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Display.R
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###############################################################################################
library(data.table)
library(plyr)
library(dplyr)
library(ISOcodes)
library(countrycode)
library(tidyr)
library(BBmisc)
library(shiny)
library(lubridate)
library(shinyWidgets)
library(leaflet)
library(shinydashboard)
library(maptools)
library(rworldmap)
library(scales)
library(ggplot2)
library(directlabels)
library(rsconnect)
source("Prepare.R", local = TRUE)
###Shiny App
header <- dashboardHeader(title = "Covid-19 Vizualisation")
sidebar <- dashboardSidebar(
sidebarMenu(
menuItem("World Map", tabName = "map", icon = icon("globe")),
menuItem("Timeline Graph", tabName = "timeline", icon = icon("chart-line")),
menuItem("Info", tabName = "info", icon = icon("info"))
)
)
body <- dashboardBody(
#tags$style(type = "text/css", "#map {height: calc(100vh - 20vh) !important;}"),
tabItems(
tabItem(tabName = "map",
leafletOutput("map", width = "100%", height = "75vh"),
absolutePanel(top = '10%', left = '20vw', height = "8vh", width = "25vh", fixed = FALSE,
textOutput("text1")
),
absolutePanel(top = '85vh', left = '20vw', height = "8vh", width = "20vw", fixed = FALSE,
setSliderColor("black", 1),
sliderInput(inputId = "Day", "Pick a date:",
min = min(countries$Day), max = max(countries$Day),
value = max(countries$Day), step = 1,
animate =
animationOptions(interval = 1000, loop = FALSE))
),
absolutePanel(top = '85vh', left = '45vw', height = "8vh", width = "20vw", fixed = FALSE,
selectInput(inputId = "Info",
label = "Pick a variable to display",
choices = list("Absolute numbers" = list(
"Cases" = "Cases",
"Active" = "Active",
"Deaths" = "Deaths",
"Recovered" = "Recovered"
),
"Daily Change in Absolute Numbers" = list(
"New Cases Daily" = "New Cases Daily",
"Change in Active Cases Daily" = "Change in Active Cases Daily",
"New Deaths Daily" = "New Deaths Daily"
),
"Relative numbers" = list(
"Cases per Million" = "Cases per Million",
"Active Cases per Million" = "Active Cases per Million",
"Deaths per Million" = "Deaths per Million",
"Recovered Cases per Million" = "Recovered Cases per Million"
),
"Ratios" = list(
"Death Ratio of all Cases" = "Death ratio",
"Active Ratio of all Cases" = "Active ratio",
"Death Ratio of all Known Outcomes" = "Death ratio of Outcomes"
),
"Daily Growth Rates" = list(
"Daily Growth Rate of Cases" = "Daily Growth Rate of Cases" ,
"Daily Growth Rate of Active Cases" = "Daily Growth Rate of Active Cases",
"Daily Growth Rate of Deaths" = "Daily Growth Rate of Deaths"
)),
selected = "Cases per Million",
multiple = FALSE,
selectize = FALSE,
width = '100%',
size = 1)
)
),
tabItem(tabName = "timeline",
plotOutput("timeline", height = "75vh"),
absolutePanel(top = '85vh', left = '20vw', height = "8vh", width = "20vw", fixed = FALSE,
selectInput(
inputId = "Country_plot",
label = "Pick Countries",
choices = as.character(unique(countries$Country)),
multiple = TRUE,
#select top three countries in cases for default plot
selected = countries[is.element(countries$Cases,sort(countries[which(countries$Day==max(countries$Day,na.rm = TRUE)),"Cases"], decreasing = TRUE)[1:3]),"Country"]
)),
absolutePanel(top = '85vh', left = '45vw', height = "8vh", width = "15vw", fixed = FALSE,
selectInput(
inputId = "Variable_plot",
label = "Pick Variable",
choices = list("Absolute numbers" = list(
"Cases" = "Cases",
"Active" = "Active",
"Deaths" = "Deaths",
"Recovered" = "Recovered"
),
"Daily Change in Absolute Numbers" = list(
"New Cases Daily" = "New Cases Daily",
"Change in Active Cases Daily" = "Change in Active Cases Daily",
"New Deaths Daily" = "New Deaths Daily"
),
"Relative numbers" = list(
"Cases per Million" = "Cases per Million",
"Active Cases per Million" = "Active Cases per Million",
"Deaths per Million" = "Deaths per Million",
"Recovered Cases per Million" = "Recovered Cases per Million"
),
"Ratios" = list(
"Death Ratio of all Cases" = "Death ratio",
"Active Ratio of all Cases" = "Active ratio",
"Death Ratio of all Known Outcomes" = "Death ratio of Outcomes"
),
"Daily Growth Rates" = list(
"Daily Growth Rate of Cases" = "Daily Growth Rate of Cases" ,
"Daily Growth Rate of Active Cases" = "Daily Growth Rate of Active Cases",
"Daily Growth Rate of Deaths" = "Daily Growth Rate of Deaths"
)),
multiple = FALSE,
selected = "Cases",
selectize = FALSE,
size = 1
)),
absolutePanel(top = '85vh', left = '65vw', height = "8vh", width = "20vw", fixed = FALSE,
dateRangeInput(inputId = "daterange",
label = "Pick Start and End Dates:",
start = "2020-02-01",
end = max(countries$Day),
min = min(countries$Day),
max = max(countries$Day),
format = "yyyy-mm-dd",
startview = "month",
weekstart = 1,
language = "en",
separator = " - ",
width = NULL)
),
),
tabItem(tabName = "info",
titlePanel("Info"),
mainPanel(
HTML(paste0("<b>Data source: </b> <a href='https://github.com/CSSEGISandData/COVID-19' > Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) </a> </br> </br>
<b>Last updated: </b>",textOutput("timestamp"),"</br>
<b>Country flags from: </b> <a href='https://github.com/stefangabos/world_countries' > https://github.com/stefangabos/world_countries </a> </br> </br>
<b>Source code: </b> <a href='https://github.com/captaincaracho/CoronaVIZ'> https://github.com/captaincaracho/CoronaVIZ </a> ")
))
))
)
# Define UI for application
ui <- dashboardPage(header, sidebar, body, skin = "black")
server <- function(input, output, session) {
#Worldmap
output$map <- renderLeaflet({
leaflet(options = leafletOptions(minZoom = 2)) %>%
addTiles() %>%
addMiniMap()
})
selected <- reactive({
#countries <- countries %>% filter(Day %in% input$Day)
countries <- countries[countries$Day == input$Day, ]
})
output$text1 <- renderText({paste("Date: ", input$Day)})
observe({
map <- joinCountryData2Map(selected(), joinCode = "ISO3",nameJoinColumn = "ISO3", verbose = TRUE)
#Colorcode
map$Color <- switch(input$Info,
"Cases" = map$Cases_color,
"Active" = map$Active_color,
"Deaths" = map$Deaths_color,
"Recovered" = map$Recovered_color,
"New Cases Daily" = map$Delta_Cases_color,
"Change in Active Cases Daily" = map$Delta_Active_color,
"New Deaths Daily" = map$Delta_Deaths_color,
"Cases per Million" = map$CpC_color,
"Active Cases per Million" = map$ApC_color,
"Deaths per Million" = map$DpC_color,
"Recovered Cases per Million" = map$RpC_color,
"Death ratio" = map$D2C_color,
"Active ratio" = map$A2C_color,
"Death ratio of Outcomes" = map$D2O_color,
"Daily Growth Rate of Cases" = map$CdG_color,
"Daily Growth Rate of Active Cases" = map$AdG_color,
"Daily Growth Rate of Deaths" = map$DdG_color
)
#Number that shows up in label
map$Info <- switch(input$Info,
"Cases" = map$Cases,
"Active" = map$Active,
"Deaths" = map$Deaths,
"Recovered" = map$Recovered,
"New Cases Daily" = map$Delta_Cases,
"Change in Active Cases Daily" = map$Delta_Active,
"New Deaths Daily" = map$Delta_Deaths,
"Cases per Million" = map$CpC,
"Active Cases per Million" = map$ApC,
"Deaths per Million" = map$DpC,
"Recovered Cases per Million" = map$RpC,
"Death ratio" = map$D2C,
"Active ratio" = map$A2C,
"Death ratio of Outcomes" = map$D2O,
"Daily Growth Rate of Cases" = map$CdG,
"Daily Growth Rate of Active Cases" = map$AdG,
"Daily Growth Rate of Deaths" = map$DdG
)
#Number that shows up in legend
map_legend <- switch(input$Info,
"Cases" = legend_Cases,
"Active" = legend_Active,
"Deaths" = legend_Deaths,
"Recovered" = legend_Recovered,
"New Cases Daily" = legend_Delta_Cases,
"Change in Active Cases Daily" = legend_Delta_Active,
"New Deaths Daily" = legend_Delta_Deaths,
"Cases per Million" = legend_CpC,
"Active Cases per Million" = legend_ApC,
"Deaths per Million" = legend_DpC,
"Recovered Cases per Million" = legend_RpC,
"Death ratio" = legend_D2C,
"Active ratio" = legend_A2C,
"Death ratio of Outcomes" = legend_D2O,
"Daily Growth Rate of Cases" = legend_CdG,
"Daily Growth Rate of Active Cases" = legend_AdG,
"Daily Growth Rate of Deaths" = legend_DdG
)
#Explaining text next to number
map_title <- switch(input$Info,
"Cases" = "Cases",
"Active" = "Active",
"Deaths" = "Deaths",
"Recovered" = "Recovered",
"New Cases Daily" = "New Cases Daily",
"Change in Active Cases Daily" = "New Active Cases Daily",
"New Deaths Daily" = "New Deaths Daily",
"Cases per Million" = "Cases per Million Inhabitants",
"Active Cases per Million" = "Active Cases per Million Inhabitants",
"Deaths per Million" = "Deaths per Million Inhabitant",
"Recovered Cases per Million" = "Recovered Cases per Million Inhabitants",
"Death ratio" = "Percentage of Deaths of all Cases",
"Active ratio" = "Percentage of Active Cases of all Cases",
"Death ratio of Outcomes" = "Percentage of Deaths of all known Outcomes",
"Daily Growth Rate of Cases" = "Daily Growth Rate of Cases" ,
"Daily Growth Rate of Active Cases" = "Daily Growth Rate of Active Cases",
"Daily Growth Rate of Deaths" = "Daily Growth Rate of Deaths"
)
measure <- switch(input$Info,
"Cases" = "",
"Active" = "",
"Deaths" = "",
"Recovered" = "",
"New Cases Daily" = "",
"Change in Active Cases Daily" = "",
"New Deaths Daily" = "",
"Cases per Million" = "",
"Active Cases per Million" = "",
"Deaths per Million" = "",
"Recovered Cases per Million" = "",
"Death ratio" = "%",
"Active ratio" = "%",
"Death ratio of Outcomes" = "%",
"Daily Growth Rate of Cases" = "%" ,
"Daily Growth Rate of Active Cases" = "%",
"Daily Growth Rate of Deaths" = "%"
)
leafletProxy("map", data = map) %>%
addTiles() %>%
#clearControls() %>%
addPolygons(fillColor = map$Color,
weight = 2,
opacity = 1,
color = "white",
dashArray = "3",
fillOpacity = 0.7,
highlight = highlightOptions(
weight = 5,
color = "white",
dashArray = "3",
fillOpacity = .8,
bringToFront = TRUE),
label = paste0(map$Country,": ", ifelse(is.na(map$Info),"No data or not not enough cases", paste0(format(round(map$Info,2), big.mark =","), measure))),
popup = paste0("<head>
<style>
table, th, td {
border: 1 px grey;
border-collapse: collapse;
}
th, td {
padding: 5px;
}
</style>
</head>",
"<h3> <img src='https://raw.githubusercontent.com/captaincaracho/world_countries/master/flags/32x32/",tolower(map$ISO2),".png', width = 35 > <b>",map$Country,"</b> </h3>",
"<table>
<tr align = 'left'>
<th>",map$Day,"</th>
<th> Absolute </th>
<th> Daily Change </th>
<th> Daily Growth </th>
<th> per Million </th>
</tr> <tr align= 'right'>
<td>Cases</td>
<td>",ifelse(is.na(map$Cases),"-", format(map$Cases, big.mark =",", nsmall = 0)),"</td>
<td>",ifelse(is.na(map$Delta_Cases),"-", format(map$Delta_Cases, big.mark =",", nsmall = 0)),"</td>
<td>",ifelse(is.na(map$CdG),"-", format(round(map$CdG,2), big.mark =",")),"% </td>
<td>",ifelse(is.na(map$CpC),"-", format(round(map$CpC,2), big.mark =",")),"</td>
</tr> <tr align= 'right'>
<td>Deaths </td>
<td>", ifelse(is.na(map$Deaths),"-", format(map$Deaths, big.mark =",", nsmall = 0)),"</td>
<td>", ifelse(is.na(map$Delta_Deaths),"-", format(map$Delta_Deaths, big.mark =",", nsmall = 0)),"</td>
<td>", ifelse(is.na(map$DdG),"-", format(round(map$DdG,2), big.mark =",")),"% </td>
<td>",ifelse(is.na(map$DpC),"-", format(round(map$DpC,2), big.mark =",")),"</td>
</tr> <tr align= 'right'>
<td>Active Cases</td>
<td>",ifelse(is.na(map$Active),"-", format(map$Active, big.mark =",", nsmall = 0)),"</td>
<td>",ifelse(is.na(map$Delta_Active),"-", format(map$Delta_Active, big.mark =",", nsmall = 0)),"</td>
<td>",ifelse(is.na(map$AdG),"-", format(round(map$AdG,2), big.mark =",")),"% </td>
<td>",ifelse(is.na(map$ApC),"-", format(round(map$ApC,2), big.mark =",")),"</td>
</tr>
</table>"
),
popupOptions = popupOptions(closeOnClick = TRUE, closeButton = FALSE, autoPan = TRUE, minWidth = 400)
) %>%
addLegend("topright", colors = unique(map_legend$color), labels = map_legend$label,
title = map_title, layerId = 1,
opacity = 1
)
#Timeline
selected_plot <- reactive({
countries %>%
filter(Country %in% input$Country_plot) %>%
filter(Day %in% (input$daterange[1]:input$daterange[2])) %>%
arrange(desc(Country))
})
selected_colors <- reactive({
countries %>%
filter(Country %in% input$Country_plot) %>%
filter(Day == input$daterange[2]) %>%
arrange(desc(Country))
})
plotvar <- switch(input$Variable_plot,
"Cases" = "Cases",
"Active" = "Active",
"Deaths" = "Deaths",
"Recovered" = "Recovered",
"New Cases Daily" = "Delta_Cases",
"Change in Active Cases Daily" = "Delta_Active",
"New Deaths Daily" = "Delta_Deaths",
"Cases per Million" = "CpC",
"Active Cases per Million" = "ApC",
"Deaths per Million" = "DpC",
"Recovered Cases per Million" = "RpC",
"Death ratio" = "D2C",
"Active ratio" = "A2C",
"Death ratio of Outcomes" = "D2O",
"Daily Growth Rate of Cases" = "CdG",
"Daily Growth Rate of Active Cases" = "AdG",
"Daily Growth Rate of Deaths" = "DdG"
)
output$timeline <- renderPlot({
ggplot(data = selected_plot(), aes(x=Day, y=!!as.name(plotvar)))+
geom_line(size=1.5, aes(color=Country))+
geom_point(size=3, aes(fill=Country), shape = 21)+
geom_dl(aes(label=Country), method= list( dl.trans(x = x+0.2), "last.bumpup", cex= 1))+
coord_cartesian(clip = 'off') +
labs(x = "Date",y = input$Variable_plot)+
scale_fill_manual(values = selected_colors()[order(selected_colors()$Country),"color_2"])+ #sort in same order as selected data frame
scale_color_manual(values = selected_colors()[order(selected_colors()$Country),"color_1"])+ #scale_color_manual(values = selected_plot()[order(selected_plot()$Country), ][selected_plot()$Day == input$End_Day,"color1"])+
scale_x_date(labels = date_format("%m-%d"), date_breaks = "1 week")+
scale_y_continuous(labels = function(x) format(x, scientific = FALSE, big.mark = ","))+
theme(axis.text = element_text(size = 12),
axis.title = element_text(size=14),
legend.title = element_text(size=14),
legend.text = element_text(size=12),
panel.background = element_rect(fill="white"),
panel.grid.major = element_line(colour = "grey"))
})
output$timestamp <- renderText(paste0(time," UTC"))
})
}
shinyApp(ui, server)