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overlapping texts (plot.PCA in FactoMineR)

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

enter image description here

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

I couldn't figure it out.

Please, someone help me!!

Thank you!!!

r factominer
• 13,701 views • link
written by mbk0asis mbk0asis

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.

• 2 views • link
written by GouthamAtla GouthamAtla

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

• 1 views • link
written by venu venu

Thank you, all! You guys been great help!

• 1 views • link
written by mbk0asis mbk0asis

1 answer

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.

enter image description here

Figure is taken from this blog post.

• 1 views • link
written by Sukhi Singh Sukhi Singh

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

• 1 views • link
written by Manu Prestat Manu Prestat

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