v1.0.0 - MRA manuscript release

flu-crew · Nov 18, 2021 · 6614f67 · 6614f67
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: octoflushow 
 Title: A Shiny app for the swine surveillence data
-Version: 0.0.0.9000
+Version: 1.0.0
 Authors@R: c( 
         person(given = "Zebulun",
                family = "Arendsee",

diff --git a/R/plots.R b/R/plots.R
@@ -419,7 +419,8 @@ barchart_bytime <- function(df, value="n", variable="H1", palette=octoflushow::g
                             tunit="month",
                             fed=FALSE,
                             xfontsize=10,
-                            yfontsize=10) {
+                            yfontsize=10,
+                            ytitle="Number of Swine Isolates") {
 
   # local format of federal quarter
   format_Q <- function(ddf){
@@ -439,7 +440,7 @@ barchart_bytime <- function(df, value="n", variable="H1", palette=octoflushow::g
   p <- ggplot2::ggplot(data = df, ggplot2::aes_string(x = "Date", y = value, fill = variable)) +
     ggplot2::geom_bar(stat = "identity", position = bartype) +
     ggplot2::scale_fill_manual(values = palette) +
-    ggplot2::labs(y="Number of Swine Isolates", x="", title=title) +
+    ggplot2::labs(y=ytitle, x="", title=title) +
     ggplot2::theme_bw() +
     ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, size = 10, vjust = 0.5),
                    axis.text.y = ggplot2::element_text(size = 10),

diff --git a/README.md b/README.md
@@ -113,3 +113,13 @@ Check the website address see if site is working.
    ```
 
    Click through the [documentation](https://httpd.apache.org/docs/2.4/mod/directives.html) for what the tags mean in `000-default.conf` so you can configure it properly.
+
+# Debugging
+
+If downloading plots returns an HTML file containing the error messages
+"polygon edge not found", then you may need to update the font database. In the
+R shell, run the following command:
+
+```R
+extrafont::font_import()
+```
diff --git a/inst/app/server.R b/inst/app/server.R
@@ -1,9 +1,9 @@
 library(shiny)
+
 require(magrittr)
 
 d <- octoflushow::load_current()
 
-
 # update data in various ways prior to plotting
 plot_munge <- function(d, collapse_n2_clade, collapse_gamma_clade, collapse_c4_clade, global_ha="us"){
   if(collapse_n2_clade){
@@ -39,15 +39,15 @@ server <- function(input, output, session) {
   })
 
   output$time_plot <- renderPlot({
-      print(basic_plot_rct())
+      print(time_plot_rct())
   })
 
   output$hana_time_plot <- renderPlot({
-      print(hana_basic_plot_rct())
+      print(hana_time_plot_rct())
   })
 
   output$triple_time_plot <- renderPlot({
-      print(triple_basic_plot_rct())
+      print(triple_time_plot_rct())
   })
 
   output$state_plot <- renderPlot({
@@ -62,18 +62,18 @@ server <- function(input, output, session) {
     print(constellation_plot_rct())
   })
 
-  basic_plot_rct <- reactive({
+  time_plot_rct <- reactive({
     plot_munge(d_rct(), input$collapse_n2_bar, input$collapse_gamma_bar, input$collapse_c4_bar, input$global_bar) %>%
       octoflushow::plot_basic(floorDateBy=input$floorDateBy, segment=input$segmentChoiceBar)
   })
 
-  hana_basic_plot_rct <- reactive({
-    plot_munge(d_rct(), input$collapse_n2_hana_bar, input$collapse_gamma_hana_bar, input$collapse_c4_hana_bar) %>%
+  hana_time_plot_rct <- reactive({
+    plot_munge(d_rct(), input$collapse_n2_hana_bar, input$collapse_gamma_hana_bar, input$collapse_c4_hana_bar, input$global_hana_bar) %>%
       octoflushow::hana_barplots(floorDateBy=input$floorDateByHanaBar, global=input$global_hana_bar == "global")
   })
 
-  triple_basic_plot_rct <- reactive({
-    plot_munge(d_rct(), input$collapse_n2_triple_bar, input$collapse_gamma_triple_bar, input$collapse_c4_triple_bar) %>%
+  triple_time_plot_rct <- reactive({
+    plot_munge(d_rct(), input$collapse_n2_triple_bar, input$collapse_gamma_triple_bar, input$collapse_c4_triple_bar, input$global_triple_bar) %>%
       octoflushow::triple_barplots(floorDateBy=input$floorDateByTripleBar, global=input$global_triple_bar == "global")
   })
 
@@ -92,47 +92,28 @@ server <- function(input, output, session) {
     octoflushow::plot_constellation()
   })
 
-  output$download_time_plot <- downloadHandler(
-    filename = function(){"swine-survey-time_plot.pdf"},
-    content = function(file){
-        ggplot2::ggsave(file, basic_plot_rct(), device="pdf", width = input$shiny_width_time_plot/72, height = input$shiny_height_time_plot/72)
-    }
-  )
-
-  output$download_hana_time_plot <- downloadHandler(
-    filename = function(){"swine-survey-hana_time_plot.pdf"},
-    content = function(file){
-        ggplot2::ggsave(file, hana_basic_plot_rct(), device="pdf", width = input$shiny_width_time_plot/72, height = input$shiny_height_time_plot/72)
-    }
-  )
+  make_downloader <- function(function_name){
+    reactive_function = get(glue::glue("{function_name}_rct"))
+    width_field = glue::glue("shiny_width_{function_name}")
+    height_field = glue::glue("shiny_height_{function_name}")
+    downloadHandler(
+      filename = function(){glue::glue("swine-survey-{function_name}.pdf")},
+      content = function(file){
+          ggplot2::ggsave(file,
+            reactive_function(),
+            device="pdf",
+            width = input[[width_field]]/72,
+            height = input[[height_field]]/72)
+      }
+    )
+  }
 
-  output$download_triple_time_plot <- downloadHandler(
-    filename = function(){"swine-survey-triple_time_plot.pdf"},
-    content = function(file){
-        ggplot2::ggsave(file, triple_basic_plot_rct(), device="pdf", width = input$shiny_width_time_plot/72, height = input$shiny_height_time_plot/72)
-    }
-  )
-
-  output$download_state_plot <- downloadHandler(
-    filename = function(){"swine-survey-state_plot.pdf"},
-    content = function(file){
-      ggplot2::ggsave(file, state_plot_rct(), device="pdf", width = input$shiny_width_state_plot/72, height = input$shiny_height_state_plot/72)
-    }
-  )
-
-  output$download_heatmap_plot <- downloadHandler(
-    filename = function(){"swine-survey-heatmap_plot.pdf"},
-    content = function(file){
-      ggplot2::ggsave(file, heatmap_plot_rct(), device="pdf", width = input$shiny_width_heatmap_plot/72, height = input$shiny_height_heatmap_plot/72)
-    }
-  )
-
-  output$download_constellation_plot <- downloadHandler(
-    filename = function(){"swine-survey-constellation_plot.pdf"},
-    content = function(file){
-      ggplot2::ggsave(file, constellation_plot_rct(), device="pdf", width = input$shiny_width_constellation_plot/72, height = input$shiny_height_constellation_plot/72)
-    }
-  )
+  output$download_time_plot <- make_downloader("time_plot")
+  output$download_hana_time_plot <- make_downloader("hana_time_plot")
+  output$download_triple_time_plot <- make_downloader("triple_time_plot")
+  output$download_state_plot <- make_downloader("state_plot")
+  output$download_heatmap_plot <- make_downloader("heatmap_plot")
+  output$download_constellation_plot <- make_downloader("constellation_plot")
 
   output$downloadExcel <- downloadHandler(
     filename = 'swine-surveillance-data.xlsx',

diff --git a/inst/config.yaml b/inst/config.yaml
@@ -15,6 +15,7 @@ colors:
     pandemic: "#01665e"
     1A.3.3.2: "#01665e"
     gamma2-beta-like: "#8c000a"
+    LAIV: "#8c000a"
     1A.2-3-like:      "#8c000a"
     delta1: "#bf812d"
     1B.2.2: "#bf812d"
@@ -33,6 +34,7 @@ colors:
     3.2010.2: "#996633"
     other-human: "#F90005"
     I:        "#542788"
+    LAIV:     "#542788"
     3.1990.1: "#542788"
     II:        "#d73027"
     3.1990.2 : "#d73027"
@@ -73,6 +75,7 @@ colors:
     Pandemic: "#F03B20"
     Human_seasonal: "#BD2D2B"
     MN99: "#91BFDB"
+    LAIV: "#91BFDB"
     N6: "#FF0000"
 #    No_data: "#EDF881"
   N2:
@@ -102,12 +105,14 @@ colors:
     Human-like: "#969696"
     Human_N2: "#969696"
     TX98: "#FF9F02"
+    LAIV: "#FF9F02"
     unknown: "#800000"
 #    No_data: "#EDF8B1"
   PB2:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "#FF0000"
@@ -116,6 +121,7 @@ colors:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "#FF0000"
@@ -124,6 +130,7 @@ colors:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "###FF0000"
@@ -132,6 +139,7 @@ colors:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "#FF0000"
@@ -140,6 +148,7 @@ colors:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "#FF0000"
@@ -148,6 +157,7 @@ colors:
     PDM: "#762A83"
     TRIG: "#C2A5CF"
     TX98: "#C7EAE5"
+    LAIV: "#C7EAE5"
     Human-seasonal: "#969696"
     Human-seasonal_H3: "#969696"
     classicalSwine: "#FF0000"

diff --git a/man/barchart_bytime.Rd b/man/barchart_bytime.Rd