Area plot with missing values in base R - r

Question

I want to draw an area plot for which the base of the polygon is zero and the data lines are connected to the base by vertical segments at every data break (that is the beginning, the end and possible NAs/NaN).
I drew this:
I had to force vertical down ward segments where the serie is interrupted with NAs, and I did this transforming NAs in 0s. But that doesn't produce vertical segments but polygon lines that reach the following 0s. I solved the problem for the beginning and the end of the series, adding a (y = 0, x = 0) point on both sides on the serie.
But this doesn't fix the problem if the NAs are inside the serie.
Any idea?
here's an example code (different image):
pollen <- c(45, 257.4, 24.67, 54.6, 89.4, 297, 471.25, 1256.5, 312.25, 969.2, 787.5, 425, NaN, 76.6, 42.67, 38.5, 20.2, 5.67, 15.8, 13.2, 11, 6.25, 6.67, 2.3, 0.5, 30.8, 3.75, 3, 2, 2.2, 3.25, 4.5, 9.6, 15.8, 200.2, NaN)
weeks.vec <- c(5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40)
plot.ts(y = pollen, x = weeks.vec, col = 'red', ylab = 'Pollen', xlab = 'Weeks', lwd = 3, xy.labels = F, xy.lines = T)
pollen[is.na(pollen)] <- 0
poly.y <- c(0,pollen,0)
poly.x <- c(weeks.vec[1], weeks.vec, weeks.vec[length(weeks.vec)])
polygon(y = poly.y, x = poly.x, density = NA,border = NA, col = rgb(1,0,0, .3))

Answer 1

I'd use ggplot2:
pollen <- c(45, 257.4, 24.67, 54.6, 89.4, 297, 471.25, 1256.5, 312.25, 969.2, 787.5, 425, NaN, 76.6, 42.67, 38.5, 20.2, 5.67, 15.8, 13.2, 11, 6.25, 6.67, 2.3, 0.5, 30.8, 3.75, 3, 2, 2.2, 3.25, 4.5, 9.6, 15.8, 200.2, NaN)
weeks.vec <- c(5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40)
DF <- data.frame(pollen, weeks.vec)
library(ggplot2)
ggplot(DF, aes(x = weeks.vec, y = pollen)) +
geom_ribbon(aes(ymin = 0, ymax = pollen),
colour = NA, fill = "red", alpha = 0.3) +
geom_line(colour = "red") +
geom_point(colour = "red", size = 3) +
xlab("Week") + ylab("Pollen") +
theme_bw()
But if you must use base plots:
plot.ts(y = pollen, x = weeks.vec, col = 'red',
ylab = 'Pollen', xlab = 'Weeks', lwd = 3,
xy.labels = F, xy.lines = T)
g <- cumsum(!is.finite(pollen))
for (i in unique(g)) {
y <- pollen[g == i]
x <- weeks.vec[g == i]
x <- x[is.finite(y)]
y <- y[is.finite(y)]
x <- c(x, rev(x))
y <- c(y, y * 0)
polygon(y = y, x = x, density = NA,border = NA, col = rgb(1,0,0, .3))
}