Exemplo de atualização de gráfico do Plotly no shiny.

exemplo.R

library(shiny)
library(dplyr)
library(plotly)


ui <- fluidPage(
  mainPanel(
    tags$style(".recalculating {opacity: 1.0}"),  # Comente esta linha para ver o comportamento normal do shiny
    plotly::plotlyOutput("grafico")
  )
)

server <- function(input, output, session) {
  output$grafico <- plotly::renderPlotly({
    data() %>% 
      plot_ly(x = ~Sepal.Length, y = ~Sepal.Width, type = "scatter", mode = "markers") %>% 
      layout(
        images = list(
          list(source = "https://raw.githubusercontent.com/rstudio/shiny/master/man/figures/logo.png",
               xref = "x", yref = "y", x = 5, y = 4, sizex = 1, sizey = 1, opacity = 0.8)
        )
      )
  })
  
  data <- reactive({
    invalidateLater(3000, session)
    Sys.sleep(1)
    iris %>%
      sample_n(30)
  })
  
}

shinyApp(ui, server)

exemplo2.R

library(shiny)
library(dplyr)
library(plotly)


ui <- fluidPage(
  mainPanel(
    # tags$style(".recalculating {opacity: 1.0;}"),
    plotly::plotlyOutput("grafico")
  )
)

server <- function(input, output, session) {
  output$grafico <- plotly::renderPlotly({
    iris %>% sample_n(30) %>% # dados iniciais
      plot_ly(x = ~Sepal.Length, y = ~Sepal.Width, type = "scatter", mode = "markers") %>% 
      layout(
        images = list(
          list(source = "https://raw.githubusercontent.com/rstudio/shiny/master/man/figures/logo.png",
               xref = "x", yref = "y", x = 5, y = 4, sizex = 1, sizey = 1, opacity = 0.8)
        )
      )
  })
  
  
  observe({
    x = data() %>% pull(Sepal.Length)
    y = data() %>% pull(Sepal.Width)
    
    plotlyProxy("grafico", session) %>% 
      plotlyProxyInvoke("deleteTraces", list(as.integer(0))) %>% 
      plotlyProxyInvoke("addTraces", list(
        x = x, y = y, type = "scatter", mode = "markers"
      ))
      
  })
  
  data <- reactive({
    invalidateLater(3000, session)
    Sys.sleep(1)
    iris %>%
      sample_n(30)
  })
  
}

shinyApp(ui, server)