R Studio Shiny Crashes (iMac M1) - r

I am trying to plot some epidemiological data. To do this, I am using the shiny app (following the steps of this tutorial).
When I start the app, a further tab opens and i can see the graphs, a map and an input . When I change the date input on the app (using reactivity), the app crashes and all I see is a gray display. I am forced to exit RStudio. It is really strange, because I already did some tests using an older Macbook Pro (2,7 GHz Dual-Core Intel Core i5 Prozessor) and although it was slow, RStudio did not crash. Is it maybe something related to the Apple M1 chip?
library(shiny)
library(shinyWidgets)
library(rgdal)
library(DT)
library(dygraphs)
library(xts)
library(leaflet)
# ui object
ui <- fluidPage(
titlePanel(p("Spatial app", style = "color:#3474A7")),
sidebarLayout(
sidebarPanel(
selectInput(
inputId = "variableselected",
label = "Select variable",
choices = c("n", "Pop", "incidence_rate")
),
dateRangeInput('dateRange',label = "Pédiode d'analyse : ",format = "yyyy-mm-dd",
start = Sys.Date(), end=Sys.Date(),startview = "year",separator = " - "),
p("Made with", a("Shiny",
href = "http://shiny.rstudio.com"
), "."),
img(
src = "imageShiny.png",
width = "70px", height = "70px"
)
),
mainPanel(
leafletOutput(outputId = "map"),
dygraphOutput(outputId = "timetrend"),
DTOutput(outputId = "table")
)
)
)
# server()
server <- function(input, output) {
output$table <- renderDT(data)
output$timetrend <- renderDygraph({
dataxts <- NULL
counties <- unique(data$COD_MUN_N)
for (l in 1:length(counties)) {
datacounty <- data[data$COD_MUN_N == counties[l], ]
dd <- xts(
datacounty[, input$variableselected],
as.Date(paste0(datacounty$weekly_cases, "-01-01"))
)
dataxts <- cbind(dataxts, dd)
}
colnames(dataxts) <- counties
dygraph(dataxts) %>%
dyHighlight(highlightSeriesBackgroundAlpha = 0.2) -> d1
d1$x$css <- "
.dygraph-legend > span {display:none;}
.dygraph-legend > span.highlight { display: inline; }
"
d1
})
output$map <- renderLeaflet({
# Add data to map
datafiltered <- data[data$weekly_cases >= input$dateRange[1] & data$weekly_cases <= input$dateRange[2], ]
# this returns positions of map#data$NAME in datafiltered$county
ordercounties <- match(map#data$MPIO_CCDGO, datafiltered$COD_MUN_N)
map#data <- datafiltered[ordercounties, ]
map$variableplot <- as.numeric(
map#data[, input$variableselected]
)
# Create leaflet
pal <- colorBin("YlOrRd", domain = map$variableplot, bins = 7)
labels <- sprintf("%s: %g", map$COD_MUN_N, map$variableplot) %>%
lapply(htmltools::HTML)
l <- leaflet(map) %>%
addTiles() %>%
addPolygons(
fillColor = ~ pal(variableplot),
color = "white",
dashArray = "3",
fillOpacity = 0.7,
label = labels
) %>%
leaflet::addLegend(
pal = pal, values = ~variableplot,
opacity = 0.7, title = NULL
)
})
}
# shinyApp()
shinyApp(ui = ui, server = server)

Related

how to avoid flickering while refreshing valueboxes in Shiny dashboard

I use shiny modules to update a large number of value boxes.
The annoying part is the value boxes donot seem to scale above 10 or 20 as their updating is causing annoying flickers.
Even those boxes whose values are not changing on the next invalidation, flicker. Ideally if the value is not changing the box should not refresh.
A representative shiny app using shiny modules is presented to replicate the problem.
When the value of N is 4 or 5 the number of boxes are small and the updates happen instantaneously. As you increase N to 10 it gets noticeable and at N = 20 the flicker is unbearable.
### ui.R
## reprex ui.r
suppressPackageStartupMessages(library(shiny))
suppressPackageStartupMessages(library(magrittr))
suppressPackageStartupMessages(library(shinydashboard))
suppressPackageStartupMessages(library(shinydashboardPlus))
suppressPackageStartupMessages(library(lubridate))
suppressPackageStartupMessages(library(shinyjs))
ui <- dashboardPage(
header = dashboardHeader(title = "Reprex"),
sidebar = dashboardSidebar(
sidebarMenu(id = "sidebar",
menuItem(text = "Fuel prediction",tabName = "LIVE",icon = icon("tachometer-alt"))
)
), # end of sidebarMenu
body = dashboardBody(id="body",useShinyjs(),
tabItems(
tabItem(tabName = "LIVE",h1("FUEL DISPENSATION"),
fluidRow(id = "parameters",
column(width = 2,h3("STATION")),
column(width = 2,h4("TIME UPDT")),
column(width = 2,h4("TANK LEVEL")),
column(width = 2,h4("DISPENSED")),
column(width = 2,h4("REFUELLED"))
),
uiOutput("st1"),
uiOutput("st2"),
uiOutput("st3"),
uiOutput("st4"),
uiOutput("st5"),
uiOutput("st6"),
uiOutput("st7"),
uiOutput("st8"),
uiOutput("st9"),
uiOutput("st10"),
uiOutput("st11"),
uiOutput("st12"),
uiOutput("st13"),
uiOutput("st14"),
uiOutput("st15"),
uiOutput("st16"),
uiOutput("st17"),
uiOutput("st18"),
uiOutput("st19"),
uiOutput("st20")
)
)
) # End of body
) # end of dashboard page
And this is the server.R:
## reprex server.R
suppressPackageStartupMessages(library(shiny))
suppressPackageStartupMessages(library(shinydashboard))
suppressPackageStartupMessages(library(data.table))
source("modules.R")
shinyServer(function(input, output,session) {
seqno <- reactiveVal(5)
timer <- reactiveTimer(3000)
observeEvent(timer(),{
seqno((seqno() + 1))
for(i in seq_len(N)){ ## the for loop generates all the output assignment statements using shiny module.
genrVB(i = i,output = output,s = seqno())
}
})
# This is just to stop the app when session ends. Ignore for the purposes of this reprex.
session$onSessionEnded(function() {
print("Session ended")
stopApp()
})
})
And this is the modules.R
### Shiny module reprex
library(shiny)
library(purrr)
library(maps)
# take N cities and N data.tables randomly generated to serve our input data for the shiny app
N <- 4
cities <- world.cities %>% as.data.table() %>% .$name %>% sample(N)
### Generate N simulated data.tables for the N cities.
### Notice the values of the column 2,3,4 donot change every minute.
simdata <- purrr::map(seq_len(N),
~data.table(ts = seq.POSIXt(Sys.time(),by = 60,length.out = 100),
fuel = rep(c(5000:5004),each = 2),
out = rep(c(100,110),each = 25),
fill = rep(c(100,200),each = 10)
))
fuelrowUI <- function(id,label = "Site X",n = 1){
ns <- NS(id)
fluidRow(id = ns("siteid"),
column(2,h3(cities[n])),
valueBoxOutput(ns("upd"),width = 2),
valueBoxOutput(ns("tank"),width = 2),
valueBoxOutput(ns("out"),width = 2),
valueBoxOutput(ns("fill"),width = 2)
)
}
fuelrowServer <- function(id,datarow=1,n = 1){
moduleServer(id,
function(input,output,session){
output$upd <- renderValueBox(vbtime(n,k = datarow))
output$tank <- renderValueBox(vblevel(n,k = datarow))
output$out <- renderValueBox(vbout(n,k = datarow))
output$fill <- renderValueBox(vbin(n,k = datarow))
})
}
# Function to loop through the output$.. in server.R using the two shiny modules
genrVB <- function(i,s,output = output){
stn <- paste0("st",i)
output[[stn]] <- renderUI(fuelrowUI(stn,label = "DUMMY",n = i))
fuelrowServer(stn,datarow = s,n = i)
}
##### Value box helper functions ##########
vblevel <- function(n = 1,k=1){
val <- simdata[[n]][k,round(fuel,0)]
valueBox(value = paste(val,"L"),
subtitle = tags$h4(cities[n]),
color = case_when(
val < 1000 ~ "red",
val >= 1000 ~ "green"
))
}
vbout <- function(n = 1,k=1){
val = simdata[[n]][k,out]
valueBox(value = paste(val,"L"),
subtitle = tags$h4(cities[n]),
color = case_when(
val < 100 ~ "aqua",
val >= 100 ~ "purple"
))
}
vbin <- function(n = 1,k=1){
val = simdata[[n]][k,fill]
valueBox(value = paste(val,"L"),
subtitle = tags$h4(cities[n]),
color = case_when(
val < 100 ~ "teal",
val >= 100 ~ "olive"
))
}
# Time Value box
vbtime <- function(n = 1,k = 1){
time <-simdata[[n]][k,ts]
timestr <- format(time,"%H:%M")
valueBox(value = timestr,
subtitle = "Last Updated",color = "aqua")
}
Please load the three code sections in three files: ui.R, server.R and modules.R.
Note: In the modules.R the first line has a line N <- 4. Please set it to 20 to see the annoying flicker.
If you only want to stop the flashing while recalculating all you'll have to do is adding
tags$style(".recalculating { opacity: inherit !important; }")
to your UI - taken from here.
Still I'd encourage you to simplify your app for better performance.
Here is an example for the approach I mentioned in the comments:
library(shiny)
library(shinydashboard)
library(data.table)
ui <- dashboardPage(
dashboardHeader(),
dashboardSidebar(),
dashboardBody(
tags$style(".recalculating { opacity: inherit !important; }"),
fluidPage(
sliderInput(
inputId = "nBoxesRows",
label = "rows of Boxes",
min = 1L,
max = 100L,
value = 20L
),
uiOutput("myValueBoxes")
)
)
)
server <- function(input, output, session) {
DT <- reactive({
invalidateLater(1000)
data.table(replicate(4, round(runif(input$nBoxesRows), digits = 2)))
})
output$myValueBoxes <- renderUI({
longDT <- melt(DT(), measure.vars = names(DT()))
longDT[, subtitle := paste0(variable, "_", seq_len(.N)), by = variable]
tagList(mapply(valueBox, subtitle = longDT$subtitle, value = longDT$value, MoreArgs = list(width = 3), SIMPLIFY = FALSE))
})
}
shinyApp(ui, server)

Double calls to plot/load functions in shiny app

I have an app with a map, dropdown, calendar and line plot (my real app is much bigger but I have simplified as much as I can). The problem with it is that when I modify any of the uicontrol features, the data loading and plotting routines run twice (as evidenced from the print statements). In the full app the plots display a reasonable amount of data so running them twice leads to poor performance.
The app is structured so that I can select 1 of 2 predefined points on the map and it will change the dropdown and graph. A new location can also be selected with the dropdown menu (which in turn updates the map). There is also a checkbox to lock the timeframe and when this is not selected the timeframe gets reset to the extents of the timeseries for the new location.
I have isolated the problem to the updateDateRangeInput that is called in the server.R file (line 35). I can comment this out and the problem goes away, but then I lose the functionality to reset the calendar to the new timeframe. Does anyone know how I can keep that functionality but stop the data loading and plotting code from running twice?
Example app below:
app.R
library(shiny)
library(rsconnect)
source('ui.R')
source('server.R')
ui <- ui_page()
server <- server_page(input, output, session)
shinyApp(ui=ui, server=server)
ui.R
library(shiny)
library(leaflet)
library(dygraphs)
inc_level <- 5
ui_page <- function(){
fluidPage(
titlePanel("TEST APP"),
sidebarLayout(
sidebarPanel(
leafletOutput('region_map'),
selectInput(inputId = "Site",label = "Pick a site",choices = c("A","B"), selected = "A"),
fluidRow(
column(6,
dateRangeInput(inputId = "timeframe",label="Select time range", start ="2015-07-01", end = "2016-07-01")),
column(4,checkboxInput(inputId = "lock_timeframe",label = "Lock Time Range"))
)
),
mainPanel(
tabsetPanel(
tabPanel("Plot 1", dygraphOutput(outputId = "plot1"))
)
)
)
)
}
server.R
library(shiny)
library(ggplot2)
library(dygraphs)
library(xts)
server_page <- function(input, output, session){
# Create Data -------------------------------------------------------------
Y1 <- c(21000, 23400, 26800)
Time1 <- startdate <- as.Date(c('2007-11-1','2008-3-25','2010-3-14'))
Y2 <- c(11000, 11400, 16800)
Time2 <- startdate <- as.Date(c('2001-11-1','2003-3-25','2005-3-14'))
Lat <-c(-39.095980, -39.605823)
Lon <- c(173.887903, 173.824561)
Site <- c("A","B")
# Extract Data -------------------------------------------------------
df1 <- reactive({
print("load data")
if (input$Site=="A"){
df1 <- data.frame(Time1, Y1)
}
else if (input$Site=="B"){
df1 <- data.frame(Time2, Y2)
}
names(df1) <- c("Time","Y")
if (1){ # IF YOU CHANGE THIS TO A 0 FUNCTIONLITY IS LOST BUT PROBLEM GOES AWAY
lockTest <- input$lock_timeframe
if (lockTest==FALSE){
updateDateRangeInput(session, "timeframe",
start = df1$Time[1],
end =df1$Time[length(df1$Time)])
}
}
df1 <- df1[df1$Time >= format(input$timeframe[1]) & df1$Time <= format(input$timeframe[2]),]
validate(need(nrow(df1)!=0, "No Data In Range"))
return(df1)
}) #%>% bindCache(input$Site) # I woudl like to cache based on location to stop reloading of data from file in the full app
# Line Plot --------------------------------------------------------
output$plot1 <- renderDygraph({
print("Plotting")
data <- df1()
data <- xts(x = data$Y, order.by = data$Time)
dyPlt <- dygraph(data,width = 800, height = 400)
})
# Plot Map -----------------------------------------------------
output$region_map <- renderLeaflet({
y <- Lat
x <- Lon
id <- Site
leaflet() %>%
addProviderTiles(providers$OpenStreetMap, options = providerTileOptions(noWrap = TRUE)) %>%
setView(lng = 174.051515, lat = -39.301619, zoom = 8) %>%
addCircleMarkers(lng = x, lat = y ,color="green", radius = 2, layerId = id, label = id,
labelOptions = labelOptions(noHide = F, direction = "bottom",
style = list("color" = "green","border-color" = "rgba(0,0,0,0.5)"))
)
})
# Map Click Behaviour -----------------------------------------------------
#When map is clicked: update map and change dropdown value
observeEvent(input$region_map_marker_click, {
event <- input$region_map_marker_click
updateSelectInput(session,
inputId = "Site",
label = "Pick a site",
choices = Site,
selected = event$id)
})
# Update map when a new site is selected from the dropdown
observeEvent(input$Site, {
update_markers()
})
# Function to redraw markers and highlight the selected location
update_markers <- function(){
y <- Lat
x <- Lon
id <- Site
sitInd <- id == input$Site
leafletProxy("region_map") %>% clearMarkers() %>% addCircleMarkers(lng = x, lat = y ,color="green", radius = 2, layerId = id, label = id,
labelOptions = labelOptions(noHide = F, direction = "bottom",
style = list("color" = "green","border-color" = "rgba(0,0,0,0.5)")),
options = list(zIndex = 200)) %>%
addCircleMarkers(lng = x[sitInd], lat = y[sitInd] ,color="blue", radius = 4, layerId = id[sitInd], label = id[sitInd],
labelOptions = labelOptions(noHide = F, direction = "bottom",
style = list("color" = "blue","border-color" = "rgba(0,0,0,0.5)")),
options = list(zIndex = 300) )
}
}

Restyling traces using plotlyProxy in a scatterplot is unstable when points are colored according to category

I have a Shiny app that builds a scatterplot and highlights the clicked points by restyling the marker outline via plotlyProxy.
The app also subsets the data and moves the entries corresponding to the clicked points from the original "Data table" to an "Outlier table".
This seems to work fine when the markers are all the same color, or when they are colored by a continuous variable. But when I color the points by a categorical variable (like "Species"), it has a weird behavior, restyling a marker from each category instead of the clicked one. The data subsets correctly.
I think the restyle function should update all traces unless specified otherwise, so I am not sure where exactly lies the problem.
Here is my code:
library(plotly)
library(DT)
ui <- fluidPage(
mainPanel(
fluidRow(
div(
column(
width = 2,
uiOutput('chartOptions')),
column(width = 5,
h3("Scatter plot"),
plotlyOutput("scatterplot"),
verbatimTextOutput("click")
)
)
),
hr(),
div(
column(width = 6,
h2("Data Table"),
div(
DT::dataTableOutput(outputId = "table_keep"),
style = "height:auto; overflow-y: scroll;overflow-x: scroll;")),
column(width = 6,
h2("Outlier Data"),
div(
DT::dataTableOutput(outputId = "table_outliers"),
style = "height:auto; overflow-y: scroll;overflow-x: scroll;"))
)
))
server <- function(input, output, session){
datasetInput <- reactive({
df <- iris
return(df)
})
output$chartOptions <- renderUI({#choose variables to plot
if(is.null(datasetInput())){}
else {
list(
selectizeInput("xAxisSelector", "X Axis Variable",
colnames(datasetInput())),
selectizeInput("yAxisSelector", "Y Axis Variable",
colnames(datasetInput())),
selectizeInput("colorBySelector", "Color By:",
c(c("Do not color",colnames(datasetInput()))))
)
}
})
vals <- reactiveValues(#define reactive values for:
data = NULL,
data_keep = NULL,
data_exclude = NULL)
observe({
vals$data <- datasetInput()
vals$data_keep <- datasetInput()
})
## Datatable
output$table_keep <- renderDT({
vals$data_keep
},options = list(pageLength = 5))
output$table_outliers <- renderDT({
vals$data_exclude
},options = list(pageLength = 5))
# mechanism for managing selected points
keys <- reactiveVal()
observeEvent(event_data("plotly_click", source = "outliers", priority = "event"), {
req(vals$data)
is_outlier <- NULL
key_new <- event_data("plotly_click", source = "outliers")$key
key_old <- keys()
if (key_new %in% key_old){
keys(setdiff(key_old, key_new))
} else {
keys(c(key_new, key_old))
}
is_outlier <- rownames(vals$data) %in% keys()
vals$data_keep <- vals$data[!is_outlier, ]
vals$data_exclude <- vals$data[is_outlier, ]
plotlyProxy("scatterplot", session) %>%
plotlyProxyInvoke(
"restyle",
list(marker.line = list(
color = as.vector(ifelse(is_outlier,'black','grey')),
width = 2
))
)
})
observeEvent(event_data("plotly_doubleclick", source = "outliers"), {
req(vals$data)
keys(NULL)
vals$data_keep <- vals$data
vals$data_exclude <- NULL
plotlyProxy("scatterplot", session) %>%
plotlyProxyInvoke(
"restyle",
list(marker.line = list(
color = 'grey',
width = 2
)
))
})
output$scatterplot <- renderPlotly({
req(vals$data,input$xAxisSelector,input$yAxisSelector)
dat <- vals$data
key <- rownames(vals$data)
x <- input$xAxisSelector
y <- input$yAxisSelector
if(input$colorBySelector != "Do not color"){
color <- dat[, input$colorBySelector]
}else{
color <- "orange"
}
scatterplot <- dat %>%
plot_ly(x = dat[,x], y = dat[,y], source = "outliers") %>%
add_markers(key = key,color = color,
marker = list(size = 10, line = list(
color = 'grey',
width = 2
))) %>%
layout(showlegend = FALSE)
return(scatterplot)
})
output$click <- renderPrint({#click event data
d <- event_data("plotly_click", source = "outliers")
if (is.null(d)) "click events appear here (double-click to clear)" else d
})
}
shinyApp(ui, server)
The problem with your above code is that no traceIndices argument is provided for restyle. Please see this.
In your example, once you switch coloring to the factor Species plotly no longer creates one trace, but three. This happens in JS so counting is done from 0 to 2.
To restyle those traces you can address them via curveNumber (in this case 0:2) and pointNumber (50 data points in each trace 0:49)
With a single trace your example works as your key and your trace have the same length (150).
As your provided code is pretty long I just focused on the "Species" problem. It won't work in all other cases, but you should be able to deduce a more general approach from it:
library(shiny)
library(plotly)
library(DT)
ui <- fluidPage(
mainPanel(
fluidRow(
div(
column(
width = 2,
uiOutput('chartOptions')),
column(width = 5,
h3("Scatter plot"),
plotlyOutput("scatterplot"),
verbatimTextOutput("click")
)
)
),
hr(),
div(
column(width = 6,
h2("Data Table"),
div(
DT::dataTableOutput(outputId = "table_keep"),
style = "height:auto; overflow-y: scroll;overflow-x: scroll;")),
column(width = 6,
h2("Outlier Data"),
div(
DT::dataTableOutput(outputId = "table_outliers"),
style = "height:auto; overflow-y: scroll;overflow-x: scroll;"))
)
))
server <- function(input, output, session){
datasetInput <- reactive({
df <- iris
df$is_outlier <- FALSE
return(df)
})
output$chartOptions <- renderUI({#choose variables to plot
if(is.null(datasetInput())){}
else {
list(
selectizeInput("xAxisSelector", "X Axis Variable",
colnames(datasetInput())),
selectizeInput("yAxisSelector", "Y Axis Variable",
colnames(datasetInput())),
selectizeInput("colorBySelector", "Color By:",
c(c("Do not color",colnames(datasetInput()))))
)
}
})
vals <- reactiveValues(#define reactive values for:
data = NULL,
data_keep = NULL,
data_exclude = NULL)
observe({
vals$data <- datasetInput()
vals$data_keep <- datasetInput()
})
## Datatable
output$table_keep <- renderDT({
vals$data_keep
},options = list(pageLength = 5))
output$table_outliers <- renderDT({
vals$data_exclude
},options = list(pageLength = 5))
# mechanism for managing selected points
keys <- reactiveVal()
myPlotlyProxy <- plotlyProxy("scatterplot", session)
observeEvent(event_data("plotly_click", source = "outliers", priority = "event"), {
req(vals$data)
is_outlier <- NULL
plotlyEventData <- event_data("plotly_click", source = "outliers")
key_new <- plotlyEventData$key
key_old <- keys()
if (key_new %in% key_old){
keys(setdiff(key_old, key_new))
} else {
keys(c(key_new, key_old))
}
vals$data[keys(),]$is_outlier <- TRUE
is_outlier <- vals$data$is_outlier
vals$data_keep <- vals$data[!is_outlier, ]
vals$data_exclude <- vals$data[is_outlier, ]
print(paste("pointNumber:", plotlyEventData$pointNumber))
print(paste("curveNumber:", plotlyEventData$curveNumber))
plotlyProxyInvoke(
myPlotlyProxy,
"restyle",
list(marker.line = list(
color = as.vector(ifelse(vals$data[vals$data$Species %in% vals$data[plotlyEventData$key, ]$Species, ]$is_outlier,'black','grey')),
width = 2
)), plotlyEventData$curveNumber
)
})
observeEvent(event_data("plotly_doubleclick", source = "outliers"), {
req(vals$data)
keys(NULL)
vals$data_keep <- vals$data
vals$data_exclude <- NULL
plotlyProxyInvoke(
myPlotlyProxy,
"restyle",
list(marker.line = list(
color = 'grey',
width = 2
)
))
})
output$scatterplot <- renderPlotly({
req(datasetInput(),input$xAxisSelector,input$yAxisSelector)
dat <- datasetInput()
key <- rownames(dat)
x <- input$xAxisSelector
y <- input$yAxisSelector
if(input$colorBySelector != "Do not color"){
color <- dat[, input$colorBySelector]
}else{
color <- "orange"
}
scatterplot <- dat %>%
plot_ly(x = dat[,x], y = dat[,y], source = "outliers") %>%
add_markers(key = key,color = color,
marker = list(size = 10, line = list(
color = 'grey',
width = 2
))) %>%
layout(showlegend = FALSE)
return(scatterplot)
})
output$click <- renderPrint({#click event data
d <- event_data("plotly_click", source = "outliers")
if (is.null(d)) "click events appear here (double-click to clear)" else d
})
}
shinyApp(ui, server)
As a quick workaround, to avoid creating 3 traces, I simply converted the categorical variable assigned to color to numeric, and I hid the colorbar, so the output looks like this:
output$scatterplot <- renderPlotly({
req(vals$data,input$xAxisSelector,input$yAxisSelector)
dat <- vals$data
key <- rownames(vals$data)
x <- input$xAxisSelector
y <- input$yAxisSelector
if(input$colorBySelector != "Do not color"){
color <- as.numeric(dat[, input$colorBySelector])
}else{
color <- "orange"
}
scatterplot <- dat %>%
plot_ly(x = dat[,x], y = dat[,y], source = "outliers") %>%
add_markers(key = key,color = color,
marker = list(size = 10, line = list(
color = 'grey',
width = 2
))) %>%
layout(showlegend = FALSE) %>%
hide_colorbar()%>%
event_register("plotly_click")
return(scatterplot)
})
Update:
Another solution that I found is to make a loop of plotly proxies for each trace / category in the click event.
So the click event looks like this:
observeEvent(event_data("plotly_click", source = "outliers", priority = "event"), {
req(vals$data)
is_outlier <- NULL
key_new <- event_data("plotly_click", source = "outliers")$key
key_old <- keys()
#keys(c(key_new, key_old))
if (key_new %in% key_old){
keys(setdiff(key_old, key_new))
} else {
keys(c(key_new, key_old))
}
is_outlier <- rownames(vals$data) %in% keys()
vals$data_keep <- vals$data[!is_outlier, ]
vals$data_exclude <- vals$data[is_outlier, ]
indices <- list()
p <- plotlyProxy("scatterplot", session)
if(input$colorBySelector != "Do not color"){
if(is.factor(vals$data[,input$colorBySelector])){
for (i in 1:length(levels(vals$data[,input$colorBySelector]))){
indices[[i]] <- rownames(vals$data[which(vals$data[,input$colorBySelector] == levels(vals$data[,input$colorBySelector])[i]), ]) #retrieve indices for each category
plotlyProxyInvoke(p,
"restyle",
list(marker.line = list(
color = as.vector(ifelse(is_outlier[as.numeric(indices[[i]])],'black','grey')),
width = 2
)), c(i-1) #specify the trace (traces are indexed from 0)
)
}
}else{
p %>%
plotlyProxyInvoke(
"restyle",
list(marker.line = list(
color = as.vector(ifelse(is_outlier,'black','grey')),
width = 2
))
)
}
}else{
p %>%
plotlyProxyInvoke(
"restyle",
list(marker.line = list(
color = as.vector(ifelse(is_outlier,'black','grey')),
width = 2
))
)
}
})

Reactive Shiny Application

I am trying to create an interactive shiny application that displays a leaflet plot based on a user's date and plot type specification. Ideally, I would like the user to specify whether they would like to view a state-wide or a county-wide plot. Then, based on their answers, I would like them to decide whether to use the regular data or the standardized data. After this, they would hit a submit button and the plot would render. I don't want the plot to render until the user presses the "Submit" action button. This is my idea so far, but it fails whenever I try to implement.
library(ggplot2)
library(shapefiles)
library(sp)
library(CARBayes)
library(leaflet)
library(rgdal)
library(leaflet)
library(shiny)
## County Data
dta <- read.csv()
## County Data (percentage)
perc <-read.csv()
## Date Specification Function
selectdates <- function(data, start, end){
keep <- data[, 1:5]
data <- data[, -c(1:5)]
tmp1 <- as.Date(names(data))
tmp2 <- which(tmp1 >= as.Date(start) & tmp1 <= as.Date(end))
tmp <- data[, tmp2]
Sum <- rowSums(tmp)
tmp <- cbind(keep, Sum)
return(tmp)
}
# Define UI for application that draws a histogram
ui <- fluidPage(
# Application title
titlePanel("Mapping"),
tags$em(""),
tags$hr(),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
dateRangeInput("daterange", "Date Range:",
start = as.character(Sys.Date() - 6),
end = as.character(Sys.Date())),
selectInput("ptChoice", "Type of Plot:", choices = c("", "County-Wise", "State-Wise")),
selectInput("typeChoice", "Data Type:", choices = c("", "Raw", "Percentage")),
actionButton("submitButton", "Submit", class = "btn btn-primary")
),
# Display leaflet plot of cases
mainPanel(
leafletOutput("countyPlot"),
leafletOutput("statePlot")
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
observeEvent(input$ptChoice, {
req(input$ptchoice)
if(input$ptChoice == "County-Wide"){
hide("statePlot")
show("countyPlot")
}
else{
hide("countyPlot")
show("statePlot")
}
})
fdta <- eventReactive(input$typeChoice, {
if (input$typeChoice == "Raw"){
df <- selectdates(data = tmp, start = input$daterange[1], end = input$daterange[2])
row.names(df) <- df$FIPS
}else if (input$typeChoice == "Percentage"){
df <- selectdates(data = perc, start = input$daterange[1], end = input$daterange[2])
}else {return(NULL)}
df
})
observeEvent(input$submitButton, {
output$statePlot <- renderLeaflet({
## INSERT STATE PLOT CODE HERE
})
output$countyPlot <- renderLeaflet({
## Loads SHP and DBF File
shp <- read.shp()
dbf <- read.dbf()
sp <- combine.data.shapefile(data = fdta, shp = shp, dbf = dbf)
proj4string(sp) <- CRS("+proj=longlat +datum=WGS84 +no_defs")
sp <- spTransform(sp, CRS("+proj=longlat +datum=WGS84 +no_defs"))
colours <- colorNumeric(palette = "YlOrRd", domain = sp#data$Sum)
leaflet(sp) %>%
addTiles() %>%
addPolygons(
fillColor = ~ colours(Sum),
weight = 1,
opacity = 0.7,
color = "white",
dashArray = '3',
fillOpacity = 0.7,
highlight = highlightOptions(
weight = 5,
color = "#666",
dashArray = "",
fillOpacity = 0.7,
bringToFront = TRUE
)
) %>%
addLegend(
pal = colours,
values = sp#data$Sum,
opacity = 1,
title = "Count"
) %>%
addScaleBar(position = "bottomleft")
})
})
}
# Run the application
shinyApp(ui = ui, server = server)
You can put the two plots inside an observeEvent, if you want it only after someone clicks on submit button. To use the appropriate dataframe, create a reactive dataframe and then use it as dfa() to generate the appropriate plot. Try this
server = function(input, output) {
observeEvent(input$ptChoice,{
req(input$ptChoice)
if(input$ptChoice == "County-Wide"){
hide("statePlot")
show("countyPlot")
}else{
hide("countyPlot")
show("statePlot")
}
})
dfa <- eventReactive(input$typechoice, {
if (input$typechoice == "Regular") {
df <- dta
}else if (input$typechoice == "Standardized") {
df <- dta2
}else {return(NULL)}
df
})
observeEvent(input$submitButton,{
output$stateplot <- renderLeaflet({
state <- CODE FOR STATE PLOT
})
output$countyPlot <- renderLeaflet({
county <- CODE FOR COUNTY PLOT
})
})
}
You might want to have your leaflet plot be stored in reactiveValues (rv) - then, you can have one output for your plot, and show what is stored in rv.
To change the plot when the submit button is pressed, be sure to reference the input$submitButton with your observeEvent.
Here is a working example that can be adapted. You could use an additional function to generate the plots based on your input values.
library(ggplot2)
library(leaflet)
library(shiny)
ui = fluidPage(
titlePanel("Leaflet Plot"),
tags$em(""),
tags$hr(),
sidebarLayout(
sidebarPanel(
selectInput("plotChoice", "Type of Plot:", choices = c("", "Boston", "Chicago")),
actionButton("submitButton", "Submit", class = "btn btn-primary")
),
# Display leaflet plot of cases
mainPanel(
leafletOutput("leafletPlot")
)
)
)
server = function(input, output) {
rv <- reactiveValues(plot = NULL)
output$leafletPlot <- renderLeaflet({
rv$plot
})
observeEvent(input$submitButton, {
if (input$plotChoice == "Boston") {
rv$plot <- leaflet() %>% setView(lng = -71.0589, lat = 42.3601, zoom = 12) %>% addTiles()
} else {
rv$plot <- leaflet() %>% setView(lng = -87.6298, lat = 41.8781, zoom = 12) %>% addTiles()
}
})
}
shinyApp(ui = ui, server = server)

Applying leaflet map bounds to filter data, within Shiny

The code below is meant to reproduce that which is found in this example with the exception of adding an additional parameter for "speed". However, my map-datatable link has broken - Can anyone help me spot the bug? The original code updates the table based on the bounds of the map, while in my code changing the map zoom has no effect on my table. I'm also not able to get the "speed" filter to work on the table and map, which is a functionality I am looking for. Any pointers would be appreciated.
library(shiny)
library(magrittr)
library(leaflet)
library(DT)
ships <-
read.csv(
"https://raw.githubusercontent.com/Appsilon/crossfilter-demo/master/app/ships.csv"
)
ui <- shinyUI(fluidPage(
titlePanel(""),
sidebarLayout(
sidebarPanel(width = 3,
numericInput(
"speed", label = h5("Ship's Speed"), value = 100
)),
mainPanel(tabsetPanel(
type = "tabs",
tabPanel(
"Leaflet",
leafletOutput("leafletmap", width = "350px"),
dataTableOutput("tbl")
)
))
)
))
server <- shinyServer(function(input, output) {
in_bounding_box <- function(data, lat, long, bounds, speed) {
data %>%
dplyr::filter(
lat > bounds$south &
lat < bounds$north &
long < bounds$east & long > bounds$west & ship_speed < input$speed
)
}
output$leafletmap <- renderLeaflet({
leaflet() %>%
addProviderTiles("Esri.WorldImagery", group = "ESRI World Imagery") %>%
addCircleMarkers(
data = ships,
~ long ,
~ lat,
popup = ~ speed,
radius = 5 ,
stroke = FALSE,
fillOpacity = 0.8,
popupOptions = popupOptions(closeButton = FALSE)
)
})
data_map <- reactive({
if (is.null(input$map_bounds)) {
ships
} else {
bounds <- input$map_bounds
in_bounding_box(ships, lat, long, bounds, speed)
}
})
output$tbl <- DT::renderDataTable({
DT::datatable(
data_map(),
extensions = "Scroller",
style = "bootstrap",
class = "compact",
width = "100%",
options = list(
deferRender = TRUE,
scrollY = 300,
scroller = TRUE,
dom = 'tp'
)
)
})
})
shinyApp(ui = ui, server = server)
Two small changes:
In the example you linked, input$map_bounds works, because the leaflet output object is called map. However, you renamed it to leafletmap, so we should refer to input$leafletmap_bounds.
in the dplyr statement, we should refer to speed, not ship_speed.
Working code is given below, hope this helps!
library(shiny)
library(magrittr)
library(leaflet)
library(DT)
ships <-
read.csv(
"https://raw.githubusercontent.com/Appsilon/crossfilter-demo/master/app/ships.csv"
)
ui <- shinyUI(fluidPage(
titlePanel(""),
sidebarLayout(
sidebarPanel(width = 3,
numericInput(
"speed", label = h5("Ship's Speed"), value = 100
)),
mainPanel(tabsetPanel(
type = "tabs",
tabPanel(
"Leaflet",
leafletOutput("leafletmap", width = "350px"),
dataTableOutput("tbl")
)
))
)
))
server <- shinyServer(function(input, output) {
in_bounding_box <- function(data, lat, long, bounds, speed) {
data %>%
dplyr::filter(
lat > bounds$south &
lat < bounds$north &
long < bounds$east & long > bounds$west & speed < input$speed
)
}
output$leafletmap <- renderLeaflet({
leaflet() %>%
addProviderTiles("Esri.WorldImagery", group = "ESRI World Imagery") %>%
addCircleMarkers(
data = ships,
~ long ,
~ lat,
popup = ~ speed,
radius = 5 ,
stroke = FALSE,
fillOpacity = 0.8,
popupOptions = popupOptions(closeButton = FALSE)
)
})
data_map <- reactive({
if (is.null(input$leafletmap_bounds)) {
ships
} else {
bounds <- input$leafletmap_bounds
in_bounding_box(ships, lat, long, bounds, speed)
}
})
output$tbl <- DT::renderDataTable({
DT::datatable(
data_map(),
extensions = "Scroller",
style = "bootstrap",
class = "compact",
width = "100%",
options = list(
deferRender = TRUE,
scrollY = 300,
scroller = TRUE,
dom = 'tp'
)
)
})
})
shinyApp(ui = ui, server = server)
The leaflet map you are rendering is called leafletmap. So rather than referring to map_bounds try changing it to leafletmap_bounds:
data_map <- reactive({
if (is.null(input$leafletmap_bounds)) {
ships
} else {
bounds <- input$leafletmap_bounds
in_bounding_box(ships, lat, long, bounds, speed)
}
})
Also in the filter, change ship_speed to speed. Should hopefully work.

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