diff --git a/DESCRIPTION b/DESCRIPTION
index b096c955..d58da749 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: toxEval
Type: Package
Title: ToxCast Evaluations
-Version: 0.1.0
-Date: 2015-08-05
+Version: 0.1.1
+Date: 2015-08-10
Authors@R: c( person("Steven", "Corsi", role = c("aut"),
email = "srcorsi@usgs.gov"),
person("Laura", "DeCicco", role = c("aut","cre"),
diff --git a/inst/shiny/server.R b/inst/shiny/server.R
index 2ce2f8bc..879f46b8 100644
--- a/inst/shiny/server.R
+++ b/inst/shiny/server.R
@@ -58,29 +58,95 @@ interl <- function (a,b) {
c(p1,p2)
}
+makePlots <- function(boxData, noLegend, boxPlot, yRange){
+
+ siteToFind <- unique(boxData$site)
+
+ if(yRange == 0) yRange <- 100
+
+ boxData <- boxData %>%
+ group_by(site,date,cat) %>%
+ summarise(sumEAR=sum(EAR)) %>%
+ data.frame( )%>%
+ mutate(grouping=factor(cat, levels=unique(cat)))
+
+ lowerPlot <- ggplot(boxData)
+
+ if(!boxPlot){
+ lowerPlot <- lowerPlot + geom_point(aes(x=cat, y=sumEAR, color=cat))
+ } else {
+ lowerPlot <- lowerPlot + geom_boxplot(aes(x=cat, y=sumEAR, fill=cat))
+ }
+
+ lowerPlot <- lowerPlot + theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25),
+ legend.position = "none") +
+ xlab("") +
+ geom_hline(yintercept=0.1) +
+ scale_y_log10("sumEAR")
+
+ chemGroupBP_group <- boxData
+
+ uniqueChoices <- as.character(unique(chemGroupBP_group$cat))
+
+ siteLimits <- stationINFO %>%
+ filter(shortName %in% unique(chemGroupBP_group$site))
+
+ if(length(siteToFind) > 1){
+
+ chemGroupBPAllSite <- chemGroupBP_group %>%
+ group_by(site, cat) %>%
+ summarise(maxEAR=max(sumEAR))
+
+ upperPlot <- ggplot(chemGroupBPAllSite, aes(x=site, y=maxEAR, fill = cat)) +
+ geom_bar(stat="identity") +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25,
+ colour=siteLimits$lakeColor)) +
+ scale_x_discrete(limits=siteLimits$Station.shortname) +
+ xlab("") +
+ scale_fill_discrete("") +
+ coord_cartesian(ylim = c(0,yRange))
+
+ if(noLegend){
+ upperPlot <- upperPlot + guides(fill=FALSE)
+ }
+
+ } else {
+
+ chemGroupBPOneSite <- chemGroupBP_group %>%
+ select(-site)
+
+ levels(chemGroupBPOneSite$cat) <- uniqueChoices
+
+ upperPlot <- ggplot(chemGroupBPOneSite, aes(x=date, y=sumEAR, fill = cat)) +
+ geom_bar(stat="identity") +
+ theme(axis.text.x=element_blank(),
+ axis.ticks=element_blank())+
+ xlab("Individual Samples") +
+ scale_fill_discrete(drop=FALSE) +
+ labs(fill="") +
+ coord_cartesian(ylim = c(0,yRange))
+
+ if(noLegend){
+ upperPlot <- upperPlot + guides(fill=FALSE)
+ }
+ }
+
+ return(list(upperPlot=upperPlot, lowerPlot=lowerPlot))
+}
+
shinyServer(function(input, output) {
#############################################################
chemicalSummary <- reactive({
- if(is.null(input$data)){
- chemicalSummary <- rbind(chemicalSummaryWS, chemicalSummaryPS)
+ if(is.null(input$data) | input$data == "Water Sample"){
+ chemicalSummary <- chemicalSummaryWS
} else if (input$data == "Passive Samples"){
chemicalSummary <- chemicalSummaryPS
- } else if (input$data == "Water Sample"){
- chemicalSummary <- chemicalSummaryWS
} else {
chemicalSummary <- rbind(chemicalSummaryWS, chemicalSummaryPS)
}
- if(is.null(input$sites) | input$sites == "All"){
- siteToFind <- summaryFile$site
- } else if (input$sites == "Potential 2016"){
- siteToFind <- df2016$Site
- } else {
- siteToFind <- input$sites
- }
-
chemicalSummary
})
@@ -123,29 +189,6 @@ shinyServer(function(input, output) {
chemicalSummaryFiltered
})
-
- endpointSummary <- reactive({
-
- chemicalSummaryFiltered <- chemicalSummaryFiltered()
-
- if(is.null(input$groupCol)){
- groupCol <- names(endPointInfo)[20]
- } else {
- groupCol <- input$groupCol
- }
-
- if(is.null(input$group)){
- group <- unique(endPointInfo[,20])[3]
- } else {
- group <- input$group
- }
-
- endpointSummary <- chemicalSummaryFiltered %>%
- filter_(paste0(groupCol," == '", group, "'")) %>%
- group_by(site, date) %>%
- summarise(sumEAR = sum(EAR),
- nHits = sum(hits))
- })
statsOfColumn <- reactive({
@@ -247,7 +290,7 @@ shinyServer(function(input, output) {
})
- statsOfGroup <- reactive({
+ statsOfGroupOrdered <- reactive({
if(is.null(input$groupCol)){
groupCol <- names(endPointInfo)[20]
@@ -258,7 +301,7 @@ shinyServer(function(input, output) {
if(is.null(input$sites) | input$sites == "All"){
siteToFind <- summaryFile$site
} else if (input$sites == "Potential 2016"){
- siteToFind <- df2016$Site
+ siteToFind <- df2016$Site
} else {
siteToFind <- input$sites
}
@@ -285,120 +328,38 @@ shinyServer(function(input, output) {
statsOfGroup <- statsOfGroup %>%
mutate(category = choices)
}
-
- statsOfGroup <- statsOfGroup %>%
+
+ statsOfGroupOrdered <- statsOfGroup %>%
group_by(site, date,category) %>%
- summarise(hits = length(category[EAR > 0.1]),
- sumEAR = sum(EAR)) %>%
+ summarise(sumEAR = sum(EAR)) %>%
group_by(site,category) %>%
- summarise(count = sum(hits > 0),
- max = max(sumEAR),
- mean = mean(sumEAR))
-
- statsOfGroup
-
+ summarise(max = sum(sumEAR > 0.1),
+ mean = sum(mean(sumEAR) > 0.1),
+ hit = as.numeric(any(sumEAR > 0.1)) )%>%
+ data.frame()
- })
-
- statsOfGroupOrdered <- reactive({
-
- statsOfGroup <- statsOfGroup()
-
- if(is.null(input$sites) | input$sites == "All"){
- siteToFind <- summaryFile$site
- } else if (input$sites == "Potential 2016"){
- siteToFind <- df2016$Site
- } else {
- siteToFind <- input$sites
- }
-
- statsOfGroup <- statsOfGroup %>%
- filter(site %in% siteToFind)
-
if(length(siteToFind) > 1){
-
- statsOfGroupOrdered <- statsOfGroup %>%
- gather(calc, value, -site, -category) %>%
- unite(choice_calc, category, calc, sep=" ") %>%
- spread(choice_calc, value)
-
- maxCat <- grep("max",names(statsOfGroupOrdered))
-
- maxCatordered <- order(apply(statsOfGroupOrdered[,maxCat], 2, max),decreasing = TRUE)
-
- if(length(maxCat) > 9){
- statsOfGroupOrdered <- statsOfGroupOrdered[,c(1,interl3((maxCat[maxCatordered[1:9]]-1),maxCat[maxCatordered[1:9]],(maxCat[maxCatordered[1:9]]+1)))]
- maxCat <- maxCat[1:9]
- } else {
- if(length(maxCat) > 1){
- statsOfGroupOrdered <- statsOfGroupOrdered[,c(1,interl3((maxCat[maxCatordered]-1),maxCat[maxCatordered],(maxCat[maxCatordered]+1)))]
- }
- }
-
+ statsOfGroupOrdered <- statsOfGroupOrdered %>%
+ group_by(site) %>%
+ summarise(max=sum(max > 0),
+ mean=sum(mean > 0))
} else {
- statsOfGroupOrdered <- statsOfGroup
+ statsOfGroupOrdered <- statsOfGroupOrdered %>%
+ data.frame() %>%
+ left_join(summaryFile[c("site","nSamples")], by="site") %>%
+ select(-site, -hit)
}
statsOfGroupOrdered
})
- chemGroupBP_group <- reactive({
-
- if(is.null(input$radioMaxGroup)){
- radioMaxGroup <- "1"
- } else {
- radioMaxGroup <- input$radioMaxGroup
- }
-
- chemGroup <- chemGroup()
-
- chemGroupBP_group <- chemGroup %>%
- # data.frame() %>%
- mutate(date = factor(as.numeric(date) - min(as.numeric(date))))
-
- if(radioMaxGroup == "1"){
- chemGroupBP_group <- mutate(chemGroupBP_group, cat=choices)
- } else if (radioMaxGroup == "2"){
- chemGroupBP_group <- mutate(chemGroupBP_group, cat=chnm)
- } else {
- chemGroupBP_group <- mutate(chemGroupBP_group, cat=class)
- }
-
- chemGroupBP_group
-
- })
-
- chemGroupBP <- reactive({
-
- if(is.null(input$radio)){
- radioMaxGroup <- "1"
- } else {
- radioMaxGroup <- input$radio
- }
-
- chemGroup <- chemGroup()
-
- chemGroupBP <- chemGroup %>%
- # data.frame() %>%
- mutate(date = factor(as.numeric(date) - min(as.numeric(date))))
-
- if(radioMaxGroup == "2"){
- chemGroupBP <- mutate(chemGroupBP, cat=class)
- } else {
- chemGroupBP <- mutate(chemGroupBP, cat=chnm)
- }
-
- chemGroupBP
-
- })
-
#############################################################
output$table <- DT::renderDataTable({
if(is.null(input$radio)){
- radio <- 1
+ radio <- "1"
} else {
radio <- input$radio
}
@@ -487,9 +448,6 @@ shinyServer(function(input, output) {
siteToFind <- input$sites
}
- statsOfGroupOrdered <- statsOfGroupOrdered %>%
- filter(site %in% siteToFind)
-
if(length(siteToFind) > 1){
if (input$data == "Water Sample"){
@@ -501,69 +459,40 @@ shinyServer(function(input, output) {
meanChem <- grep("mean",names(statsOfGroupOrdered))
maxChem <- grep("max",names(statsOfGroupOrdered))
- nChem <- grep(" count",names(statsOfGroupOrdered))
-
- colors <- brewer.pal(length(maxChem),"Blues") #"RdYlBu"
tableGroup <- DT::datatable(statsOfGroupOrdered,
rownames = FALSE,
filter = 'top',
options = list(pageLength = nrow(statsOfGroupOrdered),
order=list(list(2,'desc'))))
- tableGroup <- formatRound(tableGroup, names(statsOfGroupOrdered)[c(meanChem, maxChem)], 2)
-
-
- for(i in 1:length(maxChem)){
- tableGroup <- formatStyle(tableGroup,
- names(statsOfGroupOrdered)[maxChem[i]],
- backgroundColor = colors[i])
- tableGroup <- formatStyle(tableGroup,
- names(statsOfGroupOrdered)[meanChem[i]],
- backgroundColor = colors[i])
- tableGroup <- formatStyle(tableGroup,
- names(statsOfGroupOrdered)[nChem[i]],
- backgroundColor = colors[i])
-
- tableGroup <- formatStyle(tableGroup, names(statsOfGroupOrdered)[maxChem[i]],
- background = styleColorBar(range(statsOfGroupOrdered[,maxChem[i]],na.rm=TRUE), 'goldenrod'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center' )
-
- tableGroup <- formatStyle(tableGroup, names(statsOfGroupOrdered)[meanChem[i]],
- background = styleColorBar(range(statsOfGroupOrdered[,meanChem[i]],na.rm=TRUE), 'wheat'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center')
-
- tableGroup <- formatStyle(tableGroup, names(statsOfGroupOrdered)[nChem[i]],
- background = styleColorBar(range(statsOfGroupOrdered[,nChem[i]],na.rm=TRUE), 'seashell'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center')
- }
-
+
+ tableGroup <- formatStyle(tableGroup, names(statsOfGroupOrdered)[maxChem],
+ background = styleColorBar(range(statsOfGroupOrdered[,maxChem],na.rm=TRUE), 'goldenrod'),
+ backgroundSize = '100% 90%',
+ backgroundRepeat = 'no-repeat',
+ backgroundPosition = 'center' )
+
+ tableGroup <- formatStyle(tableGroup, names(statsOfGroupOrdered)[meanChem],
+ background = styleColorBar(range(statsOfGroupOrdered[,meanChem],na.rm=TRUE), 'wheat'),
+ backgroundSize = '100% 90%',
+ backgroundRepeat = 'no-repeat',
+ backgroundPosition = 'center')
+
} else {
- statsOfGroupOrdered <- statsOfGroupOrdered[, -1]
-
- tableGroup <- DT::datatable(statsOfGroupOrdered,
+ tableGroup <- DT::datatable(statsOfGroupOrdered[,c("category","max","nSamples")],
rownames = FALSE,
+ colnames = c('hits' = 2),
filter = 'top',
options = list(pageLength = nrow(statsOfGroupOrdered),
order=list(list(1,'desc'))))
- tableGroup <- formatRound(tableGroup, c("max","mean"), 2)
- tableGroup <- formatStyle(tableGroup, "max",
+
+ tableGroup <- formatStyle(tableGroup, "hits",
background = styleColorBar(range(statsOfGroupOrdered[,"max"],na.rm=TRUE), 'goldenrod'),
backgroundSize = '100% 90%',
backgroundRepeat = 'no-repeat',
backgroundPosition = 'center' )
-
- tableGroup <- formatStyle(tableGroup, "mean",
- background = styleColorBar(range(statsOfGroupOrdered[,"mean"],na.rm=TRUE), 'wheat'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center')
+
}
tableGroup
@@ -634,158 +563,27 @@ shinyServer(function(input, output) {
#############################################################
output$stackBarGroup <- renderPlot({
- print(topPlotsGroup())
+ print(groupPlots()$upperPlot)
})
output$stackBar <- renderPlot({
- print(topPlots())
+ print(plots()$upperPlot)
})
output$graph <- renderPlot({
- print(bottomPlots())
+ print(plots()$lowerPlot)
})
output$graphGroup <- renderPlot({
- print(bottomPlotsGroups())
+ print(groupPlots()$lowerPlot)
})
- bottomPlots <- reactive({
-
-# if(is.null(input$sites) | input$sites == "All"){
-# siteToFind <- summaryFile$site
-# } else if (input$sites == "Potential 2016"){
-# siteToFind <- df2016$Site
-# } else {
-# siteToFind <- input$sites
-# }
-#
-# if(is.null(input$radioMaxGroup)){
-# radio <- 2
-# } else {
-# radio <- input$radio
-# }
-#
-# if(length(siteToFind) > 1){
-#
-# endpointSummary <- endpointSummary()
-#
-# siteLimits <- stationINFO %>%
-# filter(shortName %in% siteToFind) %>%
-# filter(fullSiteID %in% unique(endpointSummary$site))
-#
-# if(nrow(endpointSummary) == 0){
-# endpointSummary$site <- stationINFO$fullSiteID
-# }
-#
-# endPointSummBP <- endpointSummary %>%
-# filter(site %in% siteToFind) %>%
-# data.frame()%>%
-# mutate(lake = as.character(lakeKey[site])) %>%
-# mutate(lake = factor(lake, levels=c("Lake Superior","Lake Michigan",
-# "Lake Huron","Lake Erie","Lake Ontario"))) %>%
-# mutate(site = siteKey[site]) %>%
-# mutate(site = factor(site, levels=siteLimits$Station.shortname)) %>%
-# mutate(sumEARnoZero = sumEAR)
-#
-#
-# ndLevel <- 0.1*min(endPointSummBP$sumEARnoZero[endPointSummBP$sumEARnoZero != 0])
-#
-# endPointSummBP$sumEARnoZero[endPointSummBP$sumEARnoZero == 0] <- ndLevel
-#
-#
-# sToxWS <- ggplot(endPointSummBP)
-#
-# if(!is.null(input$data) && input$data != "Passive Samples"){
-# sToxWS <- sToxWS + geom_boxplot(aes(x=site, y=sumEARnoZero, fill = lake)) +
-# scale_fill_manual(values=c("tomato3",
-# "black",
-# "springgreen3",
-# "brown",
-# "blue"))
-# } else {
-# sToxWS <- sToxWS + geom_point(aes(x=site, y=sumEARnoZero,
-# colour = lake))+
-# scale_colour_manual(values=c("tomato3",
-# "black",
-# "springgreen3",
-# "brown",
-# "blue"))
-# }
-#
-# sToxWS <- sToxWS + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.25,
-# colour=siteLimits$lakeColor))+
-# scale_x_discrete(limits=siteLimits$Station.shortname) +
-# scale_y_log10("Summation of EAR per sample") +
-# coord_cartesian(ylim = c(0.1, 1.1*max(endPointSummBP$sumEARnoZero))) +
-# xlab("")
-#
-# } else {
-#
-# chemicalSummaryFiltered <- chemicalSummaryFiltered()
-#
-# g <- ggplot_build(topPlots())
-# fillColors <- g$data[[1]]["fill"][[1]]
-# groupings <- g$plot$data$grouping
-#
-# dfNames <- data.frame(grouping = names(table(groupings)[table(groupings) != 0]),
-# freq = as.numeric(table(groupings)[table(groupings) != 0]),stringsAsFactors = FALSE)
-# dfCol <- data.frame(colors = names(table(fillColors)),
-# freq = as.numeric(table(fillColors)),stringsAsFactors = FALSE)
-#
-# colorKey <- left_join(dfNames, dfCol, by="freq")
-#
-# if(radio == "3"){
-# chemicalSummaryFiltered <- chemicalSummaryFiltered %>%
-# mutate(grouping=class)
-# } else {
-# chemicalSummaryFiltered <- chemicalSummaryFiltered %>%
-# mutate(grouping=chnm)
-# }
-#
-# chemSiteSumm <- chemicalSummaryFiltered %>%
-# filter_(paste0(groupCol," == '", group, "'")) %>%
-# mutate(site = siteKey[site]) %>%
-# filter(site %in% siteToFind) %>%
-# group_by(grouping, date) %>%
-# summarise(sumEAR = sum(EAR),
-# nHits = sum(hits))%>%
-# mutate(sumEARnoZero = sumEAR)
-#
-# ndLevel <- 0.1*min(chemSiteSumm$sumEARnoZero[chemSiteSumm$sumEARnoZero != 0])
-#
-# if(is.finite(ndLevel)){
-# chemSiteSumm$sumEARnoZero[chemSiteSumm$sumEARnoZero == 0] <- ndLevel
-#
-# chemicals <- unique(chemSiteSumm$grouping)[!(unique(chemSiteSumm$grouping) %in% colorKey$grouping)]
-#
-# noFill <- data.frame(grouping=chemicals,
-# colors=rep("#FFFFFF",length(chemicals)),
-# stringsAsFactors = FALSE)
-# fillTotal <- rbind(colorKey[,c('colors','grouping')], noFill)
-#
-# sToxWS <- ggplot(chemSiteSumm)
-#
-# if(!is.null(input$data) && input$data != "Passive Samples"){
-# sToxWS <- sToxWS + geom_boxplot(aes(x=grouping, y=sumEAR,
-# fill=grouping)) +
-# scale_fill_manual(values=setNames(fillTotal$colors,fillTotal$grouping))
-# } else {
-# sToxWS <- sToxWS + geom_point(aes(x=grouping, y=sumEAR))
-# }
-# sToxWS <- sToxWS + theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25),
-# legend.position = "none")+
-# xlab("") +
-# scale_y_log10("Summation of EAR per sample") +
-# geom_hline(yintercept=0.1)
-# }
-# }
-#
-# sToxWS
+ boxData2 <- reactive({
if(is.null(input$radio)){
- radio <- "1"
+ noLegend <- TRUE
} else {
- radio <- input$radio
+ noLegend <- input$radio == "1"
}
if(is.null(input$groupCol)){
@@ -799,7 +597,7 @@ shinyServer(function(input, output) {
} else {
group <- input$group
}
-
+
if(is.null(input$sites) | input$sites == "All"){
siteToFind <- summaryFile$site
} else if (input$sites == "Potential 2016"){
@@ -807,14 +605,13 @@ shinyServer(function(input, output) {
} else {
siteToFind <- input$sites
}
-
+
chemGroup <- chemGroup()
chemGroupBP_group <- chemGroup %>%
- # data.frame() %>%
mutate(date = factor(as.numeric(date) - min(as.numeric(date))))
- if(radio == "1"){
+ if(noLegend){
chemGroupBP_group <- mutate(chemGroupBP_group, cat=chnm)
} else {
chemGroupBP_group <- mutate(chemGroupBP_group, cat=class)
@@ -825,105 +622,37 @@ shinyServer(function(input, output) {
filter(choices %in% group) %>%
filter(EAR > 0)
- sToxWS <- ggplot(boxData)
+ return(boxData)
- if(!is.null(input$data) && input$data != "Passive Samples"){
- sToxWS <- sToxWS + geom_boxplot(aes(x=cat, y=EAR, fill=cat))
- } else {
- sToxWS <- sToxWS + geom_point(aes(x=cat, y=EAR, color=cat))
- }
-
- sToxWS <- sToxWS + theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25),
- legend.position = "none")+
- xlab("") +
- scale_y_log10("EAR") +
- geom_hline(yintercept=0.1)
+ })
+
+ plots <- reactive({
- sToxWS
+ boxData <- boxData2()
- })
-
- topPlotsGroup <- reactive({
-
- if(is.null(input$sites) | input$sites == "All"){
- siteToFind <- summaryFile$site
- } else if (input$sites == "Potential 2016"){
- siteToFind <- df2016$Site
+ if(is.null(input$radio)){
+ noLegend <- TRUE
} else {
- siteToFind <- input$sites
+ noLegend <- input$radio == "1"
}
- if(is.null(input$radioMaxGroup)){
- radio <- "2"
+ if(is.null(input$yRange2)){
+ yRange <- 1000
} else {
- radio <- input$radioMaxGroup
+ yRange <- input$yRange2
}
-
- chemGroupBP_group <- chemGroupBP_group()
- chemGroupBP_group <- chemGroupBP_group %>%
- group_by(site, date, cat) %>%
- summarise(sumEAR = sum(EAR)) %>%
- mutate(grouping=factor(cat, levels=unique(cat))) %>%
- filter(site %in% siteToFind)
-
- uniqueChoices <- as.character(unique(chemGroupBP_group$cat))
-
- siteLimits <- stationINFO %>%
- filter(shortName %in% unique(chemGroupBP_group$site))
-
- if(length(siteToFind) > 1){
-
- chemGroupBPAllSite <- chemGroupBP_group %>%
- group_by(site, cat) %>%
- summarise(maxEAR=max(sumEAR))
-
- sToxWS <- ggplot(chemGroupBPAllSite, aes(x=site, y=maxEAR, fill = cat)) +
- geom_bar(stat="identity") +
- theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25,
- colour=siteLimits$lakeColor)) +
- scale_x_discrete(limits=siteLimits$Station.shortname) +
- xlab("") +
- scale_fill_discrete("")
-
- if(radio == "2"){
- sToxWS <- sToxWS + guides(fill=FALSE)
- }
-
+ if(is.null(input$data)){
+ boxPlot <- TRUE
} else {
-
- chemGroupBPOneSite <- chemGroupBP_group %>%
- select(-site)
-
- levels(chemGroupBPOneSite$cat) <- uniqueChoices
-
-
- sToxWS <- ggplot(chemGroupBPOneSite, aes(x=date, y=sumEAR, fill = cat)) +
- geom_bar(stat="identity") +
- theme(axis.text.x=element_blank(),
- axis.ticks=element_blank())+
- xlab("Individual Samples") +
- scale_fill_discrete(drop=FALSE) +
- labs(fill="")
-
- if(radio == "2"){
- sToxWS <- sToxWS + guides(fill=FALSE)
- }
-
+ boxPlot <- !(input$data == "Passive Samples" & length(siteToFind) == 1)
}
- sToxWS
- })
-
- topPlots <- reactive({
+ return(makePlots(boxData, noLegend, boxPlot, yRange))
- chemGroup <- chemGroup()
+ })
- if(is.null(input$group)){
- group <- unique(endPointInfo[,20])[3]
- } else {
- group <- input$group
- }
+ boxData <- reactive({
if(is.null(input$sites) | input$sites == "All"){
siteToFind <- summaryFile$site
@@ -933,99 +662,52 @@ shinyServer(function(input, output) {
siteToFind <- input$sites
}
- if(is.null(input$radio)){
- radio <- "2"
+ if(is.null(input$radioMaxGroup)){
+ radioMaxGroup <- "1"
} else {
- radio <- input$radio
+ radioMaxGroup <- input$radioMaxGroup
}
- chemGroupBP <- chemGroupBP()
-
- chemGroupBP_group <- chemGroupBP %>%
- filter(choices %in% group) %>%
- group_by(site, date, cat) %>%
- summarise(sumEAR = sum(EAR)) %>%
- mutate(grouping=factor(cat, levels=unique(cat))) %>%
- filter(site %in% siteToFind)
-
- uniqueChoices <- as.character(unique(chemGroupBP_group$cat))
-
- siteLimits <- stationINFO %>%
- filter(shortName %in% unique(chemGroupBP_group$site))
-
- if(length(siteToFind) > 1){
-
- chemGroupBPAllSite <- chemGroupBP_group %>%
- group_by(site, cat) %>%
- summarise(maxEAR=max(sumEAR)) %>%
- filter(site %in% siteToFind)
-
- sToxWS <- ggplot(chemGroupBPAllSite, aes(x=site, y=maxEAR, fill = cat)) +
- geom_bar(stat="identity") +
- theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25,
- colour=siteLimits$lakeColor)) +
- scale_x_discrete(limits=siteLimits$Station.shortname) +
- xlab("") +
- scale_fill_discrete("")
- if(radio == "1"){
- sToxWS <- sToxWS + guides(fill=FALSE)
- }
-
- } else {
-
- chemGroupBPOneSite <- chemGroupBP_group %>%
- select(-site)
-
- levels(chemGroupBPOneSite$cat) <- uniqueChoices
-
-
- sToxWS <- ggplot(chemGroupBPOneSite, aes(x=date, y=sumEAR, fill = cat)) +
- geom_bar(stat="identity") +
- theme(axis.text.x=element_blank(),
- axis.ticks=element_blank())+
- xlab("Individual Samples") +
- scale_fill_discrete(drop=FALSE) +
- labs(fill="")
-
- if(radio == "1"){
- sToxWS <- sToxWS + guides(fill=FALSE)
- }
- }
+ chemGroup <- chemGroup()
- sToxWS
- })
-
- bottomPlotsGroups <- reactive({
+ chemGroupBP_group <- chemGroup %>%
+ mutate(date = factor(as.numeric(date) - min(as.numeric(date))))
- if(is.null(input$sites) | input$sites == "All"){
- siteToFind <- summaryFile$site
- } else if (input$sites == "Potential 2016"){
- siteToFind <- df2016$Site
+ if(radioMaxGroup == "1"){
+ chemGroupBP_group <- mutate(chemGroupBP_group, cat=choices)
+ } else if (radioMaxGroup == "2"){
+ chemGroupBP_group <- mutate(chemGroupBP_group, cat=chnm)
} else {
- siteToFind <- input$sites
+ chemGroupBP_group <- mutate(chemGroupBP_group, cat=class)
}
- chemGroupBP_group <- chemGroupBP_group()
-
boxData <- chemGroupBP_group %>%
filter(site %in% siteToFind) %>%
filter(EAR > 0)
- sToxWS <- ggplot(boxData)
+ return(boxData)
+
+ })
+
+ groupPlots <- reactive({
- if(!is.null(input$data) && input$data != "Passive Samples"){
- sToxWS <- sToxWS + geom_boxplot(aes(x=cat, y=EAR, fill=cat))
+ boxData <- boxData()
+
+ if(is.null(input$yRange)){
+ yRange <- 1000
} else {
- sToxWS <- sToxWS + geom_point(aes(x=cat, y=EAR, color=cat))
+ yRange <- input$yRange
}
- sToxWS <- sToxWS + theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust=0.25),
- legend.position = "none")+
- xlab("") +
- scale_y_log10("EAR") +
- geom_hline(yintercept=0.1)
+ if(is.null(input$radioMaxGroup)){
+ noLegend <- FALSE
+ radioMaxGroup <- "1"
+ } else {
+ noLegend <- input$radioMaxGroup == "2"
+ radioMaxGroup <- input$radioMaxGroup
+ }
- sToxWS
+ return(makePlots(boxData, noLegend, TRUE, yRange))
})
#############################################################
@@ -1048,9 +730,25 @@ shinyServer(function(input, output) {
siteToFind <- input$sites
}
- endpointSummary <- endpointSummary()
+ if(is.null(input$groupCol)){
+ groupCol <- names(endPointInfo)[20]
+ } else {
+ groupCol <- input$groupCol
+ }
+
+ if(is.null(input$group)){
+ group <- unique(endPointInfo[,20])[3]
+ } else {
+ group <- input$group
+ }
+
+ chemicalSummaryFiltered <- chemicalSummaryFiltered()
- sumStat <- endpointSummary %>%
+ sumStat <- chemicalSummaryFiltered %>%
+ filter_(paste0(groupCol," == '", group, "'")) %>%
+ group_by(site, date) %>%
+ summarise(sumEAR = sum(EAR),
+ nHits = sum(hits)) %>%
group_by(site) %>%
summarise(meanEAR = mean(sumEAR),
maxEAR = max(sumEAR),
@@ -1104,11 +802,11 @@ shinyServer(function(input, output) {
output$groupControl <- renderUI({
-# if(is.null(input$groupCol)){
-# groupCol <- names(endPointInfo)[20]
-# } else {
-# groupCol <- input$groupCol
-# }
+ if(is.null(input$groupCol)){
+ groupCol <- names(endPointInfo)[20]
+ } else {
+ groupCol <- input$groupCol
+ }
#
# statCol <- statsOfColumn()
#
@@ -1134,8 +832,8 @@ shinyServer(function(input, output) {
# nEndPointsInChoice <- as.character(table(endPointInfo[,input$groupCol])[namesToUse])
# dropDownHeader <- paste0(namesToUse," (",nEndPointsInChoice,")")
- ChoicesInGroup <- names(table(endPointInfo[,input$groupCol]))
- nEndPointsInChoice <- as.character(table(endPointInfo[,input$groupCol]))
+ ChoicesInGroup <- names(table(endPointInfo[,groupCol]))
+ nEndPointsInChoice <- as.character(table(endPointInfo[,groupCol]))
dropDownHeader <- paste0(ChoicesInGroup," (",nEndPointsInChoice,")")
selectInput("group", label = "Group in annotation (# End Points)",
@@ -1144,10 +842,39 @@ shinyServer(function(input, output) {
})
+ output$numControl2 <- renderUI({
+
+ boxData <- boxData2()
+
+ maxOut <- ifelse(round(max(boxData$EAR)) < 10, 10, round(max(boxData$EAR)))
+
+ numericInput("yRange2", "Y Max:",
+ min=10, max=maxOut, value=maxOut)
+ })
+
+ output$numControl1 <- renderUI({
+
+ boxData <- boxData()
+
+ maxOut <- ifelse(round(max(boxData$EAR)) < 10, 10, round(max(boxData$EAR)))
+
+ numericInput("yRange", "Y Max:",
+ min=10, max=maxOut, value=maxOut)
+ })
+
output$TableHeader <- renderUI({
HTML(paste("", input$group,"-",input$data,": ",input$sites, "
"))
})
+ output$mapFooter <- renderUI({
+ if(input$data == "Water Sample"){
+ HTML("Size range represents number of collected samples from 1-64
")
+ } else {
+ HTML("One sample per site
")
+ }
+
+ })
+
output$BoxHeader <- renderUI({
HTML(paste("", input$group,"-",input$data,": ",input$sites, "
"))
})
@@ -1163,18 +890,37 @@ shinyServer(function(input, output) {
} else {
radio <- input$radioMaxGroup
}
+
+ if(is.null(input$sites) | input$sites == "All"){
+ siteToFind <- summaryFile$site
+ } else if (input$sites == "Potential 2016"){
+ siteToFind <- df2016$Site
+ } else {
+ siteToFind <- input$sites
+ }
+
if(radio == "2"){
- word <- "chemicals"
+ word <- "chemicals"
} else if (radio == "3") {
word <- "classes"
} else {
word <- "choices"
}
- textUI <- paste("max = Maximum of number of",word,"with hits per sample
",
- "mean = Mean number of",word,"with hits per sample
",
- "count = Number of",word,"with hits per sample
")
+ if(length(siteToFind) > 1){
+ place <- "per site"
+ } else {
+ place <- ""
+ }
+ if(length(siteToFind) > 1){
+ textUI <- paste("max = Maximum of number of",word,"with hits per site
",
+ "mean = Mean number of",word,"with hits per site
",
+ "nSamples = Number of samples per site
")
+ } else {
+ textUI <- paste("hits = Number of",word,"with hits
",
+ "nSamples = Number of samples per site
")
+ }
HTML(textUI)
})
diff --git a/inst/shiny/ui.R b/inst/shiny/ui.R
index 34017c0c..90803f66 100644
--- a/inst/shiny/ui.R
+++ b/inst/shiny/ui.R
@@ -29,7 +29,7 @@ shinyUI(
),
column(6,
leaflet::leafletOutput("mymap"),
- h5("Size range represents number of collected samples from 1-64")
+ htmlOutput("mapFooter")
),
column(1)),
@@ -44,6 +44,7 @@ shinyUI(
selected = 1),
tabsetPanel(
tabPanel("Visualizations",
+ uiOutput("numControl1"),
plotOutput("stackBarGroup"),
h4("All EARs"),
plotOutput("graphGroup")),
@@ -66,11 +67,10 @@ shinyUI(
tabsetPanel(
tabPanel("Visualizations",
htmlOutput("BoxHeader"),
- h5("Only shading EARs with hits (> 0.1)"),
+ uiOutput("numControl2"),
plotOutput("stackBar"),
h5("All EARs"),
plotOutput("graph")
-
),
tabPanel("Table",
htmlOutput("TableHeader"),