Invert PCA generated graph

General
1

How can I invert/flip of PCA graph, please?

Here is the code:

library("FactoMineR")
library("factoextra")
mydata<- read.csv("Ikizdere.csv", TRUE, ",")
mydata[is.na(mydata)]=0
attach(mydata)
X=cbind (Temp., pH, EC, Perm_Ind, DO, CaCO3, o_PO4, TP, TSS, NO3_N, NO2_N, Chl_a, NH4_N, LAS, As, Cr, Cu, Mn, Ni, Pb, Zn)
summary(X)
cor(X)
res.pca <- princomp(X, scores=TRUE, cor=TRUE)
summary(res.pca)

fviz_pca_var(res.pca, col.var="contrib",
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE # Avoid text overlapping
)

PCA%20plot

2

what exactly do you mean by invert/flip? Do you want to sort the y axis in the opposite direction? Reverse the x axis?

Because what you asked could be interpreted as this:

image

which is may or may not be what you want.

3

Thanks for the kind reply. From here you can check my two graphs (https://drive.google.com/file/d/1NzBy5qix7DOCqQ6F88J2aEtga-sp-lY5/view?usp=sharing)

Both graphs are same (of course with same meaning) but the direction of the vectors is in the opposite direction. I want to invert the first plot.

4

Please download the file so you could see both plots.

5

the direction of the vectors has meaning and it hardly seems something one would arbitrarily reverse. But you could swap the axes like this:

fviz_pca_var(res.pca, axes=c(2,1), col.var="contrib",
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE # Avoid text overlapping
)
6

I may be late in answering this, but I noticed the same difference when plot my PCA, wherein the axes were flipped depending on whether I used vegan or factominer.

A quick solution is to add + xlim(c(1,-1) + ylim(c(1,-1)). For instance,

fviz_pca_var(res.PCA, axes=c(1,2), repel=TRUE, col.var="contrib", gradient.cols=c("white","#f47a27", "#ed4040"), ggtheme=theme_minimal()) + xlim(c(1,-1) + ylim(c(1,-1))

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