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Bottom plot
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@ldecicco-USGS
ldecicco-USGS committed Aug 8, 2015
1 parent e019138 commit ea9e184
Showing 1 changed file with 176 additions and 116 deletions.
292 changes: 176 additions & 116 deletions inst/shiny/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -434,7 +434,7 @@ shinyServer(function(input, output) {
}

statTable <- chemicalSummaryFiltered %>%
filter_(paste0(groupCol," == '", group, "'"))
filter_(paste0(groupCol," == '", group, "'")) %>%
mutate(site = siteKey[site]) %>%
filter(site %in% siteToFind) %>%
group_by(grouping, date) %>%
Expand Down Expand Up @@ -651,6 +651,155 @@ shinyServer(function(input, output) {

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

if(is.null(input$radio)){
radio <- "1"
} else {
radio <- input$radio
}

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
}

if(is.null(input$sites) | input$sites == "All"){
siteToFind <- summaryFile$site
} else if (input$sites == "Potential 2016"){
Expand All @@ -659,128 +808,39 @@ shinyServer(function(input, output) {
siteToFind <- input$sites
}

if(is.null(input$radioMaxGroup)){
radio <- 2
chemGroup <- chemGroup()

chemGroupBP_group <- chemGroup %>%
# data.frame() %>%
mutate(date = factor(as.numeric(date) - min(as.numeric(date))))

if(radio == "1"){
chemGroupBP_group <- mutate(chemGroupBP_group, cat=chnm)
} else {
radio <- input$radio
chemGroupBP_group <- mutate(chemGroupBP_group, cat=class)
}

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("")

boxData <- chemGroupBP_group %>%
filter(site %in% siteToFind) %>%
filter(choices %in% group) %>%
filter(EAR > 0)

sToxWS <- ggplot(boxData)

if(!is.null(input$data) && input$data != "Passive Samples"){
sToxWS <- sToxWS + geom_boxplot(aes(x=cat, y=EAR, fill=cat))
} 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 <- 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)

sToxWS

})

topPlotsGroup <- reactive({
Expand Down

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