Update with 22/23 data and convert chart from plotly to highcharter

.gitignore

@@ -8,6 +8,7 @@ allergies_chart.Rproj
 deploying_app.R
 testing.R
 create_credentials.R
+credentials.R
 
 # packrat library folder (automatically added due to packract being initialised)
 packrat/lib*/
@@ -21,6 +22,9 @@ www/
 # folder created when deploying an app #
 rsconnect/
 
+# admin folder #
+admin/
+
 # Common text files that may contain data #
 *.[cC][sS][vV]
 *.[tT][xX][tT]

data_preparation.R

@@ -2,13 +2,15 @@
 library(tidyr)
 library(dplyr)
 
-data_allergy <- readRDS("/PHI_conf/ScotPHO/Website/Topics/Allergy/sept2022_update/allergy_scotland_chart.rds") %>%
+filepath <- "/PHI_conf/ScotPHO/Website/Charts/Health Conditions/Allergic Conditions/"
+
+data_allergy <- readRDS(paste0(filepath, "allergy_scotland_chart.rds")) |> 
   mutate(rate = round(rate, 1), # round numbers more (one decimal place)
          numerator = case_when(numerator < 5 ~ NA_real_,
-                               TRUE ~ numerator)) %>%  # supression of under 5
-  gather(measure, value, -c(type, year)) %>%
+                               TRUE ~ numerator))  |>   # supression of under 5
+  gather(measure, value, -c(type, year))  |> 
   mutate(measure = recode(measure, "numerator" = "Number", "rate" = "Rate"))
 
-saveRDS(data_allergy, "shiny_app/allergy_scotland_chart.rds")
+saveRDS(data_allergy, paste0(filepath, "allergy_scotland_chart.rds"))
 
-## END
+## END

shiny_app/global.R

@@ -6,18 +6,14 @@
 
 library(dplyr) #data manipulation
 library(plotly) #charts
+library(highcharter) #charts
 library(shiny)
 library(shinymanager)
+library(phsstyles) #chart colours
 
 data_allergy <- readRDS("allergy_scotland_chart.rds")
 
 #Use for selection of conditions
 condition_list <- sort(unique(data_allergy$type))
 
-#ScotPHO logo. 
-#Needs to be https address or if local in code 64 (the latter does not work with 4.7 plotly)
-scotpho_logo <-  list(source ="https://raw.githubusercontent.com/ScotPHO/plotly-charts/master/scotpho.png",
-                      xref = "paper", yref = "paper",
-                      x= -0.09, y= 1.2, sizex = 0.22, sizey = 0.18, opacity = 1)
-
 ## END

shiny_app/server.R

@@ -1,18 +1,18 @@
 ############################.
 ## Server ----
 ############################.
-credentials_allergy <- readRDS("credentials.rds")
+#credentials_allergy <- readRDS("admin/credentials.rds")
 
 function(input, output) {
 
-  # Shinymanager Auth
-  res_auth <- secure_server(
-    check_credentials = check_credentials(credentials_allergy)
-  )
-
-  output$auth_output <- renderPrint({
-    reactiveValuesToList(res_auth)
-  })
+  # # Shinymanager Auth
+  # res_auth <- secure_server(
+  #   check_credentials = check_credentials(credentials_allergy)
+  # )
+  # 
+  # output$auth_output <- renderPrint({
+  #   reactiveValuesToList(res_auth)
+  # })
 
   # Allowing user to download data
   output$download_data <- downloadHandler( 
@@ -21,29 +21,22 @@ function(input, output) {
 
   ############################.
   #Visualization
-  output$chart <- renderPlotly({
+  output$line_chart <- renderHighchart({
 
     #Data for condition
-    data_condition <- data_allergy %>% subset(type %in% input$conditions & measure==input$measure)
+    data_condition <- data_allergy |> subset(type %in% input$conditions & measure == input$measure)
 
     #y axis title
     yaxistitle <- case_when(input$measure == "Number" ~ "Number of hospital admissions",
                             input$measure == "Rate" ~ "Hospital admissions <br>per 100,000 population")
 
-    plot <- plot_ly(data=data_condition, x=~year, y = ~value, color = ~type,
-                    colors = c('#abd9e9', '#74add1', '#4575b4', '#313695', '#022031'),
-                    type = "scatter", mode = 'lines',
-                    width = 650, height = 350) %>% 
-      #Layout
-      layout(annotations = list(), #It needs this because of a buggy behaviour
-             yaxis = list(title = yaxistitle, rangemode="tozero", fixedrange=TRUE), 
-             xaxis = list(title = "Financial year",  fixedrange=TRUE, tickangle = 270),  
-             font = list(family = 'Arial, sans-serif'), #font
-             margin = list(pad = 4, t = 50, r = 30), #margin-paddings
-             hovermode = 'false',  # to get hover compare mode as default
-             images = scotpho_logo) %>% 
-      config(displayModeBar= T, displaylogo = F) # taking out plotly logo and collaborate button
-  }
-  ) 
+    data_condition |> 
+      hchart("line", hcaes(y = value, x = year, group = type)) |> 
+      hc_colors(c('#abd9e9', '#74add1', '#4575b4', '#313695', '#022031')) |> 
+      hc_xAxis(title = list(text = "Year")) |> 
+      hc_yAxis(title = list(text = yaxistitle), min = 0) |> 
+      hc_legend(align = "left", verticalAlign = "top")
+
+  })
 
-} # end of server part
+} # end of server part

shiny_app/ui.R

@@ -3,7 +3,7 @@
 ############################.
 #Height and widths as percentages to allow responsiveness
 #Using divs as issues with classing css 
-secure_app(
+#secure_app(
 fluidPage(style="width: 650px; height: 500px; ", 
                 div(style= "width:100%", #Filters on top of page
                     h4("Chart 1. Hospital admissions for different allergic conditions"),
@@ -12,14 +12,15 @@ fluidPage(style="width: 650px; height: 500px; ",
                                     choices = c("Number", "Rate"), selected = "Rate")
                     ),
                     div(style = "width: 50%; float: left;",
-                        selectizeInput("conditions", label = "Select one or more allergic conditions (up to four)", 
+                        selectizeInput("conditions", label = "Select up to four allergic conditions", 
                                        choices = condition_list, multiple = TRUE, selected = "All allergies",
                                        options = list(maxItems =4L)))
                 ),
                 div(style= "width:100%; float: left;", #Main panel
-                    plotlyOutput("chart", width = "100%", height = "350px"),
+                    #plotlyOutput("chart", width = "100%", height = "350px"),
+                    highchartOutput("line_chart"),
                     p(div(style = "width: 25%; float: left;", #Footer
-                          HTML("Source: <a href='https://beta.isdscotland.org/find-publications-and-data/health-services/hospital-care/'>PHS, SMR 01</a>")),
+                          HTML("Source: <a href='https://publichealthscotland.scot/resources-and-tools/health-intelligence-and-data-management/national-data-catalogue/national-datasets/search-the-datasets/general-acute-inpatient-and-day-case-scottish-morbidity-record-smr01/' target='_blank'>PHS, SMR 01</a>")),
                       div(style = "width: 25%; float: left;",
                           downloadLink('download_data', 'Download data')),
                       div(style = "width: 100%; float: left;",
@@ -30,4 +31,4 @@ fluidPage(style="width: 650px; height: 500px; ",
                     )
                 )
 )#fluid page bracket
-)
+#)