Merge branch 'master' of https://github.com/Flavjack/GerminaR

NEWS.md

@@ -10,6 +10,7 @@
 - Include examples in the functions
 - Update vignettes
 - Update functions to tidyverse.
+- Conditional data viewer in the app.
 
 ## Bug fixes
 

R/fplot.R

@@ -115,8 +115,8 @@ fplot <- function(data
 
   # -------------------------------------------------------------------------
 
-  min_value <- min(plot_dt$min)
-  max_value <- max(plot_dt$max)
+  min_value <- min(plot_dt$min, na.rm = TRUE)
+  max_value <- max(plot_dt$max, na.rm = TRUE)
 
   if ( is.null(brakes) ) { brakes <- abs(round(max_value*1.2, 1))/5 } 
 

R/ger_intime.R

@@ -16,19 +16,19 @@
 #' 
 #' library(GerminaR)
 #' data <- prosopis
-#' grt <- ger_intime(Factor = "nacl"
+#' grt <- ger_intime(Factor = "temp"
 #'                   , SeedN = "seeds"
 #'                   , evalName = "D"
-#'                   , method = "relative"
+#'                   , method = "rel"
 #'                   , data = data
-#'                   )
+#'                   ) 
 #' head(grt, 10)
 #'  
 #' fplot(data = grt
 #'       , type = "line"
 #'       , x = "evaluation"
 #'       , y = "mean"
-#'       , groups = "nacl"
+#'       , groups = "temp"
 #'       , sig = NULL
 #'       ) 
 
@@ -74,22 +74,21 @@ ger_intime <- function(Factor
       pivot_longer(names(evd)
                   , names_to = "evaluation"
                   , values_to = "germination"
+                  , values_drop_na = TRUE
                   ) %>% 
       group_by(.data[[Factor]], evaluation) %>% 
-      summarise(mean = mean(germination)
+      summarise(mean = mean(germination, rm.na = TRUE)
                , r = dplyr::n()
                , std = sd(germination)
                , min = min(germination)
                , max = max(germination)
                ) %>% 
       ungroup() %>% 
-      mutate(ste = std/sqrt(r)) %>% 
+      mutate(ste = std/sqrt(r)) %>%
       mutate(evaluation = gsub("\\D", "", evaluation)) %>% 
       mutate(across(evaluation, ~ as.numeric(.))) %>% 
       arrange(evaluation) %>% 
-      mutate(across( {{Factor}},  ~ as.factor(.))) %>% 
-      mutate(across(where(is.numeric), ~replace(., is.na(.), 0))) %>% 
-      mutate(across(where(is.numeric), ~replace(., is.nan(.), 0)))
+      mutate(across( {{Factor}},  ~ as.factor(.))) 
 
 # result ------------------------------------------------------------------
 

inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf

@@ -5,9 +5,9 @@ account: flavjack
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 136814
-bundleId: 3491410
+bundleId: 3501356
 url: https://flavjack.shinyapps.io/germinaquant/
-when: 1596923423.23757
+when: 1597144329.23554
 asMultiple: FALSE
 asStatic: FALSE
 ignoredFiles: setup.R

inst/GerminaQuant/server.R

@@ -16,8 +16,8 @@ library(shinydashboard)
 library(shinyWidgets)
 library(gsheet)
 library(readxl)
-library(DT)
 library(ggpubr)
+library(DT)
 
 # app ---------------------------------------------------------------------
 # -------------------------------------------------------------------------
@@ -60,16 +60,68 @@ shinyServer(function(input, output) {
 
   }, ignoreNULL = FALSE)
 
-
-# -------------------------------------------------------------------------
 
-output$fbook <- renderUI({
+# data viewer -------------------------------------------------------------
+# -------------------------------------------------------------------------
+
+output$fb_excel <- DT::renderDataTable(server = FALSE, {
+
+    DT::datatable(data = data_fb(),
+                filter = 'top',
+                extensions = c('Buttons', 'Scroller'),
+                rownames = FALSE,
+
+                options = list(
+
+                  searchHighlight = TRUE,
+                  searching = TRUE,
+
+                  dom = 'Bfrtip',
+                  buttons = list(
+                    'copy',
+                    list(extend = 'csv', filename = input$stat_rsp),
+                    list(extend = 'excel', filename = input$stat_rsp)
+                  ),
+
+                  autoWidth = TRUE,
+                  columnDefs = list(list(className = 'dt-center', targets ="_all")),
+                  deferRender=TRUE,
+                  scrollY = 400,
+                  scrollX = TRUE,
+                  scroller = TRUE,
+
+                  initComplete = DT::JS(
+                    "function(settings, json) {",
+                    "$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
+                    "}")
+                ))
+  })
 
-  gss <- tags$iframe(src = input$import_gsheet,
-    style="height:450px; width:100%; scrolling=no")
+# -------------------------------------------------------------------------
 
-  print(gss)
+output$fb_gsheets <- renderUI({
+
+  tags$iframe(src = input$import_gsheet,
+              style="height:450px; width:100%; scrolling=no")
+
+})
+
+output$data_viewer <- renderUI({
+
+  if ( !is.null(input$import_excel) & input$import_gsheet != "" ) {
+
+    DT::dataTableOutput("fb_excel")
 
+  } else if ( input$import_gsheet != "" ) {
+
+    htmlOutput("fb_gsheets")
+
+  } else if ( !is.null(input$import_excel) ) {
+
+    DT::dataTableOutput("fb_excel")
+
+  } else { "Insert a Google spreadsheet URL or xlsx file" }
+
 })
 
 # filter ------------------------------------------------------------------

inst/GerminaQuant/setup.R

@@ -20,7 +20,7 @@ cran <- c("devtools"
 
 git <- c(
   "Flavjack/GerminaR"
-)
+  )
 
 installed <- c(cran, sub(".*/", "", git)) %in% rownames(installed.packages())
 
@@ -41,3 +41,5 @@ rm(cran, git, installed)
 # open https://shiny.rstudio.com/tutorial/written-tutorial/lesson3/
 
 # http://r-pkgs.had.co.nz/release.html
+
+# open https://realfavicongenerator.net/

inst/GerminaQuant/ui.R

@@ -16,8 +16,8 @@ library(shinydashboard)
 library(shinyWidgets)
 library(gsheet)
 library(readxl)
-library(DT)
 library(ggpubr)
+library(DT)
 
 # app ---------------------------------------------------------------------
 # -------------------------------------------------------------------------
@@ -50,14 +50,14 @@ shinyUI(dashboardPage(skin = "green",
       ),
 
       tags$head(includeHTML(("www/analytics.html"))),
-      tags$head(tags$link(rel="shortcut icon", href="https://flavjack.shinyapps.io/germinaquant/_w_6f298bc3/icon.png")),
-      
+      tags$head(tags$link(rel="shortcut icon", href="https://raw.githubusercontent.com/Flavjack/GerminaR/master/inst/GerminaQuant/www/favicon/android-chrome-256x256.png")),
+
       meta() %>%
         meta_social(
           title = "GerminaR",
           description = "Indices and Graphics for Assess Seed Germination Process",
           url = "https://flavjack.shinyapps.io/germinaquant/",
-          image = "https://flavjack.shinyapps.io/germinaquant/_w_4854280b/icon.png",
+          image = "https://raw.githubusercontent.com/Flavjack/GerminaR/master/inst/GerminaQuant/www/favicon/android-chrome-256x256.png",
           image_alt = "GerminaR"
         ), 
 
@@ -243,7 +243,7 @@ shinyUI(dashboardPage(skin = "green",
           solidHeader = T,
           width = 10,
 
-        htmlOutput("fbook")
+          htmlOutput("data_viewer")
 
         ),
 
@@ -614,7 +614,7 @@ shinyUI(dashboardPage(skin = "green",
             column(width = 12,
 
                    numericInput('plot_width', 'Width (cm)',
-                                value = 15,
+                                value = 20,
                                 min = 5,
                                 step = 5)
 
@@ -799,7 +799,7 @@ tabItem(tabName = "germint",
         column(width = 12,
 
                numericInput('intime_width', 'Width (cm)',
-                            value = 15,
+                            value = 20,
                             min = 5,
                             step = 5)
         ),

inst/GerminaQuant/www/favicon/browserconfig.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="utf-8"?>
+<browserconfig>
+    <msapplication>
+        <tile>
+            <square150x150logo src="/mstile-150x150.png"/>
+            <TileColor>#da532c</TileColor>
+        </tile>
+    </msapplication>
+</browserconfig>

inst/GerminaQuant/www/favicon/icons.html

@@ -0,0 +1,7 @@
+<link rel="apple-touch-icon" sizes="180x180" href="/favicon/apple-touch-icon.png">
+<link rel="icon" type="image/png" sizes="32x32" href="/favicon/favicon-32x32.png">
+<link rel="icon" type="image/png" sizes="16x16" href="/favicon/favicon-16x16.png">
+<link rel="manifest" href="/favicon/site.webmanifest">
+<link rel="mask-icon" href="/favicon/safari-pinned-tab.svg" color="#5bbad5">
+<meta name="msapplication-TileColor" content="#2d89ef">
+<meta name="theme-color" content="#ffffff">

inst/GerminaQuant/www/favicon/site.webmanifest

@@ -0,0 +1,19 @@
+{
+    "name": "GerminaQuant",
+    "short_name": "GerminaQuant",
+    "icons": [
+        {
+            "src": "/android-chrome-192x192.png",
+            "sizes": "192x192",
+            "type": "image/png"
+        },
+        {
+            "src": "/android-chrome-256x256.png",
+            "sizes": "256x256",
+            "type": "image/png"
+        }
+    ],
+    "theme_color": "#ffffff",
+    "background_color": "#ffffff",
+    "display": "standalone"
+}