" = 2)) %>%
  add_header_above(c(" ", "Group 6" = 6))
```

## Group rows via labeling
Sometimes we want a few rows of the table being grouped together. They might be items under the same topic (e.g., animals in one species) or just different data groups for a categorical variable (e.g., age < 40, age > 40). With the new function `group_rows()` in `kableExtra`, this kind of task can be completed in one line. Please see the example below. Note that when you count for the start/end rows of the group, you don't need to count for the header rows nor other group label rows. You only need to think about the row numbers in the "original R dataframe".
```{r}
kable(mtcars[1:10, 1:6], "html", caption = "Group Rows") %>%
  kable_styling("striped", full_width = F) %>%
  group_rows("Group 1", 4, 7) %>%
  group_rows("Group 2", 8, 10)
```

Another way to use `group_rows` is to provide an grouping index, similar with `add_header_above()`. This feature is only available in kableExtra > 0.5.2.
```{r, eval = F}
# Not evaluated. This example generates the same table as above.
kable(mtcars[1:10, 1:6], "html", caption = "Group Rows") %>%
  kable_styling("striped", full_width = F) %>%
  group_rows(index = c(" " = 3, "Group 1" = 4, "Group 2" = 3))
```

For advanced users, you can even define your own css for the group labeling.
```{r}
kable(dt, "html") %>%
  kable_styling("striped", full_width = F) %>%
  group_rows("Group 1", 3, 5, label_row_css = "background-color: #666; color: #fff;")
```

## Row indentation
Unlike `group_rows()`, which will insert a labeling row, sometimes we want to list a few sub groups under a total one. In that case, `add_indent()` is probably more apporiate. 
For advanced users, you can even define your own css for the group labeling.
```{r}
kable(dt, "html") %>%
  kable_styling("striped", full_width = F) %>%
  add_indent(c(1, 3, 5))
```

## Group rows via multi-row cell
Function `group_rows` is great for showing simple structural information on rows but sometimes people may need to show structural information with multiple layers. When it happens, you may consider to use `collapse_rows` instead, which will put repeating cells in columns into multi-row cells. 

```{r}
collapse_rows_dt <- data.frame(C1 = c(rep("a", 10), rep("b", 5)),
                 C2 = c(rep("c", 7), rep("d", 3), rep("c", 2), rep("d", 3)),
                 C3 = 1:15,
                 C4 = sample(c(0,1), 15, replace = TRUE))
kable(collapse_rows_dt, "html", align = "c") %>%
  kable_styling(full_width = F) %>%
  column_spec(1, bold = T) %>%
  collapse_rows(columns = 1:2)
```

# Table Footnote
## Notation systems
You can also use `add_footnote()` function from this package. You will need to supply a character vector with each element as one footnote. You may select from `number`, `alphabet` and `symbol` for different types of notations. Example are listed below.

### Alphabet
```{r}
kable(dt, "html") %>%
  kable_styling("striped") %>%
  add_footnote(c("Footnote 1", "Have a good day."), notation = "alphabet")
```

### Number
```{r}
kable(dt, "html") %>%
  kable_styling("striped") %>%
  add_footnote(c("Footnote 1", "Have a good day."), notation = "number")
```

### Symbol
```{r}
kable(dt, "html") %>%
  kable_styling("striped") %>%
  add_footnote(c("Footnote 1", "Footnote 2", "Footnote 3"), notation = "symbol")
```

## In-table markers
By design, `add_footnote()` will transform any `[note]` to in-table footnote markers. 

```{r}
kable(dt, "html", caption = "Demo Table[note]") %>%
  kable_styling("striped") %>%
  add_header_above(c(" ", "Group 1[note]" = 3, "Group 2[note]" = 3)) %>%
  add_footnote(c("This table is from mtcars", 
                 "Group 1 contains mpg, cyl and disp", 
                 "Group 2 contains hp, drat and wt"), 
               notation = "symbol")
```

# HTML Only Features
## Scroll box
If you have a huge table and you don't want to reduce the font size to unreadable, you may want to put your HTML table in a scroll box, of which users can pick the part they like to read. Note that scroll box isn't printer friendly, so be aware of that when you use this feature. 

When you use `scroll_box`, you can specify either `height` or `width`. When you specify `height`, you will get a vertically scrollable box and vice versa. If you specify both, you will get a two-way scrollable box. 

```{r}
kable(cbind(mtcars, mtcars), "html") %>%
  kable_styling() %>%
  scroll_box(width = "500px", height = "200px")
```