r - 有什么方法可以使 R 中散点图中的绘图点更加透明吗？

Question

我有一个 3 列矩阵；绘图由基于第 1 列和第 2 列值的点绘制，但基于第 2 列(6 个不同组)着色。我可以成功绘制所有点，但是，分配了紫色的最后一个绘图组(组 6)掩盖了其他组的绘图。有没有办法让情节更加透明？

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

否则，您可以在 scales 包中使用函数 alpha，您可以在其中直接输入颜色向量(即使它们是示例中的因子):

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%.