R/DailyBar.R

In SOMEnv: SOM Algorithm for the Analysis of Multivariate Environmental Data

#' Plot of daily percentages for each cluster
#'
#' The function produces a plot representing the the daily percentage for each cluster
#'
#' @param experimental Experimental data (must contain variable "date")
#' @param TrainClus Vector containing cluster number assignment for experimental data
#' @param Centroids Centroids matrix
#' @param colSeq Color sequence for the clusters
#' @param Total Number of observations per day
#' @param xdim x axes label dimensions
#' @param ydim y axes label dimensions
#' @import openair
#' @importFrom grDevices rainbow
#' @importFrom graphics axis barplot legend par
#' @importFrom stats quantile
#' @author Sabina Licen
#' @return Plot of daily percentages for each cluster, the latter element in the legend represents percentage of not determined data
#' @references {Licen, S., Cozzutto, S., Barbieri, P. (2020) Aerosol Air Qual. Res., 20 (4), pp. 800-809. DOI: 10.4209/aaqr.2019.08.0414
#' }
#' @export


DailyBar<-function(experimental,TrainClus,Centroids,colSeq=rainbow(nrow(data.frame(Centroids))),Total=1440,xdim=0.7,ydim=0.8)
{colSeq<-c(colSeq,"black");
 nClus<-nrow(data.frame(Centroids));
 g<-as.POSIXct(substr(experimental$date, 1, 10),format = "%Y-%m-%d",tz="GMT")#NEW!!!
 g2<-levels(as.factor(g))
 interval<-seq(as.POSIXct(g2[1],format = "%Y-%m-%d",tz="GMT"), as.POSIXct(g2[length(g2)],format = "%Y-%m-%d",tz="GMT"), by = "1 day")
 mydata<-data.frame(experimental$date,day=g,Cluster=TrainClus)
    FRE<-data.frame(Canc=rep(0,nClus+1));
    for  (j in interval) {Select<-mydata[which(mydata$day==j),];
    fre<-NULL;
    for  (i in c(1:nClus)) {n<-nrow(Select[which(Select$Cluster==i),])/Total*100;fre<-c(fre,round(n,digits=1))}
    s<-(100-sum(fre,na.rm=T));fre<-c(fre,s);FRE<-cbind(FRE,fre)}
    FRE<-data.frame(FRE)
    FRE<-FRE[,-1]
    colnames(FRE)<-paste0(substr(interval, 9, 10),"/",substr(interval, 6, 7))
    FRE2<-as.matrix(FRE)
LAB<-colnames(FRE2)
opar <- par(oma=c(0,0,0,0),xpd=T)
BAR<-barplot(FRE2,col=colSeq,ylab="",xlab="",xaxt="n",yaxt="n",ylim=c(0,100),density=c(rep(NA,nClus),10),angle=c(rep(NA,nClus),45))
    axis(1,at=BAR,labels=NA,tcl=-0.3,cex.axis=xdim)
    axis(1,at=BAR,labels=LAB,lwd=0,line=-0.5,cex.axis=xdim,las=2)
    axis(2,at=seq(0,100,25),labels=NA,tcl=-0.3,cex.axis=ydim)
    axis(2,at=seq(0,100,25),labels=seq(0,100,25),lwd=0,line=-0.5,cex.axis=ydim,las=1)
    I<-BAR[length(BAR)-1]
    F<-BAR[length(BAR)]
    legend(quantile(BAR,prob=0.1),110,ncol=nClus+1,legend=c(paste("Cl",seq(1,nClus,1),sep=""),"ND"),fill=colSeq,bty="n",cex=0.85,
    density=c(rep(NA,nClus),10),angle=c(rep(NA,nClus),45))
    on.exit(par(opar))
}