Merge pull request #177 from ldecicco-USGS/master

tests, stop button, Rdata
DOI-USGS · Apr 12, 2017 · 3036bf8 · 3036bf8
2 parents 55c9eb4 + b7f6c3b
commit 3036bf8
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Showing 10 changed files with 144 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,8 @@ Imports:
     data.table,
     RColorBrewer,
     stringi,
-    readxl
+    readxl,
+    tools
 Suggests:
     rmarkdown,
     testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -67,3 +67,4 @@ importFrom(stringi,stri_trans_totitle)
 importFrom(tidyr,gather)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
+importFrom(tools,file_ext)
diff --git a/R/explore_endpoints.R b/R/explore_endpoints.R
@@ -5,6 +5,7 @@
 #' @param browse use browser for map rendering
 #' @export
 #' @importFrom shiny runApp
+#' @importFrom tools file_ext
 #' @importFrom leaflet leaflet
 #' @importFrom leaflet addLegend
 #' @importFrom leaflet addCircles

diff --git a/R/plot_tox_endpoints.R b/R/plot_tox_endpoints.R
@@ -32,6 +32,8 @@
 #'                                         chem_site, 
 #'                                         chem_info)
 #'  plot_tox_endpoints(chemicalSummary, filterBy = "Cell Cycle")
+#'  plot_tox_endpoints(chemicalSummary, category = "Chemical Class", filterBy = "PAH")
+#'  plot_tox_endpoints(chemicalSummary, category = "Chemical", filterBy = "Atrazine")
 plot_tox_endpoints <- function(chemicalSummary, 
                               category = "Biological",
                               filterBy = "All",

diff --git a/inst/shiny/getData.R b/inst/shiny/getData.R
@@ -2,13 +2,21 @@ rawData <- reactive({
   if(!is.null(input$data)){
 
     path <- file.path(input$data$datapath)
+
     newPath <- paste0(input$data$datapath,"_",input$data$name)
     newPath <- gsub(", ","_",newPath)
+
     file.rename(from = path, to = newPath)
 
-    chem_data <- read_excel(newPath, sheet = "Data")
-    chem_info <- read_excel(newPath, sheet = "Chemicals") 
-    chem_site <- read_excel(newPath, sheet = "Sites")
+    if(tools::file_ext(input$data$name) == "xlsx" |
+       tools::file_ext(input$data$name) == "xls"){
+      chem_data <- read_excel(newPath, sheet = "Data")
+      chem_info <- read_excel(newPath, sheet = "Chemicals") 
+      chem_site <- read_excel(newPath, sheet = "Sites")     
+    } else if(tools::file_ext(input$data$name) == "RData" | 
+              tools::file_ext(input$data$name) == "rds"){
+      load(newPath)
+    }
 
     rawData <- list(chem_data=chem_data,
                     chem_info=chem_info,

diff --git a/inst/shiny/mapStuff.R b/inst/shiny/mapStuff.R
@@ -80,7 +80,7 @@ observe({
     clearMarkers() %>%
     clearControls() %>%
     addCircleMarkers(lat=~dec_lat, lng=~dec_lon,
-                     popup=paste0('<b>',mapData$`Short Name`,"</b><br/><table>",
+                     popup=paste0('<b>',mapData$site,"</b><br/><table>",
                                   "<tr><td>",maxEARWords,": </td><td>",sprintf("%.1f",mapData$meanMax),'</td></tr>',
                                   "<tr><td>Number of Samples: </td><td>",mapData$nSamples,'</td></tr>',
                                   # "<tr><td>Frequency: </td><td>",sprintf("%.1f",mapData$freq),'</td></tr>',

diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -50,6 +50,10 @@ flags <- c( "OneAbove","Noisy","HitCall")
 
 shinyServer(function(input, output,session) {
 
+  observe({
+    if (input$close > 0) stopApp()    
+  })
+
   source("getData.R",local=TRUE)$value
 
   chemicalSummary <- reactive({

diff --git a/inst/shiny/ui.R b/inst/shiny/ui.R
@@ -57,7 +57,13 @@ header <- dashboardHeader(title = "toxEval")
 
 sidebar <- dashboardSidebar(
   sidebarMenu(
-
+   tags$button(
+      id = 'close',
+      type = "button",
+      class = "btn action-button",
+      onclick = "setTimeout(function(){window.close();},500);",  # close browser
+      "Stop ToxEval"
+    ),
    fileInput("data", "Load Excel File",multiple = FALSE),
    radioButtons("radioMaxGroup", label = "",
                 choices = list("Group" = 1, "Chemical" = 2, "Class" = 3), 

diff --git a/man/plot_tox_endpoints.Rd b/man/plot_tox_endpoints.Rd
diff --git a/tests/testthat/tests_summary.R b/tests/testthat/tests_summary.R
@@ -99,6 +99,26 @@ test_that("Plotting stacked summaries", {
 
 })
 
+test_that("Plotting endpoints", {
+  testthat::skip_on_cran()
+
+  bioStackPlot <- suppressWarnings(plot_tox_endpoints(chemicalSummary, 
+                                  category = "Biological",
+                                  filterBy = "Cell Cycle"))
+  expect_true(all(names(bioStackPlot$data) %in% c("site","category","endPoint",
+                                                  "meanEAR")))
+
+  classStackPlot <- suppressWarnings(plot_tox_endpoints(chemicalSummary, 
+                                    category = "Chemical Class", filterBy = "PAH"))
+  expect_true(all(names(classStackPlot$data) %in% c("site","category","endPoint",
+                                                    "meanEAR")))
+
+  chemStackPlot <- suppressWarnings(plot_tox_endpoints(chemicalSummary, category = "Chemical", filterBy = "Atrazine"))
+  expect_true(all(names(chemStackPlot$data) %in% c("site","category","endPoint",
+                                                   "meanEAR")))
+
+})
+
 
 test_that("Internal table functions", {
   testthat::skip_on_cran()
@@ -130,4 +150,97 @@ test_that("Map stuff functions", {
                             category = "Biological")
   expect_type(mapDataList, "list")
   expect_equal(length(mapDataList), 2)
+})
+
+test_that("Table endpoint hits", {
+  testthat::skip_on_cran()
+
+  bt <- table_endpoint_hits(chemicalSummary, category = "Biological")
+  expect_type(bt, "list")
+  expect_true(all(names(bt$x$data) %in% c("endPoint","Nuclear Receptor","DNA Binding",
+                                  "Phosphatase","Steroid Hormone","Esterase")))
+
+  expect_error(table_endpoint_hits(chemicalSummary, category = "Class"))
+
+  ct <- table_endpoint_hits(chemicalSummary, category = "Chemical Class")
+  expect_type(ct, "list")
+
+  expect_true(all(names(ct$x$data) %in% c("endPoint","Antioxidant",
+                                          "Detergent Metabolites","Herbicide",
+                                          "Plasticizer")))
+
+  cht <- table_endpoint_hits(chemicalSummary, category = "Chemical")
+  expect_type(cht, "list")
+
+  expect_true(all(names(cht$x$data) %in% c("endPoint","Bisphenol A",
+                                           "4-Nonylphenol, branched","Triphenyl phosphate",
+                                           "Metolachlor","Atrazine")))
+})
+
+test_that("table_tox_endpoint", {
+  testthat::skip_on_cran()
+
+  bt <- table_tox_endpoint(chemicalSummary, category = "Biological")
+  expect_type(bt, "list")
+  expect_true("nSites" %in% names(bt$x$data))
+
+  expect_error(table_tox_endpoint(chemicalSummary, category = "Class"))
+
+  ct <- table_tox_endpoint(chemicalSummary, category = "Chemical Class")
+  expect_type(ct, "list")
+
+  expect_true(all(names(ct$x$data) %in% c(" ","Nuclear Receptor","DNA Binding",
+                                          "Phosphatase","Esterase","Steroid Hormone",
+                                          "Zebrafish")))
+
+  cht <- table_tox_endpoint(chemicalSummary, category = "Chemical")
+  expect_type(cht, "list")
+
+  expect_true(all(names(cht$x$data) %in% c(" ","Nuclear Receptor","DNA Binding",
+                                           "Phosphatase","Esterase","Steroid Hormone",
+                                           "Zebrafish")))
+})
+
+
+test_that("table_tox_sum", {
+  testthat::skip_on_cran()
+
+  bt <- table_tox_sum(chemicalSummary, category = "Biological")
+  expect_type(bt, "list")
+  expect_true(all(c("site","category","Hits.per.Sample","Individual.Hits","nSamples") %in% names(bt$x$data)))
+
+  expect_error(table_tox_sum(chemicalSummary, category = "Class"))
+
+  ct <- table_tox_sum(chemicalSummary, category = "Chemical Class")
+  expect_type(ct, "list")
+
+  expect_true(all(names(ct$x$data) %in% c("site","category","Hits.per.Sample","Individual.Hits","nSamples")))
+
+  cht <- table_tox_sum(chemicalSummary, category = "Chemical")
+  expect_type(cht, "list")
+
+  expect_true(all(names(cht$x$data) %in% c("site","category","Hits.per.Sample","Individual.Hits","nSamples")))
+})
+
+test_that("table_tox_rank", {
+  testthat::skip_on_cran()
+
+  bt <- table_tox_rank(chemicalSummary, category = "Biological")
+  expect_type(bt, "list")
+  expect_true("site" %in% names(bt$x$data))
+
+  expect_error(table_tox_rank(chemicalSummary, category = "Class"))
+
+  ct <- table_tox_rank(chemicalSummary, category = "Chemical Class")
+  expect_type(ct, "list")
+
+  expect_true(all(c("site","Antioxidant maxEAR","Antioxidant freq",
+                    "Herbicide maxEAR","Herbicide freq",
+                    "Detergent Metabolites maxEAR","Detergent Metabolites freq") %in% names(ct$x$data)))
+
+  cht <- table_tox_rank(chemicalSummary, category = "Chemical")
+  expect_type(cht, "list")
+
+  expect_true(all(c("site","Bisphenol A maxEAR","Bisphenol A freq",
+                    "4-Nonylphenol, branched maxEAR") %in% names(cht$x$data)))
 })