plotly scatterplot values shown in widget in shiny but I cannot see the points on the graph?

I am trying to create an interactive graph from a dataframe with some NA and string values. Would these values prevent a scatterplot? The string values are easy to remove as I can just remove the column with select(-column) but I am struggling with the NA values. I followed the code from this example (https://community.plotly.com/t/incorporate-a-plotly-graph-into-a-shiny-app/5329/2) but it does not work when I try to use my own data set.

I tried to use the plot_ly code to create an interactive scatterplot. I used the shiny outline (ui, server, shinyApp). I expected to see the scatterplot show the data but it would not.

library(shiny)
library(plotly)
library(tibble)
library(tidyverse)
library(tidyr)
library(readr)
library(dplyr)
library(ggplot2)

# set working directory
setwd("~/BDSWD")

#add data
gmclean <- read_csv("gapminder_clean.csv")

#remove certain columns
gmcut <- gmclean %>%
  select(-Year, -continent, -pop, -`Country Name`)

#no NA values
gmna <- replace(gmcut, is.na(gmcut), 0)

# Define UI ----
ui <- fluidPage(
  column(3,offset = 4, titlePanel("Explor Gapminder Data with Shiny")),
  headerPanel('Variables'),
  mainPanel(
    plotlyOutput('plot')
  ),
  sidebarPanel(
    #variable selection for x-axis
    selectInput(inputId ='xvrbl', #The input slot that will be used to access the value.
                label = 'X-Axis Variable', #Display label for the control, or NULL for no label.
                choices = colnames(gmcut), #List of values to select from
                selected = ""
                ),
    #variable selection for y-axis
    selectInput(inputId ='yvrbl', #The input slot that will be used to access the value.
                label = 'Y-Axis Variable', #Display label for the control, or NULL for no label.
                choices = colnames(gmcut), #List of values to select from
    )
  )
)

server <- function(input, output) {

  x <- reactive({
    gmcut[,input$xvrbl]
  })

  y <- reactive({
    gmcut[,input$yvrbl]
  })


  output$plot <- renderPlotly(
    plot1 <- plot_ly(
      x = x(),
      y = y(),
      type = 'scatter',
      mode = 'markers')
  )

}

# Run the app
shinyApp(ui = ui, server = server)

Solution

The issue is (most likely) that gmcut is a tibble. When you do e.g. gmcut[,input$xvrbl] the result is a tibble too instead of a vector (This is one of the differences between a data.frame and a tibble. In case of a data.frame the result would be a vector).

Hence, as plot_ly expects vectors you get an "empty" plot as you are passing tibbles to x and y.

To fix that use gmcut[[input$xvrbl]] instead or explicitly drop the dimensions using gmcut[, input$xvrbl, drop = TRUE].

Using the gapminder::gapminder dataset as example data:

library(shiny)
library(plotly)
library(tidyverse)

# add data
gmclean <- gapminder::gapminder |>
  rename(Year = year, "Country Name" = country)

# remove certain columns
gmcut <- gmclean %>%
  select(-Year, -continent, -pop, -`Country Name`)

# no NA values
gmna <- replace(gmcut, is.na(gmcut), 0)

# Define UI ----
ui <- fluidPage(
  column(3, offset = 4, titlePanel("Explor Gapminder Data with Shiny")),
  headerPanel("Variables"),
  mainPanel(
    plotlyOutput("plot")
  ),
  sidebarPanel(
    # variable selection for x-axis
    selectInput(
      inputId = "xvrbl", # The input slot that will be used to access the value.
      label = "X-Axis Variable", # Display label for the control, or NULL for no label.
      choices = colnames(gmcut), # List of values to select from
      selected = ""
    ),
    # variable selection for y-axis
    selectInput(
      inputId = "yvrbl", # The input slot that will be used to access the value.
      label = "Y-Axis Variable", # Display label for the control, or NULL for no label.
      choices = colnames(gmcut), # List of values to select from
    )
  )
)

server <- function(input, output) {
  x <- reactive({
    gmcut[[input$xvrbl]] ## or gmcut[, input$xvrbl, drop = TRUE]
  })

  y <- reactive({
    gmcut[[input$yvrbl]]
  })


  output$plot <- renderPlotly({
    plot1 <- plot_ly(
      x = x(),
      y = y(),
      type = "scatter",
      mode = "markers"
    )
  })
}

# Run the app
shinyApp(ui = ui, server = server)
#> 
#> Listening on http://127.0.0.1:7126