导出高分辨率、节点标记的系统发育树

Question

老读者，第一次发问者！

所以我有一个包含18个提示(A-Q)和17个内部节点的系统发育树。内部节点用一些彩色馅饼标记，如下所示：

    plot(tree, cex = 0.8, label.offset= 1)
mbv <- c(1,1,1,1,1,1,1,1,1,0,0,1,1,1,0,0,0)
nodelabels(pie = mbv, piecol = c("black", "white"), cex = 0.8)

trait <- c(0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1)
names(trait)<-tree$tip.label
tiplabels(pie = to.matrix(trait, sort(unique(trait))), piecol = c("black", "white"), 
          cex = 0.4)

我正在尝试导出高分辨率的PNG或Tiff图像的这棵树，但我有问题。

原始代码：

Cairo(filename='SpeciesTree_withBins.png', type="png", res=300)
par(mar=c(1,1,1,1))
{plot(tree, cex = 0.8, label.offset= 1)
mbv <- c(1,1,1,1,1,1,1,1,1,0,0,1,1,1,0,0,0)
nodelabels(pie = mbv, piecol = c("black", "white"), cex = 0.8)
trait <- c(0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1)
names(trait)<-tree$tip.label
tiplabels(pie = to.matrix(trait, sort(unique(trait))), piecol = c("black", "white"), 
          cex = 0.4)}
dev.off()

这导致了以下错误：

Error in symbols(xpos, ypos, circles = radius, inches = FALSE, add = TRUE,  : 
  plot.new has not been called yet

尝试的解决方案1：

Cairo(filename='SpeciesTree_withBins.png', type="png", res=300)
{plot(tree, cex = 0.8, label.offset= 1)
  mbv <- c(1,1,1,1,1,1,1,1,1,0,0,1,1,1,0,0,0)
  nodelabels(pie = mbv, piecol = c("black", "white"), cex = 0.8)    
  trait <- c(0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1)
  names(trait)<-tree$tip.label
  tiplabels(pie = to.matrix(trait, sort(unique(trait))), piecol = c("black", "white"), 
            cex = 0.4)}
dev.off()

这给了我一个不同的错误：

 Error in plot.new() : figure margins too large 

尝试的解决方案2：

Cairo(filename='SpeciesTree_withBins.png', type="png", res=300)
par(mar=c(1,1,1,1))
{plot(tree, cex = 0.8, label.offset= 1)
mbv <- c(1,1,1,1,1,1,1,1,1,0,0,1,1,1,0,0,0)
nodelabels(pie = mbv, piecol = c("black", "white"), cex = 0.8)
trait <- c(0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1)
names(trait)<-tree$tip.label
tiplabels(pie = to.matrix(trait, sort(unique(trait))), piecol = c("black", "white"), 
          cex = 0.4)}
dev.off()

这确实生成了一个PNG，但名称为'plot‘而不是’‘SpeciesTree_withBins’，结果图像被严重压缩。

Squashedplot

我不确定如何解决这个问题。有没有人可以帮我导出一个没有压缩的高分辨率的节点标记树(最好是用正确的文件名)？

Answer 1

这似乎是由于解决方案问题造成的。请注意，我无法重现您的示例，因此我可能会稍微偏离正轨(即，我不知道tree和Cairo函数从何而来--我还假设您使用的是phytools::to.matrix)。

您的解决方案2似乎运行良好，您可以使用png而不是Cairo更改文件的名称，还可以使用png中的height和width参数更改绘图尺寸

library(ape)
library(phytools)
## Making a random tree
tree <- rtree(18)

## Setting up the png output file
## you might want to change the width and height here!
png(filename = "SpeciesTree_withBins.png", res = 300,
    width = 800, height = 800)

## The margin definition
par(mar = c(1,1,1,1))

## Some tree parameters
mbv <- c(1,1,1,1,1,1,1,1,1,0,0,1,1,1,0,0,0)
trait <- c(0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1)
names(trait) <- tree$tip.label

## Plotting the tree
plot(tree, cex = 0.8, label.offset= 1)
nodelabels(pie = mbv, piecol = c("black", "white"), cex = 0.8)
tiplabels(pie = to.matrix(trait, sort(unique(trait))),
                          piecol = c("black", "white"),cex = 0.4)

## Saving the file
dev.off()