Using `ggplotly` and `DT` from a `for` loop in Rmarkdown

Question

Is that possible to use ggplotly() or datatable() in RMarkdown from inside a for loop or function? Example:

--- title: "Using `ggplotly` and `DT` from a `for` loop in Rmarkdown" output: html_document --- ```{r setup, include=FALSE} library(ggplot2); library(DT) ``` ## Without `for` loop - works ```{r} datatable(cars) g <- ggplot(cars) + geom_histogram(aes_string(x=names(cars)[1] )) ggplotly(g) ``` ## From inside the `for` loop - does not work (nothing is printed) ```{r} for( col in 1:ncol(cars)) { datatable(cars) # <-- does not work print( datatable(cars) ) # <-- does not work either g <- ggplot(cars) + geom_histogram(aes_string(x=names(cars)[col] ) ) ggplotly (g) # <-- does not work print ( ggplotly (g) ) # <-- does not work either } ```

I wonder if this is because interactive outputs cannot be print-ed at all - by design.
No such problem existing when printing non-interactive outputs.

PS This is related to: Automating the generation of preformated text in Rmarkdown using R
Looping headers/sections in rmarkdown?

Have you seen this: stackoverflow.com/questions/36234169/… — J_F
– J_F, Commented Mar 14, 2020 at 18:17
Thanks for the link - I looked int it. It does offer a solution, but only if you just want to loop ggplotly (for that you'll need to stop using ggplot2 and use plotly directly). However, I'm trying to have a combination of text,graphs,tables- all generated automatically after printing each Section header. — IVIM
– IVIM, Commented Mar 15, 2020 at 2:05
You can still use ggplotly. See stackoverflow.com/questions/61906480/…. Also it is possible to combine different htmlwidgets — stefan
– stefan, Commented Jun 24, 2020 at 10:36
Found this related link ( ggplotly from inside for loop in .Rmd file does not work). github.com/ropensci/plotly/issues/570 - Seems like it is still not resolved :( — IVIM
– IVIM, Commented Jun 26, 2020 at 16:25

stefan · Accepted Answer · 2020-06-26 16:50:14Z

24

This is the solution from the post I added in my comment adapted to your case:

--- title: "Using `ggplotly` and `DT` from a `for` loop in Rmarkdown" output: html_document --- ```{r setup, include=FALSE} library(plotly); library(DT) ``` ```{r, include=FALSE} # Init Step to make sure that the dependencies are loaded htmltools::tagList(datatable(cars)) htmltools::tagList(ggplotly(ggplot())) ``` ```{r, results='asis'} for( col in 1:ncol(cars)) { print(htmltools::tagList(datatable(cars))) g <- ggplot(cars) + geom_histogram(aes_string(x=names(cars)[col] ) ) print(htmltools::tagList(ggplotly(g))) } ```

answered Jun 26, 2020 at 16:50

stefan

130k6 gold badges42 silver badges84 bronze badges

Sign up to request clarification or add additional context in comments.

4 Comments

Ahdee Over a year ago

this is great. However I don't get why the cars need to be initiated. I tried it on my pc and without the init step it just fails. The reason why I'm asking is because I have a complicated list of tables that use the for loop through and I can't seem to initiate with a for loop!

Ahdee Over a year ago

scratch above comment: to get list to work just simply initiate with lappy, like this, l = list ( c=cars, c2=iris ) htmltools::tagList( lapply(l, datatable) )

stefan Over a year ago

Hi @Ahdee. We don't need to init cars. The init step makes sure that the javascript dependencies, i.e. plotly.js and DataTables.js, are included in the html document.

Brian D Over a year ago

Or if using %>% notation...

for(col in 1:ncol(cars)) { cars %>% select(all_of(col)) %>% DT::datatable(options = list(paging=F)) %>% print(htmltools::tagList(.)) }

IVIM · Accepted Answer · 2020-06-26 16:33:07Z

This seems to be a persistent problem with RMarkdown. Here is the work around however, found here:

lotlist = list() for (VAR in factor_vars) { p <- ggplot(mtcars, aes_string(x = "mpg", y = "wt", color = VAR)) + geom_point() plotlist[[VAR]] = ggplotly(p) } htmltools::tagList(setNames(plotlist, NULL))

Collectives™ on Stack Overflow

Using `ggplotly` and `DT` from a `for` loop in Rmarkdown

2 Answers 2

4 Comments

Comments

Linked

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

4 Comments

Comments

Linked

Related