Merge pull request #182 from ldecicco-USGS/master

More style cleanups

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: toxEval
 Type: Package
 Title: ToxCast Evaluations
-Version: 0.3.3
-Date: 2017-04-28
+Version: 0.3.4
+Date: 2017-05-02
 Authors@R: c( person("Steven", "Corsi", role = c("aut"),
     email = "[email protected]"),
     person("Laura", "DeCicco", role = c("aut","cre"),

R/plot_chemical_boxplots.R

@@ -4,6 +4,7 @@
 #' @param chemicalSummary data frame from \code{graph_chem_data}
 #' @param manual_remove vector of categories to remove
 #' @param mean_logic logical \code{TRUE} is mean, \code{FALSE} is maximum
+#' @param plot_ND logical whether or not to plot the non-detects
 #' @export
 #' @import ggplot2
 #' @importFrom stats median quantile
@@ -32,7 +33,8 @@
 #' plot_chemical_boxplots(chemicalSummary)
 plot_chemical_boxplots <- function(chemicalSummary, 
                                    manual_remove=NULL,
-                                   mean_logic = FALSE){
+                                   mean_logic = FALSE,
+                                   plot_ND = TRUE){
 
   site <- EAR <- sumEAR <- meanEAR <- groupCol <- nonZero <- ".dplyr"
   chnm <- Class <- maxEAR <- ".dplyr"
@@ -41,16 +43,20 @@ plot_chemical_boxplots <- function(chemicalSummary,
                 "#FFFF00","#78C15A","#79AEAE","#FF0000","#00FF00","#B1611D",
                 "#FFA500","#F4426e", "#800000", "#808000")
 
+  if(!plot_ND){
+    chemicalSummary <- chemicalSummary[chemicalSummary$EAR > 0,]
+  }
+
   if(length(unique(chemicalSummary$Class)) > length(cbValues)){
     n <- length(unique(chemicalSummary$Class))
 
     if(n > 20 & n<30){
       cbValues <- c(brewer.pal(n = 12, name = "Set3"),
                     brewer.pal(n = 8, name = "Set2"),
-                    brewer.pal(n = n-20, name = "Set1"))
+                    brewer.pal(n = max(c(3,n-20)), name = "Set1"))
     } else if (n <= 20){
       cbValues <- c(brewer.pal(n = 12, name = "Set3"),
-                    brewer.pal(n = n-12, name = "Set2"))     
+                    brewer.pal(n =  max(c(3,n-12)), name = "Set2"))     
     } else {
       cbValues <- colorRampPalette(brewer.pal(11,"Spectral"))(n)
     }

R/plot_group_boxplots.R

@@ -5,6 +5,7 @@
 #' @param category either "Biological", "Chemical Class", or "Chemical"
 #' @param manual_remove vector of categories to remove
 #' @param mean_logic logical \code{TRUE} is mean, \code{FALSE} is maximum
+#' @param plot_ND logical whether or not to plot the non-detects
 #' @export
 #' @import ggplot2
 #' @importFrom stats median
@@ -35,19 +36,23 @@
 plot_tox_boxplots <- function(chemicalSummary, 
                               category = "Biological",
                               manual_remove = NULL,
-                              mean_logic = FALSE){
+                              mean_logic = FALSE,
+                              plot_ND = TRUE){
 
   match.arg(category, c("Biological","Chemical Class","Chemical"))
 
   site <- EAR <- sumEAR <- meanEAR <- groupCol <- nonZero <- ".dplyr"
 
   if(category == "Chemical"){
 
-    chemPlot <- plot_chemical_boxplots(chemicalSummary, mean_logic = mean_logic)
+    chemPlot <- plot_chemical_boxplots(chemicalSummary, mean_logic = mean_logic, plot_ND = plot_ND)
     return(chemPlot)
 
   } else {
 
+    if(!plot_ND){
+      chemicalSummary <- chemicalSummary[chemicalSummary$EAR > 0,]
+    }
     single_site <- length(unique(chemicalSummary$site)) == 1
 
     bioPlot <- ggplot()+

R/plot_heat_chemical.R

@@ -98,6 +98,7 @@ plot_heat_chemicals <- function(graphData, chem_site){
 #' @param category either "Biological", "Chemical Class", or "Chemical"
 #' @param manual_remove vector of categories to remove
 #' @param mean_logic logical \code{TRUE} is mean, \code{FALSE} is maximum
+#' @param plot_ND logical whether or not to plot the non-detects
 #' @export
 #' @import ggplot2
 #' @importFrom stats median
@@ -157,12 +158,18 @@ plot_tox_heatmap <- function(chemicalSummary,
                              chem_site, 
                              category = "Biological",
                              manual_remove = NULL,
-                             mean_logic = FALSE){
+                             mean_logic = FALSE,
+                             plot_ND = TRUE){
 
   match.arg(category, c("Biological","Chemical Class","Chemical"))
 
   SiteID <- site_grouping <- `Short Name` <- chnm <- maxEAR <- ".dplyr"
   site <- EAR <- sumEAR <- meanEAR <- ".dplyr"
+
+  if(!plot_ND){
+    chemicalSummary <- chemicalSummary[chemicalSummary$EAR > 0,]
+  }
+
   if(category == "Chemical"){
     graphData <- graph_chem_data(chemicalSummary, mean_logic=mean_logic)
     plot_back <- plot_heat_chemicals(graphData=graphData, chem_site=chem_site)

inst/shiny/boxPlot.R

@@ -1,6 +1,8 @@
 output$graphGroup <- renderPlot({ 
 
   catType = as.numeric(input$radioMaxGroup)
+
+  plot_ND = input$plot_ND
 
   chemicalSummary <- chemicalSummary()
 
@@ -12,7 +14,8 @@ output$graphGroup <- renderPlot({
 
   bioPlot <- plot_tox_boxplots(chemicalSummary, 
                                category = category,
-                               mean_logic = as.logical(input$meanEAR))
+                               mean_logic = as.logical(input$meanEAR),
+                               plot_ND = plot_ND)
 
   if(catType == 2){
     ggsave("boxPlot.png",

inst/shiny/heatMap.R

@@ -3,7 +3,7 @@ output$graphHeat <- renderPlot({
   validate(
     need(!is.null(input$data), "Please select a data set")
   )
-
+  plot_ND = input$plot_ND_heat
   catType = as.numeric(input$radioMaxGroup)
 
   chemicalSummary <- chemicalSummary()
@@ -22,7 +22,8 @@ output$graphHeat <- renderPlot({
 
   heatMap <- plot_tox_heatmap(chemicalSummary,
                               chem_site,
-                              category = c("Biological","Chemical","Chemical Class")[catType])
+                              category = c("Biological","Chemical","Chemical Class")[catType],
+                              plot_ND = plot_ND)
 
   ggsave("heatPlot.png",heatMap,bg = "transparent")
 
@@ -31,11 +32,9 @@ output$graphHeat <- renderPlot({
 })
 
 output$graphHeat.ui <- renderUI({
-  # heightOfGraph <- 500
-  # if(as.numeric(input$radioMaxGroup) == 2){
-  #   heightOfGraph <- 800
-  # }
-  plotOutput("graphHeat", width = "100%")
+  height <- PlotHeight()
+
+  plotOutput("graphHeat", height = height, width = 800)
 })
 
 output$downloadHeatPlot <- downloadHandler(

inst/shiny/ui.R

@@ -140,8 +140,8 @@ body <- dashboardBody(
     ),
     tabPanel(title = tagList("Box Plots", shiny::icon("bar-chart")),
              value="summary",
+             checkboxInput("plot_ND", "Plot ND's?", TRUE),
              uiOutput("graphGroup.ui"),
-             # div(style = 'overflow-y: scroll', uiOutput("graphGroup.ui")),
             downloadButton('downloadBoxPlot', 'Download PNG')
     ),
     tabPanel(title = tagList("Bar Charts", shiny::icon("bar-chart")),
@@ -176,6 +176,7 @@ body <- dashboardBody(
     ),
     tabPanel(title = tagList("Heat Map", shiny::icon("bar-chart")),
                    value="heat",
+             checkboxInput("plot_ND_heat", "Plot ND's?", TRUE),
                    uiOutput("graphHeat.ui"),
              downloadButton('downloadHeatPlot', 'Download PNG')
     )