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rplotpca

Set axis limits for plot.PCA - strange behaviour (FactoMineR)

I want to plot the result of a PCA with the package factominer. When one plots a PCA it is good practice to resize the graph so that its H/L ratio is in proportion to the %variance explained by each axis.

So I tried first to resize the graph simply by stretching the window: it obviously fails and keep the points in the middle instead of stretching them too.

library(FactoMineR)
out <- PCA(mtcars)

enter image description here

Then I try to force the xlim and ylim arguments to be fixed (?plot.PCA)

plot.PCA(out, choix="ind", xlim=c(-6,6), ylim=c(-4, 4))

enter image description here

Same problem, the xlim limits are not respected...

Can someone explain this behaviour and knows how to fix it?

Solution

  • What you're seeing is the result of the call to plot inside plot.PCA: 

    plot(0, 0, main = titre, xlab = lab.x, ylab = lab.y, 
     xlim = xlim, ylim = ylim, col = "white", asp = 1, ...)

    plot is called with parameter asp set to 1, which guarantees that the y/x ratio stays the same, so when you try to resize the window, the xlim are recomputed.

    In plot.window you can find the "meaning" of asp:

    If asp is a finite positive value then the window is set up so that one data unit in the x direction is equal in length to asp * one data unit in the y direction.

    You can try

    plot(0, 0, main = "", xlab = "", ylab = "", xlim = c(-6, 6), ylim = c(-4, 4), col = "white", asp = 1)

    and resizing the window, and then the same with

    plot(0, 0, main = "", xlab = "", ylab = "", xlim = c(-6, 6), ylim = c(-4, 4), col = "white")

    to see the difference.