I'd like to number my tables made with the gt package in rmarkdown rendered pdf.
What I've tried
In a markdown doc, defining a function f that increments a variable every time it is called:
---
title: "."
output: bookdown::pdf_document2
---
```{r}
library(gt)
.i <- 1
f <- function() {.i <<- .i + 1 ; as.character(.i)}
```
```{r numbered_kable}
knitr::kable(head(mtcars,2), caption = "bla")|> kableExtra::kable_styling(latex_options = "HOLD_position")
```
```{r numbered_but_ugly}
mtcars |> head(2) |>
gt() |>
tab_header(
glue::glue("{f()} blabla2")
)
```
Which works, but is a bit involved if both figures and tables need to be numbered.
Question
What is the best way to number figures and tables in using the gt package?
There is a cross-referencing version that seems to be working
devtools::install_github("rstudio/gt", ref="eff3be7384365a44459691e49b9b740420cd0851")
-markdown code
---
title: "."
output: bookdown::pdf_document2
---
```{r}
library(gt)
library(dplyr)
```
```{r numbered_gt}
mtcars %>%
head(2) %>%
gt() %>%
tab_header(title="blabla2",
label="tab:tab1")
```
-output
Related
I have a list of many (can be dozens of) tables created with the gt package in R. I would like to export them all as a single HTML file with a little space between each table. Currently, I have been exporting each table individually, reading them into an RMarkdown with the xfun package, and knitting to a single HTML file. I'm curious if there is a method to cut out the intermediate step of saving each table individually and reading into the Rmd.
Example:
library(gt)
library(tidyverse)
tbl_list <- list(mtcar_tbl = mtcars %>% gt(),
iris_tbl = iris %>% gt(),
cars_tbl = cars %>% gt())
purrr::map(seq_along(tbl_list), function(rownum){
htmltools::save_html(html = tbl_list[[rownum]],
file = paste0("test",rownum,".html"))
})
RMarkdown to combine and export tables:
---
title: ""
output: html_document
---
```{r, echo=FALSE,message=FALSE,warning=FALSE}
library(xfun)
```
```{r echo=FALSE}
htmltools::includeHTML("test1.html")
```
<br><br>
```{r echo=FALSE}
htmltools::includeHTML("test2.html")
```
<br><br>
```{r echo=FALSE}
htmltools::includeHTML("test3.html")
```
One option would be to use purrr::walk with chunk option results="asis" to directly print your tables without the intermediate step. To add the line breaks after each table use cat("<br><br>"):
Note: For the reprex I just print the head of each table.
---
title: "Untitled"
output: html_document
date: "2022-09-19"
---
```{r echo=FALSE, results='asis', warning=FALSE, message=FALSE}
library(gt)
library(tidyverse)
tbl_list <- list(mtcar_tbl = mtcars,
iris_tbl = iris,
cars_tbl = cars)
tbl_list <- purrr::map(tbl_list, ~ head(.x) %>% gt() )
purrr::walk(tbl_list, function(x) { print(x); cat("<br><br>") })
```
I would like to use the < symbol in a table caption of a Rmarkdown that converts to a docx document. I am using the flextable package as this gives a lot of (needed) flexibility to tables in the docx format.
But I am really confused by the multiple conversion steps through pandoc. It does not seem so easy to get to the < as it is a special coding HTML character. I have read that in HTML you would escape it via <. This gives me the problem that the & has to be escaped, too. The conversion then turns < into < (as it converts the & into &) and \\< would yield me &lt; (as it converts the & of the & again). Latex does not seem to work either, I've tried <, $<$ and $\\textless$ but to no avail.
All combinations basically follow the same logic, i.e. that < are correctly transformed to < but then the HTML is not converted again.
Any idea how to solve this? What do I miss?
Example RMD file:
---
title: "Untitled"
author: "Unkown"
date: "1/25/2021"
output: bookdown::word_document2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(flextable)
library(tidyverse)
```
## R Markdown
This is an R Markdown document, see Table \#ref(tab:test).
```{r test, echo = F}
flextable(head(cars, n = 10)) %>%
bold(part = "header") %>%
autofit() %>%
set_caption("Table: (\\#tab:test) Example caption with less-than symbol: \\< or < or < or $<$ or $\\textless$")
```
This should answer the question about < and > in the captions
---
title: "Untitled"
output: bookdown::word_document2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(flextable)
library(tidyverse)
```
## R Markdown
This is an R Markdown document, see Table \#ref(tab:test).
```{r test, echo = F, tab.id="test"}
flextable(head(cars, n = 10)) %>%
bold(part = "header") %>%
autofit() %>%
set_caption("Example caption with less-than symbol: > and <")
```
You could use the package officedown. It will make the references as real Word references, it also offers few features to customize your captions:
---
output:
bookdown::markdown_document2:
base_format: officedown::rdocx_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, tab.cap.style="Table Caption")
library(flextable)
library(tidyverse)
```
```{r test1}
flextable(head(cars, n = 10)) %>%
bold(part = "header") %>%
autofit() %>%
set_caption("Example caption with less-than symbol: > and <")
```
```{r "test2", tab.cap="Example caption with less-than symbol: > & <"}
flextable(head(cars, n = 10)) %>%
bold(part = "header") %>%
autofit()
```
\newpage
See \#ref(tab:test1).
See \#ref(tab:test2).
Markdown does not compile after the first chunk. I am able to run all the chunk individually and run them all at once. When attempting to Knit to a HTML document, markdown does not compile right at the first chunk and stops. No Errors, No Warnings, etc., and just stops.
I have tried eval = False, which just outputs nothing, I removed several portions of the code and found it is the portion of the scrape of the HTML table. However, works when I run the chunk.
---
title: "Harry Potter Cast"
author: "Ben Tanaka"
date: "5/29/2019"
output:
html_document:
keep_md: yes
---
```{r setup, echo=FALSE, include=FALSE, warning=FALSE,message =FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(xml2)
library(rvest)
library(stringr)
library(tibble)
library(data.table)
library(knitr)
library(kableExtra)
library(dplyr)
library(tidyr)
library(ggplot2)
```
# *Harry Potter Cast*
```{r Harry_Potter}
potter_url <- 'https://www.imdb.com/title/tt1201607/fullcredits?ref_=tt_ql_1'
potter_scrape <- read_html(potter_url)
potter_cast_uf <- {potter_scrape %>% html_nodes("table") %>% .[[3]] %>% html_table()}
potter_cast_df <- potter_cast_uf[,c(2,4)]
setnames(potter_cast_df,old=c("X2","X4"),new=c("Actor","Character"))
str_replace_all(potter_cast_df$Actor, '[\r\n]' , '')
str_replace_all(potter_cast_df$Character, '[\r\n]' , '')
potter_cast_tbl <- as_tibble(potter_cast_df)
{potter_cast_tbl %>% mutate_all(funs(str_replace_all(.,'[\r\n]' , '')))}
potter_cast_tbl <- potter_cast_tbl[-1,]
potter_cast_tbl <- potter_cast_tbl[-92,]
{potter_cast_tbl %>% mutate_all(funs(str_replace_all(.,'Griphook / \n Professor Filius Flitwick' , 'Griphook / Professor Filius Flitwick')))}
{potter_cast_tbl <- potter_cast_tbl %>% separate(Actor,c("Actor_FName","Actor_MName","Actor_LName"))}
potter_cast_tbl$Actor_FName[!is.na(potter_cast_tbl$Actor_LName)]<- paste(potter_cast_tbl$Actor_FName[!is.na(potter_cast_tbl$Actor_LName)],potter_cast_tbl$Actor_MName[!is.na(potter_cast_tbl$Actor_LName)],sep=" ")
potter_cast_tbl$Actor_LName[is.na(potter_cast_tbl$Actor_LName)] <- potter_cast_tbl$Actor_MName[is.na(potter_cast_tbl$Actor_LName)]
potter_cast_tbl<-potter_cast_tbl[,-2]
output_dt <- head(potter_cast_tbl,10)
{output_dt %>% kable() %>% kable_styling()}
```
No Error messages. Just trying to get the markdown html knit output.
I am having a problem with my ztable,
I want to knit my Rmarkdown file to HTML but I cannot find a way to display the table I created with ztable:
z=ztable(loucaste) %>% makeHeatmap(palette = "Blues") %>% print(caption="Table 2.)
I tried to set
options(ztable.table="html")
and put this at the beginning as I read somewhere else
output: html_document
header-includes: \usepackage{colortbl}
but it doesn't work when I knit to HTML. My intention was to create a sort of formatting table similar to the ones made on excel and ztable looks like the only way.
Try this minimal Rmd. The key seems to be options(ztable.type = "html") and in the chunk that generates the table, r results='asis'
If that works for you, substitute your code in the appropriate place i.e. ztable(loucaste) %>% makeHeatmap(palette = "Blues") %>% print(caption="Table 2.).
---
title: "ztable"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ztable)
library(magrittr)
options(ztable.type = "html")
```
## R Markdown
```{r results='asis'}
matrix(1:100, nrow = 10) %>%
as.data.frame() %>%
ztable() %>%
makeHeatmap() %>%
print(caption = "table 2")
```
Consider this simple example:
---
title: "Untitled"
output: ioslides_presentation
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
## Slide with R Output
```{r t, warning=FALSE, message=FALSE}
library(knitr)
library(kableExtra)
library(dplyr)
for(threshold in c(20, 25)) {
cars %>%
filter(dist < threshold) %>%
kable('html') %>%
kable_styling(bootstrap_options = "striped")
}
```
Here I simply want to print each output of the for loop into a different slide. In this example, there are two calls to kablethat should go on two different slides.
The code above does not work. Am I even using the right packages for that? Any ideas?
Thanks!
You can use the asis option:
---
title: "Untitled"
output: ioslides_presentation
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(kableExtra)
library(dplyr)
# needed so r will include javascript/css dependencies needed for striped tables:
kable(cars, "html") %>% kable_styling(bootstrap_options = "striped")
```
```{r, results = "asis"}
for (threshold in c(20, 25)) {
cat("\n\n##\n\n")
x <- cars %>%
filter(dist < threshold) %>%
kable('html') %>%
kable_styling(bootstrap_options = "striped")
cat(x)
}
```
To get rid of that bogus table, you can try to put options(kableExtra.html.bsTable = T) in your setup section.
Here's the start of a solution. You can print strings with markdown, either by making the strings yourself or using pander's pandoc.* functions. If you set results="asis" for that chunk, it will get compiled the same as any other markdown. I used cat to make the ## headings, but commented out two pander functions that you could try also to make headers or horizontal rules to split slides.
There's more detail on the pander functions here, plus other SO questions such as this one.
---
title: "Untitled"
output: ioslides_presentation
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(kableExtra)
library(dplyr)
```
```{r, results='asis'}
for(threshold in c(20, 25)) {
# pander::pandoc.header(sprintf("Threshold = %s", threshold))
# pander::pandoc.horizontal.rule()
cat(paste("\n##", "Threshold =", threshold), "\n")
tbl <- cars %>%
filter(dist < threshold) %>%
kable(format = "html") %>%
kable_styling(bootstrap_options = "striped")
print(tbl)
}
```
One issue is that when I knit this, I'm not getting the striped table that you'd expect. If I add a slide before this chunk and put a table in it with these kableExtra settings, I do get stripes, but the first table is also pretty ugly...I'm not sure if that's a bug or conflicting CSS somewhere or what.