While Shiny is very powerful, there are many things that cannot be achieved in R and must be done in JavaScript. When including JavaScript code in a Shiny app, you sometimes need to send a message or a value from R to the JavaScript layer. This example how this is done.
Sending a message from Shiny to Javascript involves two steps: first, in R you need to call session$sendCustomMessage(type, message), where type is a string that specifies what message handler to call and message is an R object that gets sent to the message handler. Then you need to write the message handler in JavaScript using the code Shiny.addCustomMessageHandler(type, function(message) {...});. Whenever Shiny sends a message of type type, the corresponding function in JavaScript will get called with the message as its argument. While this may sound complicated, looking at the example code shows how simple this is. Note that for this to work, the shiny server function must be defined with the session parameter, ie. server <- function(input, output, session) {...}.
To send a message in the other direction (from JavaScript to R), see Send a message from JavaScript to R.
Another approach for calling JavaScript functions from Shiny which attempts to make the process easier is using the extendShinyjs() function from the shinyjs package.