I am trying to create an interactive shiny app that shows the user a Plotly map and allows the user to select different counties in the U.S. Then it can use the info on the selected counties to generate graphs and plots. However, it seems that the choropleth map only returns the curveNumber, pointNumber, and z value upon selection. How can I identify the selected county from this info? Or how can I make it gives the county names upon selection? Here is my ui and server function:
library(shiny)
library(shinyWidgets)
library(plotly)
library(leaflet)
ui <- fluidPage(
titlePanel("Johns Hopkins COVID-19 Modeling Visualization Map"),
setBackgroundImage(
src = "https://brand.jhu.edu/assets/uploads/sites/5/2014/06/university.logo_.small_.horizontal.blue_.jpg"
),
sidebarLayout(
sidebarPanel(
radioButtons("countyFill", "Choose the County Map Type", c("Map by total confirmed", "Map by total death"), selected = "Map by total confirmed"),
checkboxGroupInput("statesInput", "Choose the State(s)",
c("AL", "MO", "AK", "MT", "AZ", "NE",
"AR", "NV", "CA", "NH", "CO", "NJ",
"CT", "NM", "DE", "NY", "DC", "NC",
"FL", "ND", "GA", "OH", "HI", "OK",
"ID", "OR", "IL", "PA", "IN", "RI",
"IA", "SC", "KS", "SD", "KY", "TN",
"LA", "TX", "ME", "UT", "MD", "VT",
"MA", "VA", "MI", "WA", "MN", "WV",
"MS", "WI", "WY"),
inline = TRUE),
actionButton("submit", "Submit (may take 30s to load)")
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel("County Level", plotlyOutput("countyPolygonMap"),
htmlOutput("motionChart"),
verbatimTextOutput("brush")),
tabPanel("State Level", leafletOutput("statePolygonMap")),
tags$div(
tags$p(
"JHU.edu Copyright © 2020 by Johns Hopkins University & Medicine. All rights reserved."
),
tags$p(
tags$a(href="https://it.johnshopkins.edu/policies/privacystatement",
"JHU Information Technology Privacy Statement for Websites and Mobile Applications")
)
)
)
)
)
)
library(shiny)
library(leaflet)
library(magrittr)
library(rgdal)
library(plotly)
library(rjson)
library(dplyr)
library(viridis)
library(googleVis)
library(lubridate)
library(reshape2)
library(data.table)
library(shinyWidgets)
server <- function(input, output, session) {
statepolygonZip <- download.file("https://www2.census.gov/geo/tiger/GENZ2018/shp/cb_2018_us_state_500k.zip",
destfile = "cb_2018_us_state_500k.zip");
unzip("cb_2018_us_state_500k.zip");
statePolygonData <- readOGR("cb_2018_us_state_500k.shp", layer = "cb_2018_us_state_500k",
GDAL1_integer64_policy = TRUE);
## obtaning the state shape file data provided by cencus.gov
## for more categories of region shape file:
## https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html
url <- 'https://raw.githubusercontent.com/plotly/datasets/master/geojson-counties-fips.json'
countyGeo <- rjson::fromJSON(file=url)
## Obtaining the geographical file for all U.S. counties
url2<- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv"
covidCases <- read.csv(url2, header = TRUE)
fips <- sprintf("%05d",covidCases$FIPS)
colnames(covidCases)[6] <- "countyNames"
totalComfirmed <- covidCases[,c(which(names(covidCases)=="countyNames"), ncol(covidCases))]
names(totalComfirmed) <- c("countyNames", "cases")
destroyX = function(es) {
f = es
for (col in c(1:ncol(f))){ #for each column in dataframe
if (startsWith(colnames(f)[col], "X") == TRUE) { #if starts with 'X' ..
colnames(f)[col] <- substr(colnames(f)[col], 2, 100) #get rid of it
}
}
assign(deparse(substitute(es)), f, inherits = TRUE) #assign corrected data to original name
}
destroyX(covidCases)
gvisCasesData <- cbind.data.frame(covidCases$countyNames, covidCases[11,ncol(covidCases)])
gvisCasesData <- melt(data = setDT(covidCases), id.vars = "countyNames",measure.vars = c(colnames(covidCases)[c(12:ncol(covidCases))]))
colnames(gvisCasesData)[2:3] <- c("Date", "numCases")
gvisCasesData$Date <- mdy(gvisCasesData$Date)
url3 <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv"
covidDeath <- read.csv(url3, header = TRUE)
fips <- sprintf("%05d",covidCases$FIPS)
colnames(covidDeath)[6] <- "countyNames"
totalDeath <- covidDeath[,c(which(names(covidDeath)=="countyNames"), ncol(covidDeath))]
names(totalDeath) <- c("countyNames", "totalDeath")
v <- reactiveValues(data = totalComfirmed)
observeEvent(input$countyFill, {
if (input$countyFill == "Map by total confirmed") {
v$data <- totalComfirmed$cases;
v$zmin = 100;
v$zmax = 12000;
v$hover <- with(covidCases, paste(countyNames));
}
if (input$countyFill == "Map by total death") {
v$data <- totalDeath;
v$zmin = 0;
v$zmax = 1600;
v$hover <- with(covidDeath, paste(countyNames));
}
})
observeEvent(input$submit, {
req(input$submit)
output$countyPolygonMap <- renderPlotly({
countyPolygonMap <- plot_ly(source = "countyMap") %>% add_trace(
countyName <- covidCases$countyNames,
type="choroplethmapbox",
geojson=countyGeo,
locations=fips,
z=v$data,
colorscale="Viridis",
zmin= v$zmin,
zmax= v$zmax,
text = ~v$hover,
marker=list(line=list(width=0),opacity=0.5)
) %>% layout(
mapbox=list(
style="carto-positron",
zoom =2,
center=list(lon= -95.71, lat=37.09))
%>% event_register(event = "plotly_selected")
);
countyPolygonMap;
## generating the interactive plotly map
})
#output$motionChart <- renderGvis({
# selected <- event_data(event = "plotly_selected", source = "countyMap")
# selectedCountyCases <- as.integer(unlist(selected[3]))
# selectedCounties <- subset(totalComfirmed, totalComfirmed$cases %in% selectedCountyCases)
# gvisCasesDataSubset <- subset(gvisCasesData, countyNames %in% c(selectedCounties$countyNames))
# motionChart <- gvisMotionChart(gvisCasesDataSubset, "countyNames", "Date", options=list(width=800, height=400))
#})
output$brush <- renderText({
selected <- event_data(event = "plotly_selected", source = "countyMap")
brush <- selected
})
output$statePolygonMap <-renderLeaflet ({
statesAbbr <- subset(statePolygonData, input$statesInput %in% statePolygonData$STUSPS);
## subsetting the shape file with the selected states
leaflet(statesAbbr) %>%
addPolygons(color = "#444444", weight = 1, smoothFactor = 0.5,
opacity = 1.0, fillOpacity = 0.5,
fillColor = ~colorQuantile("YlOrRd", ALAND)(ALAND),
highlightOptions = highlightOptions
(color = "white", weight = 2,bringToFront = TRUE))
})
## producing the map with polygon boundary on the state level
})
}
shinyApp(ui = ui, server = server)
Thanks a lot for your help!
