server.r

library("shiny")
library("plotly")
library("ggplot2")

shinyServer(function(input, output) {
  output$text <- renderText({
    ggiris <- qplot(Petal.Width, Sepal.Length, data=iris, color=Species)
    py <- plotly("RgraphingAPI", "ektgzomjbx")
    res <- py$ggplotly(ggiris)
    iframe <- paste("<iframe height=\"600\" id=\"igraph\" scrolling=\"no\" seamless=\"seamless\" src=\"", 
          res$response$url, "\" width=\"500\" frameBorder=\"0\"></iframe>", sep = "")
    iframe
  })
})

ui.r

library("shiny")

shinyUI(pageWithSidebar(
  
  headerPanel(title=HTML("TaxMap"), windowTitle="TaxMap"),
  
  sidebarPanel(
    wellPanel("plotly in shiny")
  ),
  
  mainPanel(
    htmlOutput("text")
  )
))

If you upload this to shiny servers can you get the iframe to show? I am trying to iframe a plot.ly graph into my shiny web application and I am having trouble displaying the iframed graph.

Hi @spivotron. If you add ".embed" at the end of the plotly link, you will get an URL to embed into your Shiny app. In this case is "https://plot.ly/~sckott/22.embed". After that, you can use tags$iframe() in your ui.R to embed the plot.ly graph, for example:
mainPanel(
tags$iframe(src="https://plot.ly/~sckott/22.embed",
height=400,
width=600)
)

For more details: http://shiny.rstudio.com/articles/tag-glossary.html