I have a matrix (named ichimoku) with 516 rows and 2 columns ,each one of them containing values to be plotted, the goal is to recreate the clouds for the Ichimoku strategy.
Here is some code that works for a simple version of your problem, in which the lines only cross once. I haven't tested it for repeated crossings, however.
# Make toy data
ichimoku <- data.frame(senkouA = rep(10, 10), senkouB = c(3, 5, 4, 7, 10, 11, 15, 12, 13, 14))
# Make indices for the conditions that define the fill colors. They need to intersect for the polygons to connect.
index.green = with(ichimoku, as.logical(senkouA >= senkouB))
index.red = with(ichimoku, as.logical(senkouA <= senkouB))
# Make the line plot
matplot(ichimoku, lty=1, lwd=1, pch=20, type="l", col=c("red","blue"))
# Now add polygons with fill color based on those conditions by subsetting the task using the indices.
with(ichimoku, polygon(x = c(seq(length(senkouA))[index.green], rev(seq(length(senkouA))[index.green])),
y = c(senkouB[index.green], senkouA[index.green]), col = "green"))
with(ichimoku, polygon(x = c(seq(length(senkouA))[index.red], rev(seq(length(senkouA))[index.red])),
y = c(senkouB[index.red], senkouA[index.red]), col = "red"))
Here's my result: