I am trying to create an interactive map using Plotly in the Shiny app that allows the user to select the region by box select and lasso select on the map, then it can return a GoogleVis motion chart showing the statistics on the region selected within the Shiny app. However when it comes to the output function of GoogleVis:
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))
})
It gives the error of:
Warning: Error in $: $ operator is invalid for atomic vectors
96: renderText [/Users/b.w.h/Documents/JHU/Summer 1/COVID-19 Modeling Project/County Polygon Visualization with Shiny/USMapWithCountyPolygon/server.R#114]
95: func
82: origRenderFunc
81: output$brush
1: runApp
This is very strange because when I checked in the console, the data frame that I am trying to subset with "$" is not atomic.
is.atomic(totalComfirmed)
[1] FALSE
Why would that happen? Here is my full 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)
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$FIPS)
colnames(covidCases)[6] <- "countyNames"
totalComfirmed <- covidCases[,ncol(covidCases)]
names(totalComfirmed) <- c("countyNames", "cases")
destroyX = function(es) {
f = es
for (col in c(1:ncol(f))){ #for each column in dataframe
if (startsWith(colnames(f)[col], "X") == TRUE) { #if starts with 'X' ..
colnames(f)[col] <- substr(colnames(f)[col], 2, 100) #get rid of it
}
}
assign(deparse(substitute(es)), f, inherits = TRUE) #assign corrected data to original name
}
destroyX(covidCases)
gvisCasesData <- cbind.data.frame(covidCases$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)
colnames(covidDeath)[6] <- "countyNames"
totalDeath <- covidDeath[,ncol(covidDeath)]
v <- reactiveValues(data = totalComfirmed)
observeEvent(input$countyFill, {
if (input$countyFill == "Map by total confirmed") {
v$data <- totalComfirmed;
v$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$brush <- renderText({
# selected <- event_data(event = "plotly_selected", source = "countyMap")
# selectedCountyCases <- as.integer(unlist(selected[3]))
# brush <- selectedCounties
#})
output$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, server)
Thanks for your help!
When I run
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$FIPS)
colnames(covidCases)[6] <- "countyNames"
totalComfirmed <- covidCases[,ncol(covidCases)]
names(totalComfirmed) <- c("countyNames", "cases")
and then try is.atomic, i get
is.atomic(totalComfirmed)
# [1] TRUE
You've extracted a single column out of a data.frame which by default returns just an atomic vector. Then when you try to do
totalComfirmed$cases %in% selectedCountyCases
You'll get an error because totalComfirmed doesn't have any columns. Perhaps you meant
totalComfirmed <- covidCases[,c(which(names(covidCases)=="countyNames"), ncol(covidCases))]
Also is totalComfirmed a typo? Should it be totalConfirmed?