offline plots in for loops

[chriddyp]

a current workaround is:

```{r, results="asis"}
for(i in 1:3) {
    fig <- list(data=list(list(x=rnorm(100), type="histogram")), layout=list(title=paste(c('plot', i, sep=" "))))
    cat(knit_print.offline(fig %>% offline))
}
```

maybe there is an easier way?

[cpsievert]

It looks like ggvis suffers from the same problem. I have a feeling it's because knitr can only call knit_print() once per chunk. I suppose my advice would be to use subplot() instead

```{r}
n <- 10
df <- data.frame(
  x = c(replicate(3, rnorm(n))),
  plot = rep(1:3, each = n)
)
df %>%
  plot_ly(x = x, group = plot, xaxis = paste0("x", plot), 
          type = "histogram") %>% 
  subplot() %>% offline()
```

[cpsievert]

Looks like @yihui will provide a solution for us 😊

[yihui]

Here is the easy way:

```{r}
res <- lapply(1:3, function(i) {
    fig <- list(data=list(list(x=rnorm(100), type="histogram")), layout=list(title=paste(c('plot', i, sep=" "))))
    fig %>% offline
})
htmltools::tagList(res)
```

[cpsievert]

offline() was deprecated when plotly.js went open source.

Here is the current way to do this:

```{r}
library(plotly)
htmltools::tagList(lapply(1:3, function(x) { plot_ly(x = rnorm(10)) }))
```

Or, if you prefer a for loop:

```{r}
l <- htmltools::tagList()
for (i in 1:3) {
  l[[i]] <- plot_ly(x = rnorm(10))
}
l
```

[GegznaV]

Nice workarround. Unfortunately, I'm not able to use it in my current automated analysis where in each iteration of for loop plotly graphs are followed by tables, results of some statistical tests, etc. Printing all plots in one place would be confusing and not using for loop would mean, that analysis is not automated.
Now it is not clear for me is it a bug/limitation in knitr or in plotly, as I noticed that result of pander() also does not print from inside for loop in .Rmd file?

[timelyportfolio]

@GegznaV, what are you using to make the tables? Do you have a small code sample? This can still be made to work with a combination of plotly and tables.

[GegznaV]

simple example of .Rmd document:

---
title: "Untitled"
output: html_document
---

library(ggplot2)
library(plotly)
library(magrittr)
library(pander)

for(i in c("vs", "am", "gear", "carb")){

     print(i)

    mtcars$am <- as.factor(mtcars[[i]])
    # plot 1
    {ggplot(mtcars,aes(x = mpg, y = disp, color = am)) + geom_point()}  %>%
        ggplotly

    # plot 2
    {ggplot(mtcars,aes(x = mpg, fill = am)) + geom_density(alpha = .3)}  %>%
        ggplotly

    # table 1
    summary(mtcars[,c("mpg","disp",i)]) %>% pander

    # table 2: Kruskal-Wallis test
    kruskal.test(mtcars$mpg, mtcars[[i]])  %>% pander

}

May be it's possible to save images as .html files and insert them as in this example (section "Slidify"):
https://github.com/garthtarr/pairsD3#slidify

[timelyportfolio]

@GegznaV, this is a hack in the ugliest of forms, but it does work. Perhaps, @jcheng5, @ramnath_vaidy, or @yihui can demonstrate an easier way.

        ---
        title: "Untitled"
        output: html_document
        ---

        ```{r results='asis'}
        library(ggplot2)
        library(plotly)
        library(magrittr)
        library(htmltools)
        library(pander)

        # turn off pander auto asis
        pander::panderOptions('knitr.auto.asis', FALSE)

        # create a container for our output
        output <- list()

        # loop through columns
        for(i in c("vs", "am", "gear", "carb")){
          # get column
          mtcars$am <- as.factor(mtcars[[i]])

          # plot 1
          output[[length(output) + 1]] <- {
            ggplot(mtcars,aes(x = mpg, y = disp, color = am)) + geom_point()
          }  %>%  ggplotly %>%  as.widget

              # plot 2
          output[[length(output) + 1]] <- {
            ggplot(mtcars,aes(x = mpg, fill = am)) + geom_density(alpha = .3)
          }  %>% ggplotly %>%  as.widget

          output[[length(output) + 1]] <-  paste0(
            capture.output(summary(mtcars[,c("mpg","disp",i)]) %>% pander),
            collapse="\n"
          )
        }

        # now cat/print all of the content
        for(j in 1:length(output)){
          x <- output[[j]]
          #  we know only character and htmlwidget in this case
          #   if more need to handle appropriately
          if(inherits(x,"character")){
            # noquote critical here
            #  also turn off auto.asis very important
            cat(noquote(paste0(x,collapse="\n")))
          } else {
            # print the html piece of the htmlwidgets
            cat(renderTags(x)$html)
          }
        }

        ```

        ```{r echo=FALSE, messages=FALSE, warning=FALSE}
        # attach the Dependencies
        # since the do not get included with renderTags(...)$html
        deps <- lapply(
          Filter(function(x){inherits(x,"htmlwidget")},output),
          function(hw){
            renderTags(hw)$dependencies
          }
        )

        attachDependencies(
          tagList(),
          unlist(deps,recursive=FALSE)
        )
        ```