[英]Any way to make plot points in scatterplot more transparent in R?
我有一个3列矩阵; 绘图是根据第1列和第2列的值按点绘制的,但根据第2列(6个不同的组)进行着色。 我可以成功绘制所有点,但是最后一个被分配为紫色的绘图组(第6组)掩盖了其他组的图形。 有没有办法使绘图点更透明?
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,您将在包装scales
中具有功能alpha
,在其中可以直接输入颜色矢量(即使它们是示例中的因素):
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%.
透明度也可以在color参数中编码。 它只是另外两个十六进制数字,编码的透明度介于0(完全透明)和255(完全可见)之间。 我曾经写过这个函数来增加颜色矢量的透明度,也许在这里有用吗?
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)
如果决定使用ggplot2
,则可以使用alpha
参数设置重叠点的alpha
。
例如
library(ggplot2)
ggplot(diamonds, aes(carat, price)) + geom_point(alpha = 1/40)
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