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，分配为紫色的最后一个绘图组（第 6 组）掩盖了其他组的绘图。有没有办法让情节点更透明？
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)
否则，您alpha在包scales中有功能，您可以在其中直接输入颜色矢量（即使它们是您示例中的因素）：
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%.
创建颜色时，您可以使用rgb并设置其alpha参数：
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)
详情请参阅?rgb。
透明度也可以在颜色参数中编码。它只是另外两个十六进制数字，编码介于 0（完全透明）和 255（完全可见）之间的透明度。我曾经写过这个函数来为颜色向量添加透明度，也许它在这里有用？
addTrans <- function(color,trans)
{
# This function adds transparancy to a color.
# Define transparancy with an integer between 0 and 255
# 0 being fully transparant and 255 being fully visable
# Works with either color and trans a vector of equal length,
# or one of the two of length 1.
if (length(color)!=length(trans)&!any(c(length(color),length(trans))==1)) stop("Vector lengths not correct")
if (length(color)==1 & length(trans)>1) color <- rep(color,length(trans))
if (length(trans)==1 & length(color)>1) trans <- rep(trans,length(color))
num2hex <- function(x)
{
hex <- unlist(strsplit("0123456789ABCDEF",split=""))
return(paste(hex[(x-x%%16)/16+1],hex[x%%16+1],sep=""))
}
rgb <- rbind(col2rgb(color),trans)
res <- paste("#",apply(apply(rgb,2,num2hex),2,paste,collapse=""),sep="")
return(res)
}
一些例子：
cols <- sample(c("red","green","pink"),100,TRUE)
# Fully visable:
plot(rnorm(100),rnorm(100),col=cols,pch=16,cex=4)
# Somewhat transparant:
plot(rnorm(100),rnorm(100),col=addTrans(cols,200),pch=16,cex=4)
# Very transparant:
plot(rnorm(100),rnorm(100),col=addTrans(cols,100),pch=16,cex=4)
如果您使用的是十六进制代码，您可以在代码末尾再添加两位数字来表示 Alpha 通道：
例如半透明红色：
plot(1:100, main="Example of Plot With Transparency")
lines(1:100 + sin(1:100*2*pi/(20)), col='#FF000088', lwd=4)
mtext("use `col='#FF000088'` for the lines() function")
如果您决定使用ggplot2，您可以使用参数设置重叠点的透明度alpha。
例如
library(ggplot2)
ggplot(diamonds, aes(carat, price)) + geom_point(alpha = 1/40)