Feature/83 stackedbarplot status

DESCRIPTION

@@ -19,6 +19,8 @@ URL: https://mirai-solutions.ch,
 BugReports: https://github.com/miraisolutions/Covid19/issues
 Imports: 
     config,
+    purrr,
+    stringr,
     golem,
     shiny,
     bsplus,

NAMESPACE

@@ -40,6 +40,7 @@ export(recovered_timeseries_csv_url)
 export(remove_legend)
 export(roundUp)
 export(run_app)
+export(stackedbarplot_plot)
 export(time_evol_area_plot)
 export(time_evol_line_facet_plot)
 export(time_evol_line_plot)
@@ -48,7 +49,9 @@ import(dplyr)
 import(ggplot2)
 import(leaflet)
 import(markdown)
+import(purrr)
 import(shiny)
+import(stringr)
 import(tidyr)
 importFrom(DT,DTOutput)
 importFrom(DT,datatable)

NEWS.md

@@ -5,6 +5,8 @@
 - fix trend order of area plot both global and country tabs, added utils funtion (#74)
 - correct plot titles for modules mod_compare_nth_cases_plot and mod_growth_death_rate (#66)
 - Add angle to bar-plot labels (#68)
+- Add status split stackedbarplot (#83)
+
 
 ### Covid19 1.1.6 (2020-04-06)
 

R/mod_country_comparison.R

@@ -25,6 +25,11 @@ mod_country_comparison_ui <- function(id){
              withSpinner(uiOutput(ns("lines_points_plots")))
              )
     ),
+    fluidRow(
+      column(12,
+             withSpinner(uiOutput(ns("status_stackedbarplot")))
+      )
+    ),
     mod_add_table_ui(ns("add_table_countries"))
   )
 }
@@ -106,6 +111,11 @@ mod_country_comparison_server <- function(input, output, session, orig_data_aggr
 
     callModule(mod_compare_nth_cases_plot_server, "lines_points_plots", countries_data, n = n, n_highligth = length(input$select_countries), istop = F)
 
+    output$status_stackedbarplot <- renderUI({
+      mod_stackedbarplot_ui(ns("status_stackedbarplot"))
+    })
+    callModule(mod_stackedbarplot_status_server, "status_stackedbarplot", countries_data, n = n, n_highligth = length(input$select_countries), istop = F)
+
     # tables ----
     callModule(mod_add_table_server, "add_table_countries", countries_data, maxrowsperpage = 10)
   })

R/mod_global.R

@@ -38,6 +38,12 @@ mod_global_ui <- function(id){
       )
     ),
     hr(),
+    fluidRow(
+      column(12,
+             mod_stackedbarplot_ui(ns("plot_stackedbarplot_status"))
+      )
+    ),
+    hr(),
     mod_add_table_ui(ns("add_table_world"))
   )
 }
@@ -138,6 +144,9 @@ mod_global_server <- function(input, output, session, orig_data, orig_data_aggre
   # > growth_death_rate
   callModule(mod_growth_death_rate_server, "plot_growth_death_rate", orig_data_aggregate)
 
+  # > stacked barplot with status split
+  callModule(mod_stackedbarplot_status_server, "plot_stackedbarplot_status", orig_data_aggregate)
+
   # tables ----
   callModule(mod_add_table_server, "add_table_world", world)
 

R/mod_stackedbarplot_status.R

@@ -0,0 +1,104 @@
+#' stackedbarplot_status UI Function
+#'
+#' @description A shiny Module.
+#'
+#' @param id,input,output,session Internal parameters for {shiny}.
+#'
+#' @noRd
+#'
+#' @importFrom shiny NS tagList
+#' @importFrom shinycssloaders withSpinner
+mod_stackedbarplot_ui <- function(id, n_highligth = 5){
+  ns <- NS(id)
+  tagList(
+    fluidRow(
+      column(6,
+             uiOutput(ns("title_stackedbarplot_status")),
+             withSpinner(uiOutput(ns("plot_stackedbarplot_status"), height = 400)),
+      )
+    )
+  )
+}
+#' stackedbarplot_status Server Function
+#'
+#' @param countries_data reactive data.frame for multiple countries
+#'
+#' @import dplyr
+#' @import tidyr
+#' @import ggplot2
+#' @import purrr
+#' @importFrom plotly ggplotly layout
+#' @noRd
+mod_stackedbarplot_status_server <- function(input, output, session, df, n = 1000, w = 7, n_highligth = 5, istop = T){
+  ns <- session$ns
+  # titles
+  if (istop) {
+    output$title_stackedbarplot_status <- renderUI(div(h4(paste0("Current top ", n_highligth, " status split")), align = "center", style = "margin-top:20px; margin-bottom:20px;"))
+  } else {
+    output$title_stackedbarplot_status <- renderUI(div(h4("Status split by country"), align = "center", style = "margin-top:20px; margin-bottom:20px;"))
+  }
+
+  prep_data <- function(orig_data_aggregate, n, w){
+    df1 <- orig_data_aggregate %>%
+      Covid19:::select_countries_n_cases_w_days(n = n, w = w) %>%
+      filter( date == max(date)) %>%
+      Covid19:::align_country_names_pop() %>%
+      mutate(country_name = Country.Region) %>%
+      Covid19:::get_pop_data() %>%
+      filter(population > 10^6) %>% # dropping countries with less than 1 M pop, needed?
+      Covid19:::align_country_names_pop_reverse()
+    df1
+  }
+  df_pop <- reactive({prep_data(df(), n,w)})
+  #df_pop = prep_data(df, n = 1000, w = 7)
+
+  statuses <- c("deaths", "active", "recovered")
+
+  pick_status <- function(df, stat){
+    df <-  df  %>%
+      bind_cols(df[, stat] %>% setNames("Value"))
+    df
+  }
+  df_status = reactive({pick_status(df_pop(), "confirmed") %>%
+    arrange(desc(Value)) %>%
+    top_n(n_highligth, wt = Value)  %>%
+    select(Country.Region,!!statuses)})
+
+
+  # gather status and compute ratios
+  df_status_stack = reactive({df_status() %>%
+      gather("status", "countstatus", -Country.Region) %>%
+    group_by(Country.Region) %>%
+    mutate(n.pop = sum(countstatus),
+           ratio.over.cases  = countstatus/n.pop) %>%
+    group_by(status) %>%
+    mutate(tot.status = sum(countstatus),
+           ratio.status  = countstatus/tot.status) %>%
+    ungroup() %>%
+    mutate(Country.Region = as.factor(Country.Region),
+           status = factor(status, levels = statuses)) %>%
+    arrange(status)})
+
+  caption_explain <- "Status split per country as of today."
+
+  output$plot_stackedbarplot_status <- renderUI({
+    tagList(
+      plotlyOutput(ns("plot_stackedbarplot_status_draw"), height = 400),
+      div(p(caption_explain), align = "center")
+    )
+  })
+
+  output$plot_stackedbarplot_status_draw <- renderPlotly({
+    p = df_status_stack() %>%
+        stackedbarplot_plot() %>% fix_colors()
+    p <- p %>%
+      ggplotly(tooltip = c("text", "fill"))   %>%
+      layout(legend = list(orientation = "v", y = 1, yanchor = "left"))
+
+    p$x$data <-
+      p$x$data %>%
+      purrr::map(clean_plotly_leg, "[^\\(][^,]*")
+
+    p
+  })
+}

R/plots.R

@@ -1,3 +1,36 @@
+#' stacked barplot status
+#'
+#' @param df data.frame
+#' @param percent logical to make the y axis in percent
+#'
+#' @import ggplot2
+#'
+#' @return ggplot plot
+#' @export
+stackedbarplot_plot <- function(df, percent =  T) {
+  suffix = NULL
+  if (percent) {
+    df$ratio.over.cases <- 100*df$ratio.over.cases
+    suffix = "%"
+  }
+  p <- df %>%
+    ggplot(aes(x = Country.Region, y = ratio.over.cases, fill = status,
+               text = paste0("percentage: ", round(ratio.over.cases, 1), suffix,"</br>",
+               label = paste("count: ",
+                             formatC(countstatus, format = "f", big.mark = ",", digits  = 0)))))+
+    basic_plot_theme() +
+    geom_col(position = position_stack(reverse = TRUE)) +
+    theme(
+      axis.text.x = element_text(angle = 30)
+    )
+  if (percent) {
+    p <- p + scale_y_continuous(labels = function(x) paste0(x, "%"))
+  }
+  # p = p %>%
+  #   fix_colors()
+  p
+}
+
 #' Time evolution as line plot
 #'
 #' @rdname time_evol_line_plot

R/utils.R

@@ -195,3 +195,16 @@ align_country_names_pop_reverse <- function(data){
     )
   data
 }
+#' clean ggplotly legend
+#' @param .plotly_x ggplotly object
+#' @param .extract_str regular expression
+#' @import stringr
+clean_plotly_leg <- function(.plotly_x, .extract_str) {
+  # Inpects an x$data list in a plotly object, cleans up legend values where appropriate
+  if ("legendgroup" %in% names(.plotly_x)) {
+    # The list includes a legend group
+    .plotly_x$legendgroup <- stringr::str_extract(.plotly_x$legendgroup, .extract_str)
+    .plotly_x$name <- stringr::str_extract(.plotly_x$name, .extract_str)
+  }
+  .plotly_x
+}

man-roxygen/ex-mod_stackedbarplot_status.R

@@ -0,0 +1,27 @@
+if (interactive()) {
+  library(shiny)
+  library(Covid19)
+  library(dplyr)
+  library(tidyr)
+  library(ggplot2)
+  library(plotly)
+
+  ui <- fluidPage(
+    tagList(
+      Covid19:::golem_add_external_resources(),
+      Covid19:::mod_stackedbarplot_ui("plot", 5)
+    )
+  )
+  server <- function(input, output, session) {
+
+    orig_data_aggregate = reactive({get_timeseries_full_data() %>%
+      get_timeseries_by_contagion_day_data() %>%
+      aggregate_province_timeseries_data() %>%
+      arrange(Country.Region)})
+
+    callModule(Covid19:::mod_stackedbarplot_status_server, "plot", orig_data_aggregate)
+
+  }
+  runApp(shinyApp(ui = ui, server = server), launch.browser = TRUE)
+}
+