WQ-Review: Discrete water-quality data review and exploration toolbox

Documented in qwtsPlot

#' Parameter timeseries plot
#' 
#' Takes output data object from readNWISodbc and prints a plot of parameter vs time.
#' @param qw.data A qw.data object 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 plotparm A character vector of parameters to plot
#' @param show.q Logical to plot instantaneous hydrograph
#' @param show.smooth Logical to add a loess smooth to plot
#' @param highlightrecords A character vector of record numbers to highlight in 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 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")
#' qwtsPlot(qw.data = qw.data,
#'                        site.selection = "06733000",
#'                        plotparm = "00915",
#'                        new.threshold = 60*60*24*30,
#'                        show.q = FALSE,
#'                        show.smooth = FALSE,
#'                        highlightrecords = " ",
#'                        facet = "multisite",
#'                        scales="fixed",
#'                        wySymbol = FALSE,
#'                        labelDQI = FALSE,
#'                        printPlot = TRUE)
#' @import ggplot2
#' @importFrom stringr str_wrap
#' @export

qwtsPlot <- function(qw.data,
                     site.selection,
                     plotparm,
                     new.threshold = 60*60*24*30,
                     show.q = FALSE,
                     show.smooth = FALSE,
                     highlightrecords = " ",
                     facet = "multisite",
                     scales="fixed",
                     wySymbol = FALSE,
                     labelDQI = FALSE,
                     printPlot = TRUE){
        # ## 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 color to medium code name, not factor level, so its consistant between all plots regardles of number of medium codes in data
        # qual.shapes <- c(19,0,2,5,4,3,6,7,8,9,11)
        # names(qual.shapes) <- c("Sample","<",">","E","A","M","N","R","S","U","V")
        
        plotdata <- subset(qw.data$PlotTable,SITE_NO %in% (site.selection) & 
                                   PARM_CD == (plotparm))
        Qplotdata <- subset(qw.data$PlotTable,SITE_NO %in% (site.selection) & 
                                    PARM_CD %in% c(plotparm,"00061"))
        
        if (length(site.selection) == 1)
        {
                #maintitle <- stringr::str_wrap(unique(qw.data$PlotTable$STATION_NM[which(qw.data$PlotTable$SITE_NO == (site.selection))]), width = 25)
                maintitle <- unique(qw.data$PlotTable$STATION_NM[qw.data$PlotTable$SITE_NO == site.selection])
        } else (maintitle <- "Multisite timeseries plot")
        
        #ylabel <- stringr::str_wrap(unique(plotdata$PARM_DS[which(plotdata$PARM_CD==(plotparm))]), width = 25)
        ylabel <- unique(plotdata$PARM_DS[plotdata$PARM_CD == plotparm])
        
        p1 <- ggplot(data=plotdata,)
        p1 <- p1 + geom_point(aes(x=SAMPLE_START_DT,y=RESULT_VA,shape = REMARK_CD, color = MEDIUM_CD,
                                       text = paste('SAMPLE_START_DT:',SAMPLE_START_DT,'\n',
                                                    'REMARK_CD RESULT_VA:',REMARK_CD,RESULT_VA,'\n',
                                                    'MEDIUM_CD:',MEDIUM_CD,'\n')), size=3)
        if ( facet == "Facet")
        {
                p1 <- p1 + facet_wrap(~ STATION_NM, nrow = 1, scales=scales)
        }
        
        p1 <- p1 + ylab(paste(ylabel,"\n")) + xlab("Date")
        p1 <- p1 + scale_colour_manual("Medium code",values = medium.colors)
        p1 <- p1 + scale_shape_manual("Remark code",values = qual.shapes)
        p1 <- p1 + theme_bw()
        p1 <- p1 + ggtitle(maintitle)
        
        #check for highlighted records and put different symbols
        if(
                nrow((data=subset(plotdata, RECORD_NO %in% highlightrecords))) > 0
        ){
                
                p1 <- p1 + geom_point(data=subset(plotdata, RECORD_NO %in% highlightrecords),aes(x=SAMPLE_START_DT,y=RESULT_VA),size = 7,alpha=0.5, color ="#D55E00" ,shape=19)
        }
        
        
        ##Check for new samples and label them. 
        if(nrow(subset(plotdata, RESULT_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=RESULT_VA,color = MEDIUM_CD,label="New",hjust=1.1),show.legend=F)      
        }else{}
        
        if(labelDQI == TRUE)
        {
                p1 <- p1 + geom_text(aes(x=SAMPLE_START_DT,y=RESULT_VA,color = MEDIUM_CD,label=DQI_CD),size=7,vjust="bottom",hjust="right")
        }
        
        ##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=RESULT_VA),size=5,alpha = 0.5, color = "#F0E442",shape=19)
        }
        
        p1 <- p1 + theme(axis.text.x = element_text(angle = 90)) + theme(panel.grid.minor = element_line())
        
        ###Add smooth if checked
        if((show.smooth)==TRUE){
                p1 <- p1 + geom_smooth(data = subset(plotdata, REMARK_CD=="Sample" & 
                                                             MEDIUM_CD %in%(c("WS ","WG "))),
                                       aes(x=SAMPLE_START_DT,y=RESULT_VA))
        } 
        
        
        p3 <- ggplot(data=subset(Qplotdata, MEDIUM_CD == "WS " & 
                                         REMARK_CD == "Sample"),aes(x=SAMPLE_START_DT,y=RESULT_VA,shape = REMARK_CD, color = MEDIUM_CD))
        p3 <- p3 + facet_grid(PARM_NM~.,scales="free_y") + geom_point(data=subset(Qplotdata,PARM_CD == plotparm)) + geom_line(data=subset(Qplotdata,PARM_CD == "00061" & MEDIUM_CD=="WS "))
        p3 <- p3 + theme_bw()
        p3 <- p3 + scale_colour_manual("Medium code",values = medium.colors)
        p3 <- p3 + scale_shape_manual("Remark code",values = qual.shapes)
        p3 <- p3 + ylab("Value, see individual parameters for units") + xlab("Date")
        p3 <- p3 + ggtitle(maintitle)
        ###Add Q if checked
        if((show.q)==TRUE){ 
                p2 <- ggplot(data=subset(Qplotdata, MEDIUM_CD == "WS " & 
                                                 REMARK_CD == "Sample"),aes(x=SAMPLE_START_DT,y=RESULT_VA,shape = REMARK_CD, color = MEDIUM_CD))
                p2 <- p2 + facet_grid(PARM_NM~.,scales="free_y") + geom_point(data=subset(Qplotdata,PARM_CD == plotparm)) + geom_line(data=subset(Qplotdata,PARM_CD == "00061" & MEDIUM_CD=="WS "))
                p2 <- p2 + theme_bw()
                p2 <- p2 + scale_colour_manual("Medium code",values = medium.colors)
                p2 <- p2 + scale_shape_manual("Remark code",values = qual.shapes)
                p2 <- p2 + ylab("Value, see individual parameters for units") + xlab("Date")
                p2 <- p2 + ggtitle(maintitle)
                if((show.smooth)==TRUE){
                        p2 <- p2 + geom_smooth(data = subset(Qplotdata, REMARK_CD=="Sample" & 
                                                                     MEDIUM_CD %in%(c("WS ","WG "))),
                                               aes(x=SAMPLE_START_DT,y=RESULT_VA))
                }
                
                
                if(printPlot == TRUE)
                {
                        print(p2) 
                } else(return(p2))
                
        }
        if ((show.q)==FALSE)
        {
                if(printPlot == TRUE)
                {
                        print(p1) 
                } else(return(p1))
        }
        
}