Nothing
######################
## Haul Bubble plot ##
######################
# x <- data$SHOOTING_LONGITUDE
# y <- data$SHOOTING_LATITUDE
# data <- MEDITS.to.dd(TA)
# variable <- "SHOOTING_DEPTH"
# range <- NA # c(15.5,20,40,42.5)
# interval="equal"
# bubbleplot(x,y,data,variable, interval="equal")
bubbleplot <- function(x,y,data, variable, range=NA,inches=0.1, interval="equal",
land=countries, d1 = depth_1, d2= depth_2, d3 = depth_3){
if (FALSE){
x=m$SHOOTING_LONGITUDE;y=m$SHOOTING_LATITUDE;data=m; variable="SHOOTING_DEPTH"; range=NA; interval="quantiles";
land=countries; d1 = depth_1; d2= depth_2; d3 = depth_3
}
countries <- land
depth_1 <- d1
depth_2 <- d2
depth_3 <- d3
summary.grid <- data.frame(x,y,data[,variable])
colnames(summary.grid) <- c("MEAN_LONGITUDE_DEC","MEAN_LATITUDE_DEC", variable)
if (is.na(range[1])){
x_min <- min(summary.grid$MEAN_LONGITUDE_DEC)
x_max <- max(summary.grid$MEAN_LONGITUDE_DEC)
y_min <- min(summary.grid$MEAN_LATITUDE_DEC)
y_max <- max(summary.grid$MEAN_LATITUDE_DEC)
xdif <- 10*(x_max - x_min)/100
ydif <- 10*(y_max - y_min)/100
# range <- c(x_min,x_max,y_min,y_max)
range <- c((x_min-xdif),(x_max+xdif),(y_min-ydif),(y_max+ydif))
}
#----------------------------------------
# Plotting indices
#----------------------------------------
if (interval=="quantiles") {
cat_lim <- as.numeric(quantile(summary.grid[!is.na(summary.grid[,variable]), variable], probs = seq(0, 1,0.20) ) )
}
if (interval=="equal") {
max_val <- max(summary.grid[!is.na(summary.grid[,variable]), variable])
break_size <- max_val/5
cat_lim <- seq(0, max_val, break_size)
}
cate_label <- round(cat_lim,2)
cate_label_min <- cate_label
cate_label_max <- cate_label[2:length(cate_label)]
cate_label <- paste("(", cate_label_min, ", ", cate_label_max, "]", sep="")
cate_label[1] <- paste("[", cate_label_min[1], ", ", cate_label_max[1], "]", sep="")
#cate_label[length(cate_label)] <- paste(">", cate_label_max[length(cate_label_max)] )
cate_label <- cate_label[1: (length(cate_label)-1)]
palette_cate <- heat.colors(length(cate_label))
palette_cate <- palette_cate[length(palette_cate):1]
summary.grid_to_plot <- summary.grid
summary.grid_to_plot$cate <- "0"
summary.grid_to_plot$color <- "black"
summary.grid_to_plot$to_plot <- 0
summary.grid_to_plot$color[ summary.grid_to_plot[,variable] >= min(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable]) & summary.grid_to_plot[,variable] <=cat_lim[2]] <- palette_cate[1]
summary.grid_to_plot$color[ summary.grid_to_plot[,variable] >cat_lim[2] & summary.grid_to_plot[,variable] <=cat_lim[3]] <- palette_cate[2]
summary.grid_to_plot$color[ summary.grid_to_plot[,variable] >cat_lim[3] & summary.grid_to_plot[,variable] <=cat_lim[4]] <- palette_cate[3]
summary.grid_to_plot$color[ summary.grid_to_plot[,variable] >cat_lim[4] & summary.grid_to_plot[,variable] <=cat_lim[5]] <- palette_cate[4]
summary.grid_to_plot$color[ summary.grid_to_plot[,variable] >cat_lim[5] & summary.grid_to_plot[,variable] <=max(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable])] <- palette_cate[5]
summary.grid_to_plot$cate[ summary.grid_to_plot[,variable] >= min(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable]) & summary.grid_to_plot[,variable] <=cat_lim[2]] <- cate_label[1]
summary.grid_to_plot$cate[ summary.grid_to_plot[,variable] >cat_lim[2] & summary.grid_to_plot[,variable] <=cat_lim[3]] <- cate_label[2]
summary.grid_to_plot$cate[ summary.grid_to_plot[,variable] >cat_lim[3] & summary.grid_to_plot[,variable] <=cat_lim[4]] <- cate_label[3]
summary.grid_to_plot$cate[ summary.grid_to_plot[,variable] >cat_lim[4] & summary.grid_to_plot[,variable] <=cat_lim[5]] <- cate_label[4]
summary.grid_to_plot$cate[ summary.grid_to_plot[,variable] >cat_lim[5] & summary.grid_to_plot[,variable] <max(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable])] <- cate_label[5]
#summary.grid_to_plot$cate[ summary.grid_to_plot$meanNkm2 >cat_lim[6] ] <- cate_label[6]
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] >= min(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable]) & summary.grid_to_plot[,variable] <=cat_lim[2]] <- 2
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] >cat_lim[2] & summary.grid_to_plot[,variable] <=cat_lim[3]] <- 3
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] >cat_lim[3] & summary.grid_to_plot[,variable] <=cat_lim[4]] <- 4
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] >cat_lim[4] & summary.grid_to_plot[,variable] <=cat_lim[5]] <- 6
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] >cat_lim[5] & summary.grid_to_plot[,variable] <=max(summary.grid_to_plot[!is.na(summary.grid_to_plot[,variable]), variable])] <- 7
summary.grid_to_plot$to_plot[ summary.grid_to_plot[,variable] == 0] <- 0
plot.new()
# polygon(c(-min(summary.grid_to_plot[,"MEAN_LONGITUDE_DEC"])^2,-min(summary.grid_to_plot[,"MEAN_LONGITUDE_DEC"])^2,
# max(summary.grid_to_plot[,"MEAN_LONGITUDE_DEC"])^2,max(summary.grid_to_plot[,"MEAN_LONGITUDE_DEC"])^2),
# c(-min(summary.grid_to_plot[,"MEAN_LATITUDE_DEC"])^2,max(summary.grid_to_plot[,"MEAN_LATITUDE_DEC"])^2,
# max(summary.grid_to_plot[,"MEAN_LATITUDE_DEC"])^2,-min(summary.grid_to_plot[,"MEAN_LATITUDE_DEC"])^2), col="#1E90FF")
lx =range[2] - range[1]
ly =range[4] - range[3]
ratio <- ly/lx*1.1
img_width <- par()$fin[1]
img_height <- img_width*ratio
oldoptions <- options()$warn
old_par <- list()
old_par$mar <-par()$mar
old_par$fin <-par()$fin
if (img_height > old_par$fin[2]){
img_height <- old_par$fin[2]
img_width <- img_height/ratio
}
on.exit(c(par(mar=old_par$mar,fin=old_par$fin),options(warn=oldoptions)))
options(warn=-1)
par(new=TRUE, mar=c(4, 5, 4, 2), fin=c(img_width,img_height)) #c(bottom, left, top, right) ,bg = 'blue'
plot(1,1,type="n",xlim=c(range[1],range[2]), ylim=c(range[3],range[4]) , xlab=expression(paste("Longitude (",degree,"E)")), ylab=expression(paste("Latitude (",degree,"N)")), main=variable)
#plot(cgpmgrid, xlim=c(range[1],range[2]), ylim=c(range[3],range[4]), add=TRUE, border="light grey") #data = centroidi_coords,
plot(countries, xlim=c(range[1],range[2]), ylim=c(range[3],range[4]), border="grey", col="light grey", add=TRUE)
plot(depth_1, xlim=c(range[1],range[2]), ylim=c(range[3],range[4]), col="#C0C0C0", add=TRUE)
plot(depth_2, xlim=c(range[1],range[2]), ylim=c(range[3],range[4]), col="#A9A9A9", add=TRUE)
plot(depth_3, xlim=c(range[1],range[2]), ylim=c(range[3],range[4]), col="#808080", add=TRUE)
symbols(summary.grid_to_plot$MEAN_LONGITUDE_DEC[order(summary.grid_to_plot $to_plot, decreasing = TRUE)],
summary.grid_to_plot$MEAN_LATITUDE_DEC[order(summary.grid_to_plot $to_plot, decreasing = TRUE)],
circles=as.numeric(as.character(summary.grid_to_plot $to_plot[order(summary.grid_to_plot $to_plot, decreasing = TRUE)])), inches=inches, fg="black",
bg=summary.grid_to_plot$color[order(summary.grid_to_plot $to_plot, decreasing = TRUE)], add=TRUE) # inches=1
points(summary.grid_to_plot$MEAN_LONGITUDE_DEC[summary.grid_to_plot $to_plot==0], summary.grid_to_plot$MEAN_LATITUDE_DEC[summary.grid_to_plot $to_plot==0], pch=4, cex=0.65) # inches=1 ,
legend(range[1],range[4], cate_label, col=palette_cate, pch = 19, pt.cex=c(1,2,2.5,3,3.3), title =variable, bty = "n")
#with(centroidi_coords, text(centroidi_coords$coords.x1 - 0.5, centroidi_coords$coords.x2, labels = centroidi_coords$cgpmgrid_id, pos = 4, cex = 0.2, col="grey"))
box()
}
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