In order to show specific features from the results of my PCA (with FactomineR), I am trying to manipulate the plot of individuals and the biplot with the factoextra package.
I want to draw ellipses around my individuals, but they belong to 10 different groups and the result is not easily readable, so I would like to select the more representative groups for drawing ellipses, while keeping all the individuals represented on the graphs (as dots + names).
So far, I haven't succeed in keeping both (individuals with ellipse + individuals without) trying this kind of things
fviz_ellipses(res.pca, select.list= list(name= "active.ind"), habillage = DF$Group, addEllipses = T)
with active.ind a vector of the selected rows (individuals).
I tried adding ellipses like a geom in ggplot2, like this
fviz_pca_ind(res.pca, repel = T)+
fviz_ellipses(res.pca, select.list= list(name= "active.ind"), habillage = DF$Group, addEllipses = T)
but it returns the error Error: Don't know how to add o to a plot
I am also wondering if there is any way to separate the colours of the individuals and the ellipses, having colours matching a group and ellipses matching another (there would be a coloured circle ellipse grouping dots of different colour): habillage and addEllipses seem to always work together, but is there any other way to add a scale_color or something like that and make it prevail over habillage ?
The easier thing I could think of would be to add ellipses as an independent object, although I have no clue about how to do that.
Any thoughts would be very welcome. Thanks !