overlapping texts (plot.PCA in FactoMineR)

Question

[mbk0asis]

Hi, all!

I was trying to draw a PCA plot using FactoMineR (a R package). When I ran it, texts on the plots were overlapped with unknown numbers.

Here's the R code

library(FactoMineR)
pca<-PCA(dta.cor, scale.unit=T)
plot.PCA(pca,cex=1)

and the result plot

As you can see numbers in pink are covering sample names.

I couldn't figure it out.

Please, someone help me!!

Thank you!!!

[GouthamAtla]

You can explore the options by looking at the help. ?plot.PCA It looks like it has label= and autoLab= options which may be useful to turn off the unwanted labels. Try to troubleshoot it yourself first, which is the best way to learn.

[venu]

Adding to other suggestions check geom_text_repel form ggrepel Check its vignette here

[mbk0asis]

Thank you, all! You guys been great help!

Answer 1

[Sukhi Singh]

You can use prcomp for PCA calculations and then plot it using ggplot and add labels using ggrepel.

ggrepel provides geoms for ggplot2 to repel overlapping text labels. It works both for geom_text and geom_label.

Figure is taken from this blog post.

[Manu Prestat]

Neat! Didn't know this ggplot feature. Thanks!

[Sukhi Singh]

The labels are from ggrepel, a package by Kamil. ggrepel: repel overlapping text labels in ggplot2