dygraph in R multiple plots at once

I think the only way is to export to a external document such as html

See http://rmarkdown.rstudio.com/flexdashboard/

To plot multiple dygraphs in the same RStudio window you must first create a list of dygraphs objects, and then render the dygraphs list using package htmltools. Yihui Xie from RStudio provided the answer here: Yihui Xie answer (but without grouping).
I answered a similar question here: my answer.

Here is working R code that produces grouped (synchronized) dygraphs plots:

# create the time series
temperature <- ts(frequency = 12, start = c(1980, 1),
              data = c(7.0, 6.9, 9.5, 14.5, 18.2, 21.5, 
                       25.2, 26.5, 23.3, 18.3, 13.9, 9.6))
rainfall <- ts(frequency = 12, start = c(1980, 1),
           data = c(49.9, 71.5, 106.4, 129.2, 144.0, 176.0, 
                    135.6, 148.5, 216.4, 194.1, 95.6, 54.4))

# create a list of dygraphs objects
library(dygraphs)
library(htmltools)
plotobj <- list(
  dygraphs::dygraph(temperature, group="temp_rain", main="temperature"),
  dygraphs::dygraph(rainfall, group="temp_rain", main="rainfall")
)  # end list

# render the dygraphs objects using htmltools
htmltools::browsable(htmltools::tagList(plotobj))

The above R code produces the following grouped (synchronized) dygraphs plots: