library(ggplot2)

foo <- expand.grid(
  chr = paste('chr', 1:3, sep = ''),
  pos = seq(1, 1e8, length.out = 1e3+1),
  sp = c('Sp A', 'Sp B', 'Sp C')
)
foo$density <- runif(nrow(foo))

p1 <- ggplot(data = foo, aes(x = pos, y = density)) +
  geom_smooth(method = 'loess', span = 0.01, se = FALSE) +
  facet_grid(sp ~ chr) +
  theme_bw()

p2 <- p1 + geom_ribbon(aes(ymin = 0, fill = chr, ymax = predict(loess(density ~ pos, span = 0.01))), alpha = 0.3)

png(filename = '~/Desktop/wo_ribbon.png', width = 1000, height = 500)
print(p1)
dev.off()

png(filename = '~/Desktop/w_ribbon.png', width = 1000, height = 500)
print(p2)
dev.off()