Any way to make plot points in scatterplot more transparent in R?

Question

I have a 3 column matrix; plots are made by points based on column 1 and column 2 values, but colored based on column 2 (6 different groups). I can successfully plot all points, however, the last plot group (group 6) which was assigned the color purple, masks the plots of the other groups. Is there a way to make the plot points more transparent?

s <- read.table("/.../parse-output.txt", sep="\t")  dim(s)  [1] 67124     3 x <- s[,1]  y <- s[,2] z <- s[,3]  cols <- cut(z, 6, labels = c("pink", "red", "yellow", "blue", "green", "purple")) plot(x, y, main= "Fragment recruitment plot - FR-HIT", ylab = "Percent identity", xlab = "Base pair position", col = as.character(cols), pch=16)  

Answer 1

Otherwise, you have function alpha in package scales in which you can directly input your vector of colors (even if they are factors as in your example):

library(scales) cols <- cut(z, 6, labels = c("pink", "red", "yellow", "blue", "green", "purple")) plot(x, y, main= "Fragment recruitment plot - FR-HIT",       ylab = "Percent identity", xlab = "Base pair position",       col = alpha(cols, 0.4), pch=16)  # For an alpha of 0.4, i. e. an opacity of 40%. 

Answer 2

When creating the colors, you may use rgb and set its alpha argument:

plot(1:10, col = rgb(red = 1, green = 0, blue = 0, alpha = 0.5),      pch = 16, cex = 4) points((1:10) + 0.4, col = rgb(red = 0, green = 0, blue = 1, alpha = 0.5),        pch = 16, cex = 4) 

Please see ?rgb for details.