Changing axes labels for biplot() in R - r

Question

I am trying to visualize the results of a PCoA{ape} by making a biplot in R.
The axes now get the default labels axis 1 and axis 2, but I want to edit this.
This is the code I have tried:
biplot(pcoa.ntK, Y=NULL, plot.axes=c(1,2), rn=ntnames,
xlabs="PC1 (%)", ylabs="PC2 (%)")
But the labels don't change.
Can someone tell me what I'm doing wrong here?
And I also would like to edit the title, anyone tips for this?
My data:
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 is a generic function. The default method and the method for use with objects that come from using the prcomp function in the stats package do allow you to specify axis labels and a title, but for some reason the person that wrote the method that is called with objects of class pcoa hasn't allowed you to specify them. I think your only option would be to write your own version of biplot.pcoa (or ask the package maintainer to add this option).
This is a very quick and dirty hack of the function in the ape package that might do what you want, but no promises that it won't have broken something else!
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

You can check the source code of biplot.pcoa and you'll see it's not that hard to modify. The author of the package decided to hard-code the axis labels based on the input and also the main title of the plot. Here's a modified version that will first check if values for xlab, ylab and main were used before using the pre-defined ones:
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()
}
Then:
biplot(pcoa.ntK, Y=NULL, plot.axes=c(1,2), rn=ntnames,
xlab="PC1 (%)", main = "Main Title")
Keep in mind this won't change the original function, so you'll need to load this modified version every time you load the package and need wish to set the labels like this.