#' Chargebalance timeseries plot
#'
#' Takes output list from readNWISodbc and prints a plot of charge balance vs time.
#' @param qw.data A qw.data list generated from readNWISodbc
#' @param new.threshold The threshold value in seconds from current system time for "new" data.
#' @param site.selection A character vector of site IDs to plot
#' @param facet Character string of either "multisite" for plotting all sites on one plot or "Facet" for plotting sites on individual plots
#' @param scales Character string to define y axis on faceted plots. Options are "free","fixed","free_x", or "free_y"
#' @param show.smooth Add a loess smooth to plot
#' @param highlightrecords A character vector of record numbers to highlight in plot
#' @param wySymbol Make current water-year highlighted.
#' @param labelDQI Logical. Should points be labeled with DQI code.
#' @param printPlot Logical. Prints plot to graphics device if TRUE
#' @examples
#' data("exampleData",package="WQReview")
#' qwcbPlot(qw.data = qw.data,
#' site.selection = "06733000",
#' facet = "multisite",
#' scales="fixed",
#' new.threshold = 60*60*24*30,
#" show.smooth = FALSE,
#' highlightrecords = NULL,
#' wySymbol = FALSE,
#' labelDQI = FALSE,
#' printPlot = TRUE)
#' @importFrom stringr str_wrap
#' @import ggplot2
#' @importFrom dplyr left_join
#' @export
qwcbPlot <- function(qw.data,
site.selection,
facet = "multisite",
scales="fixed",
new.threshold = 60*60*24*30,
show.smooth = FALSE,
highlightrecords = NULL,
wySymbol = FALSE,
labelDQI = FALSE,
printPlot = TRUE){
###Run ion balance function if not run already and dplyr::left_join to qw.data$PlotTable
if(is.null(qw.data$PlotTable$perc.diff))
{
tryCatch({
chargebalance.table <- ionBalance(qw.data = qw.data,wide=FALSE)
###Check that a balance was calculated
###Join charge balance table to plot table
chargebalance.table <- chargebalance.table[c("RECORD_NO","sum_cat","sum_an","perc.diff","complete.chem")]
qw.data$PlotTable <- dplyr::left_join(qw.data$PlotTable,chargebalance.table[!duplicated(chargebalance.table$RECORD_NO), ],by="RECORD_NO")
}, error = function(e) {
stop("Insufficient data to calculate charge balance. Check your qw.data$PlotTable data")
})
} else {}
## Sets color to medium code name, not factor level, so its consistant between all plots regardles of number of medium codes in data
medium.colors <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#D55E00","#D55E00")
names(medium.colors) <- c("WS ","WG ","WSQ","WGQ","OAQ","OA ")
## Sets shape to Remark code name, not factor level, so its consistant between all plots regardles of number of medium codes in data
qual.shapes <- c(19,0,2,5)
names(qual.shapes) <- c("Complete","Incomplete")
plotdata <- subset(qw.data$PlotTable,SITE_NO %in% (site.selection) &
!duplicated(RECORD_NO) == TRUE
)
###Set the modified date to most recent modification for that record
###setup the hline from charge balance
hline <- data.frame(yint=c(-5,5,-10,10),Imbalance=c("+/- 5%","+/- 5%","+/- 10%","+/- 10%"))
if(length(site.selection) == 1)
{
#maintitle <- str_wrap(unique(plotdata$STATION_NM[which(plotdata$SITE_NO == (site.selection))]), width = 25)
maintitle <- unique(qw.data$PlotTable$STATION_NM[qw.data$PlotTable$SITE_NO == site.selection])
} else if (length(site.selection) > 1)
{
maintitle <- "Multisite charge balance plot"
} else (maintitle <- "No site selected")
ylabel <- "Charge balance Percent difference\n( [sum(cat)-sum(an)]/[tot. charge] * 100 )"
p1 <- ggplot(data=plotdata,aes(x=SAMPLE_START_DT,y=perc.diff,shape = complete.chem, color = MEDIUM_CD,
text = paste('SAMPLE_START_DT:',SAMPLE_START_DT,'\n',
'Percent Diff.:',perc.diff,'\n',
'Chemistry:',complete.chem,'\n',
'MEDIUM_CD:',MEDIUM_CD,'\n')))
p1 <- p1 + geom_point(size=3)
p1 <- p1 + ylab(paste(ylabel,"\n")) + xlab("Date")
p1 <- p1 + scale_colour_manual("Medium code",values = medium.colors)
p1 <- p1 + scale_shape_manual("Chemistry status",values = qual.shapes)
p1 <- p1 + scale_y_continuous(limits=c(-100,100))
if(facet == "Facet"){
p1 <- p1 + facet_wrap(~ STATION_NM, nrow = 1, scales=scales)
} else {}
#p1 <- p1 + scale_x_datetime(limits=c(as.POSIXct((begin.date)),as.POSIXct((end.date))))
##Highlighted records labels
if(nrow(subset(plotdata, RECORD_NO %in% highlightrecords)) >0 )
{
p1 <- p1 + geom_point(data=subset(plotdata, RECORD_NO %in% highlightrecords),aes(x=SAMPLE_START_DT,y=perc.diff),size=7,alpha = 0.5, color = "#D55E00",shape=19)
}
###New sample labels
if(nrow(subset(plotdata, RESULT_MD >= (Sys.time()-new.threshold))) > 0)
{
if(all(is.finite(plotdata$perc.diff[which(plotdata$SAMPLE_MD >= (Sys.time()-new.threshold))])) &
nrow(subset(plotdata, SAMPLE_MD >= (Sys.time()-new.threshold))) > 0)
{
p1 <- p1 + geom_text(data=subset(plotdata,RESULT_MD >= (Sys.time()-new.threshold)),
aes(x=SAMPLE_START_DT,y=perc.diff,color = MEDIUM_CD,label="New",hjust=1.1),show.legend=F)
}else{}
} else{}
##highlight this water year's data
if(wySymbol == TRUE)
{
p1 <- p1 + geom_point(data=subset(plotdata, as.character(waterYear(SAMPLE_START_DT)) == as.character(waterYear(Sys.time()))),
aes(x=SAMPLE_START_DT,y=perc.diff),size=5,alpha = 0.5, color ="#F0E442" ,shape=19)
}
if(labelDQI == TRUE)
{
p1 <- p1 + geom_text(aes(label=DQI_CD),size=5,vjust="bottom",hjust="right")
}
p1 <- p1 + ggtitle(maintitle)
p1 <- p1 + geom_hline(data = hline,aes(yintercept = yint,linetype=Imbalance),show.legend=TRUE)
p1 <- p1 + theme_bw() + theme(panel.grid.minor = element_line())
if((show.smooth)==TRUE){
p2 <- p1 + geom_smooth(data=subset(plotdata, MEDIUM_CD %in% (c("WS ","WG ")))) + theme_bw()
if(printPlot == TRUE)
{
print(p2)
} else{}
return(p2)
} else{
if(printPlot == TRUE)
{
print(p1)
}else {}
return(p1)}
}
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