Question

我试图通过在R中制作一个双色标来可视化PCoA{ape}的结果。轴现在获得默认标签轴1和轴2，但我想编辑它。

这是我尝试过的代码：

biplot(pcoa.ntK, Y=NULL, plot.axes=c(1,2), rn=ntnames,
                           xlabs="PC1 (%)", ylabs="PC2 (%)")

但标签不会发生变化。有人能告诉我这里我做错了什么吗？而且我也想编辑标题，任何有关此的提示？

我的数据：

ntK <- matrix( 
  c(0.00000, 0.01500, 0.01832, 0.02061, 0.01902, 0.01270, 0.02111, 0.01655, 0.01520, 0.01691,
    0.01667, 0.00000, 0.01175, 0.01911, 0.01759, 0.01127, 0.01854, 0.01041, 0.00741, 0.02007,
    0.02432, 0.01404, 0.00000, 0.02551, 0.01972, 0.01838, 0.02505, 0.01484, 0.01391, 0.02687,
    0.01501, 0.01252, 0.01399, 0.00000, 0.01442, 0.01294, 0.01402, 0.01132, 0.01239, 0.01455,
    0.02343, 0.01951, 0.01830, 0.02440, 0.00000, 0.01727, 0.02470, 0.02021, 0.01699, 0.02482,
    0.01320, 0.01054, 0.01439, 0.01847, 0.01457, 0.00000, 0.01818, 0.01366, 0.00977, 0.01394,
    0.02468, 0.01950, 0.02206, 0.02251, 0.02343, 0.02040, 0.00000, 0.02028, 0.01875, 0.02558,
    0.02254, 0.01276, 0.01522, 0.02117, 0.02234, 0.01790, 0.02363, 0.00000, 0.01152, 0.02557,
    0.01804, 0.00792, 0.01244, 0.02019, 0.01637, 0.01116, 0.01904, 0.01004, 0.00000, 0.02099,
    0.01862, 0.01988, 0.02227, 0.02200, 0.02218, 0.01476, 0.02408, 0.02066, 0.01947, 0.00000), 
  nrow=10, 
  ncol=10)

library(ape)
ntnames <- c("A","B","C","D","E","F","G","H","I","J")
pcoa.ntK <- pcoa(ntK)

Answer 1

biplot是一个通用函数。使用prcomp包中使用stats函数的对象的默认方法和方法允许您指定轴标签和标题，但由于某种原因，编写方法的人使用类pcoa的对象调用时，不允许您指定它们。我认为您唯一的选择是编写自己的biplot.pcoa版本（或要求软件包维护者添加此选项）。

这是ape包中可能做你想要的功能的一个非常快速和肮脏的黑客攻击，但没有任何承诺，它赢得了别的东西！

biplot.pcoa <- function (x, Y = NULL, plot.axes = c(1, 2), dir.axis1 = 1, dir.axis2 = 1, 
          rn = NULL, xlabs = NULL, ylabs = NULL, main = NULL, ...) 
{
  k <- ncol(x$vectors)
  if (k < 2) 
    stop("There is a single eigenvalue. No plot can be produced.")
  if (k < plot.axes[1]) 
    stop("Axis", plot.axes[1], "does not exist.")
  if (k < plot.axes[2]) 
    stop("Axis", plot.axes[2], "does not exist.")
  if (!is.null(rn)) 
    rownames(x$vectors) <- rn
  labels = colnames(x$vectors[, plot.axes])
  if (!is.null(xlabs)) labels[1] <- xlabs
  if (!is.null(ylabs)) labels[2] <- ylabs
  diag.dir <- diag(c(dir.axis1, dir.axis2))
  x$vectors[, plot.axes] <- x$vectors[, plot.axes] %*% diag.dir
  if (is.null(Y)) {
    limits <- apply(x$vectors[, plot.axes], 2, range)
    ran.x <- limits[2, 1] - limits[1, 1]
    ran.y <- limits[2, 2] - limits[1, 2]
    xlim <- c((limits[1, 1] - ran.x/10), (limits[2, 1] + 
                                            ran.x/5))
    ylim <- c((limits[1, 2] - ran.y/10), (limits[2, 2] + 
                                            ran.y/10))
    par(mai = c(1, 1, 1, 0.5))
    plot(x$vectors[, plot.axes], xlab = labels[1], ylab = labels[2], 
         xlim = xlim, ylim = ylim, asp = 1)
    text(x$vectors[, plot.axes], labels = rownames(x$vectors), 
         pos = 4, cex = 1, offset = 0.5)
    if (is.null(main)){
      title(main = "PCoA ordination", line = 2.5)
    } else title(main = main, line = 2.5)
  }
  else {
    n <- nrow(Y)
    points.stand <- scale(x$vectors[, plot.axes])
    S <- cov(Y, points.stand)
    U <- S %*% diag((x$values$Eigenvalues[plot.axes]/(n - 
                                                        1))^(-0.5))
    colnames(U) <- colnames(x$vectors[, plot.axes])
    par(mai = c(1, 0.5, 1.4, 0))
    biplot(x$vectors[, plot.axes], U, xlab = labels[1], ylab = labels[2])
    if (is.null(main)) {
    title(main = c("PCoA biplot", "Response variables projected", 
                   "as in PCA with scaling 1"), line = 4)
    } else title(main = main, line = 4)
  }
  invisible()
}

biplot(pcoa.ntK, xlabs = 'My x label', ylabs = 'My y label', main = 'My title')

Answer 2

您可以查看biplot.pcoa的源代码，您会发现它并不难修改。该软件包的作者决定根据输入以及图表的主标题对轴标签进行硬编码。以下是修改后的版本，在使用预定义值之前，首先会检查xlab，ylab和main的值是否已用过：

biplot.pcoa <- function (x, Y = NULL, plot.axes = c(1, 2), dir.axis1 = 1, dir.axis2 = 1, 
          rn = NULL, ...) 
{
  k <- ncol(x$vectors)
  if (k < 2) 
    stop("There is a single eigenvalue. No plot can be produced.")
  if (k < plot.axes[1]) 
    stop("Axis", plot.axes[1], "does not exist.")
  if (k < plot.axes[2]) 
    stop("Axis", plot.axes[2], "does not exist.")
  if (!is.null(rn)) 
    rownames(x$vectors) <- rn
  args <- list(...)
  labels = ifelse(c("xlab", "ylab") %in% names(args), c(args$xlab, args$ylab), colnames(x$vectors[, plot.axes]))
  diag.dir <- diag(c(dir.axis1, dir.axis2))
  x$vectors[, plot.axes] <- x$vectors[, plot.axes] %*% diag.dir
  if (is.null(Y)) {
    limits <- apply(x$vectors[, plot.axes], 2, range)
    ran.x <- limits[2, 1] - limits[1, 1]
    ran.y <- limits[2, 2] - limits[1, 2]
    xlim <- c((limits[1, 1] - ran.x/10), (limits[2, 1] + 
                                            ran.x/5))
    ylim <- c((limits[1, 2] - ran.y/10), (limits[2, 2] + 
                                            ran.y/10))
    par(mai = c(1, 1, 1, 0.5))
    title <- ifelse("main" %in% names(args), args$main, "PCoA ordination")
    plot(x$vectors[, plot.axes], xlab = labels[1], ylab = labels[2], 
         xlim = xlim, ylim = ylim, asp = 1, 
         main = title)
    text(x$vectors[, plot.axes], labels = rownames(x$vectors), 
         pos = 4, cex = 1, offset = 0.5)
    #title(main = "PCoA ordination", line = 2.5)
  }
  else {
    n <- nrow(Y)
    points.stand <- scale(x$vectors[, plot.axes])
    S <- cov(Y, points.stand)
    U <- S %*% diag((x$values$Eigenvalues[plot.axes]/(n - 
                                                        1))^(-0.5))
    colnames(U) <- colnames(x$vectors[, plot.axes])
    par(mai = c(1, 0.5, 1.4, 0))
    title <- ifelse("main" %in% names(args), args$main, c("PCoA biplot", "Response variables projected", 
                                                              "as in PCA with scaling 1"))
    biplot(x$vectors[, plot.axes], U, xlab = labels[1], ylab = labels[2], main = title)
    # title(main = c("PCoA biplot", "Response variables projected", 
    #                "as in PCA with scaling 1"), line = 4)
  }
  invisible()
}

然后：

biplot(pcoa.ntK, Y=NULL, plot.axes=c(1,2), rn=ntnames,
   xlab="PC1 (%)", main = "Main Title")

请记住，这不会改变原始功能，因此每次加载包时都需要加载此修改版本，并且需要设置这样的标签。

在R中更改biplot（）的轴标签

2 个答案: