Colored ind PCA

[Hersh]

Hi,
I would like to colored my sites/ind in my PCA but it doesn't work
I saw I have to use "habillage = " but I can't colored my ind depending on "eco" and have at the same time my var colored with the cos2

This firts code work well

eco <- as.character(Env$Clust

fviz_pca_biplot(res.pca, repel = TRUE,
                col.var = "cos2",
                gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07") 
                ) 

This one work well also and with this one I have my ind colored but I don't have my colored var with cos2

fviz_pca_biplot(res.pca, label="var", habillage=iris$Species,
               addEllipses=TRUE, ellipse.level=0.95)

How can I merge these two code ?
I tried to do that but it say "Error: Discrete value supplied to continuous scale" :

fviz_pca_biplot(res.pca, repel = TRUE,
                col.var = "cos2",
                gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
                habillage = eco
                )

[M_AcostaCH]

Hi @Hersh , remember put a reporducible example of data for better help you, like this dput() or reprex
And script for replicate the situation.

FAQ: What's a reproducible example (`reprex`) and how do I create one?

Why reprex? Getting unstuck is hard. Your first step here is usually to create a reprex, or reproducible example. The goal of a reprex is to package your code, and information about your problem so that others can run it and feel your pain. Then, hopefully, folks can more easily provide a solution. What's in a Reproducible Example? Parts of a reproducible example: background information - Describe what you are trying to do. What have you already done? complete set up - include any library() calls and data to reproduce your issue. data for a reprex: Here's a discussion on setting up data for a reprex make it run - include the minimal code required to reproduce your error on the data…

Check this documentation for know more about PCA

FactoMineR and factoextra : Principal Component Analysis Visualization - R...

[Hersh]

Hello
Thanks for your response and sorry for the late response, I was looking for a way to send a reproductible example of a df without using mine !

So here a example :

library(factoextra)
library(ggplot2)
data <- iris
habillage <- as.character(data$Species)
res.pca <- prcomp(data[,1:4],  scale = TRUE)

fviz_pca_biplot (res.pca, 
                 # Individuals
                 geom.ind = c("point","text"),
                 fill.ind = habillage,
                 pointshape = 21, pointsize=5,
                 palette = "set2",labelsize = 5, 
                 addEllipses=TRUE, ellipse.level=0.90, mean.point =FALSE, label="all",
                 repel = TRUE, 
                 #variables
                 col.var="contrib",gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07")) +
  labs(fill = "Cluster", color = "Contrib", alpha = "contrib") +
  theme_minimal()
#> Warning: ggrepel: 106 unlabeled data points (too many overlaps). Consider
#> increasing max.overlaps

I succeed to have both my Cluster color and "contrib" color but I just want to modify the Cluster color
I want to have "Setosa" in green, "Versicolor" in blue and "Virginica" in red

I tried many way but also the same problem about "discrete value supplied to continus scale" and so one...

[Hersh]

Ok, so apparently it was as simple as doing this :

palette = c("green","blue","red")

I'm not used to R being simple from time to time!
Sorry for the inconvenience, hope this post helps someone!