R/qwseasonalPlot.R

In USGS-R/WQ-Review: Discrete water-quality data review and exploration toolbox

#' Seasonal plot
#' 
#' Takes output data object from readNWISodbc and prints a boxplot of a parameter by month.
#' @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 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 Logical to 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")
#' qwseasonalPlot(qw.data = qw.data,
#'                site.selection = "06733000",
#'                plotparm = "00095",
#'                facet = "multisite",
#'                scales="fixed",
#'                new.threshold = 60*60*24*30,
#'                show.smooth = FALSE,
#'                highlightrecords = " ",
#'                wySymbol = FALSE,
#'                labelDQI = FALSE,
#'                printPlot = TRUE)
#' @import ggplot2
#' @importFrom stringr str_wrap
#' @export

qwseasonalPlot <- function(qw.data,
                           new.threshold = 60*60*24*30,
                           site.selection,
                           plotparm,
                           facet = "multisite",
                           scales="fixed",
                           show.smooth = FALSE,
                           highlightrecords = " ",
                           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))
        
        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 seasonal plot"
        } else (maintitle <- "No site selected")
        
        #ylabel <- str_wrap(unique(qw.data$PlotTable$PARM_DS[which(qw.data$PlotTable$PARM_CD==(plotparm))]), width = 25)
        ylabel <- unique(plotdata$PARM_DS[plotdata$PARM_CD == plotparm])
        
        p1 <- ggplot(data=plotdata)
        p1 <- p1 + geom_point(aes(x=DOY,y=RESULT_VA, color=MEDIUM_CD,shape = REMARK_CD,
                                  text = paste('Day-of-year:',DOY,'\n',
                                               '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)
        }else{}
        
        ##Check for new samples and label them. Tried ifelse statement for hte label but it did no recognize new.threshol as a variable for some reason
        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=DOY,y=RESULT_VA,color = MEDIUM_CD,label="New",hjust=1.1),size=7,show.legend=FALSE)      
        }else{}
        
        if(nrow(subset(plotdata, RECORD_NO %in% highlightrecords)) >0 )
        {
                p1 <- p1 + geom_point(data=subset(plotdata, RECORD_NO %in% highlightrecords),aes(x=DOY,y=RESULT_VA),size=7,alpha = 0.5, color ="#D55E00" ,shape=19)
        }
        
        ##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=DOY,y=RESULT_VA),size=7,alpha = 0.5, color = "#F0E442",shape=19)
        }
        
        if(labelDQI == TRUE)
        {
                p1 <- p1 + geom_text(aes(x=DOY,y=RESULT_VA, color=MEDIUM_CD,label=DQI_CD),size=7,vjust="bottom",hjust="right",show.legend=FALSE)
        }
        
        p1 <- p1 + scale_color_manual("Medium code",values = medium.colors)
        p1 <- p1 + scale_shape_manual("Remark code",values = qual.shapes)
        p1 <- p1 + ylab(paste(ylabel,"\n")) + xlab("Month")
        p1 <- p1 + scale_x_continuous(breaks = c(1,32,60,91,121,152,182,213,244,274,305,335),
                                      labels=c("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec")
        )
        p1 <- p1 + ggtitle(maintitle) + theme_bw() + 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=DOY,y=RESULT_VA))
        } 
        
        if(printPlot==TRUE)
        {
                print(p1)
        }else {return(p1)}
        
}