How to print HTML interactive plotly graphs within a lapply loop using knitr render from a .R source file ?

Question

Within Rstudio, I try to dynamically render plotly plots into an HTML report using knitr render from a .R source file. knitr renders the plotly plots as long as they are not within a lapply loop. But once I try to output them from within a lapply loop they are note rendered. I need to use a loop because I need to programatically build my HTML reports with various numbers of plots with various names.

Here is the command that I execute in the console to create the HTML report from my plotlytest.R source file :

render("plotlytest.R")

and here is my example source file called plotlytest.R :

#'---
#'author: "pokyah"
#'output: 
#'  html_document:
#'    theme: flatly
#'    toc: true
#'    toc_depth: 6
#'    toc_float:
#'      collapsed: false
#'      smooth_scroll: true
#'title: "Plotly test"
#'date: \`r format(Sys.Date(), " %d-%m-%Y")`\
#'---
#'
#

#+ ---------------------------------
#' ## Loading libraries
library(plotly)
library(ggplot2)

#+ ---------------------------------
#' ## plotly example
#+ plotly,echo=FALSE,warning=FALSE,message=FALSE,error=FALSE,results='asis', plotly=TRUE

mtcars.p <- ggplot(mtcars, aes(mpg, wt, colour = cyl)) + geom_point() +
  labs(colour = "Cylinders")


iris.p <- ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) + geom_point() +
  labs(colour = "Cylinders")

myPlots.l <- list(mtcars.p, iris.p)
names(myPlots.l) <- c("mtcars", "iris")

printPlots <- function(p, plots){
  cat("\n")
  cat("###", names(plots[p]))
  cat("\n")
  ggplotly(plots[[p]]) # this is not rendered
  cat("\n")
  print (plots[[p]]) # this is rendered, but of course this is not an interactive plot
  cat("\n")
}

cat("\n")
cat("## printing out of lapply -> plotly working")

cat("\n")
ggplotly(myPlots.l$mtcars) # this is rendered

cat("\n")
ggplotly(myPlots.l$iris) # this is also rendered
cat("\n")

cat("\n")
cat("## printing inside of lapply -> plotly not working")
cat("\n")
lapply(seq_along(myPlots.l), printPlots, myPlots.l )

The closer question to my problem is this one but I'm still stuck with this problem. Any idea how to solve this ?

here is my config :

R version 3.3.1 (2016-06-21)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 42.2

I'm afraid you cannot produce an HTML widget (plotly) and an R graph next to each other in one step in lapply(). What you can possibly achieve is to produce all HTML widgets in one step, then all R graphs in another step. To achieve this, see stackoverflow.com/q/30509866/559676 — Yihui Xie
It is absolutely possible to have HTML and R graphs in the same document using any method. You simply need to ensure the plot is explicitly printed, not merely returned. ggplotly does not explicitly print the output. — alan ocallaghan

RLesur RLesur · Accepted Answer · 2018-01-30T23:10:37

Here's a solution. You need to call knit_print() on "ggplotly" object (it's an htmlwidget object).
htmlwidgets needs to be attached.
The only problem I couldn't resolve is ggplotly width/height: I have to explicit these values.

#'---
#'author: "pokyah"
#'output: 
#'  html_document:
#'    theme: flatly
#'    toc: true
#'    toc_depth: 6
#'    toc_float:
#'      collapsed: false
#'      smooth_scroll: true
#'title: "Plotly test"
#'date: \`r format(Sys.Date(), " %d-%m-%Y")`\
#'---
#'
#

#+ ---------------------------------
#' ## Loading libraries
library(plotly)
library(ggplot2)
library(htmlwidgets)
library(knitr)

#+ ---------------------------------
#' ## plotly example
#+ plotly,echo=FALSE,warning=FALSE,message=FALSE,error=FALSE,results='asis', plotly=TRUE

mtcars.p <- ggplot(mtcars, aes(mpg, wt, colour = cyl)) + geom_point() +
  labs(colour = "Cylinders")


iris.p <- ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) + geom_point() +
  labs(colour = "Cylinders")

myPlots.l <- list(mtcars.p, iris.p)
names(myPlots.l) <- c("mtcars", "iris")

printPlots <- function(p, plots){
  cat("\n")
  cat("###", names(plots[p]))
  cat("\n")
  #ggplotly(plots[[p]]) # this is not rendered. Of course, no "print" method is called.
                       # This line only returns an htmlwidget object that is lost because inside a function. 
  cat(knit_print(ggplotly(plots[[p]], width = 672, height = 480))) # This works.
  cat("\n")
  print(plots[[p]]) # this is rendered, but of course this is not an interactive plot
  cat("\n")
}

cat("\n")
cat("## printing out of lapply -> plotly working")

cat("\n")
ggplotly(myPlots.l$mtcars) # this is rendered

cat("\n")
ggplotly(myPlots.l$iris) # this is also rendered
cat("\n")

cat("\n")
cat("## printing inside of lapply -> plotly not working")
cat("\n")
lapply(seq_along(myPlots.l), printPlots, myPlots.l)

How to print HTML interactive plotly graphs within a lapply loop using knitr render from a .R source file ?

2 Answers