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rpcaellipsefactoextra

Removing the inner color of the ellipse in PCA

Does anyone know how to change the transparency(or alpha) of the color in the ellipse?
I want to remain only the line of boundary in the plot.
I tried to mimic the code in this site: http://www.sthda.com/english/wiki/fviz-pca-quick-principal-component-analysis-data-visualization-r-software-and-data-mining

But I could not find the option about the alpha value of the ellipse color.

#Dataset
require(ggplot2)
require(ggfortify)
require(factoextra)

set.seed(1)
df <- structure(list(Sample = c("cat", "dog", "rabbit", "chicken", "duck", "butterfly", "ladybug", "rose", "lily", "iris", "maple tree", "pinetree", "ginkgo"), 
                     Class = c("mammalia", "mammalia", "mammalia", "bird", "bird", "insect", "insect", "flower", "flower", "flower", "tree", "tree", "tree"), 
                     Kingdom = c("animalia", "animalia", "animalia", "animalia", "animalia", "animalia", "animalia", "plantae", "plantae", "plantae", "plantae", "plantae", "plantae")), 
                class = "data.frame", row.names = c(NA, -13L))
rownames(df)<-df[,1]
df[,1]<-NULL

for(i in 3:20){
  df[,i]<-sample(100, size=nrow(df), replace=TRUE)
}
df[,c(3:20)]<-log(df[,c(3:20)]+1, base=2)

df #I ommitted the value from v13 to v20 for simplicity
              Class  Kingdom       V3       V4       V5       V6       V7       V8       V9      V10      V11      V12
cat        mammalia animalia 6.108524 5.781360 5.087463 5.357552 4.247928 5.614710 5.000000 5.129283 5.321928 6.303781
dog        mammalia animalia 5.321928 6.228819 6.409391 5.491853 4.523562 6.491853 4.169925 3.459432 4.643856 4.523562
rabbit     mammalia animalia 1.000000 3.000000 5.169925 4.700440 6.303781 4.584963 6.209453 1.000000 5.754888 6.149747
chicken        bird animalia 5.129283 6.209453 6.149747 6.149747 6.044394 6.409391 6.459432 5.459432 6.539159 4.857981
duck           bird animalia 6.459432 6.321928 6.228819 5.321928 6.149747 4.906891 6.392317 5.906891 6.442943 5.247928
butterfly    insect animalia 5.459432 6.426265 5.426265 5.700440 6.459432 3.807355 6.507795 4.754888 5.357552 5.954196
ladybug      insect animalia 3.906891 5.247928 5.285402 5.426265 6.149747 4.523562 5.614710 4.000000 6.614710 5.554589
rose         flower  plantae 6.375039 6.491853 4.392317 2.807355 6.247928 6.554589 6.022368 5.882643 6.392317 6.087463
lily         flower  plantae 5.906891 5.247928 4.857981 4.643856 6.357552 4.857981 6.569856 4.906891 6.507795 6.442943
iris         flower  plantae 5.700440 5.129283 4.392317 5.044394 6.658211 5.614710 6.599913 4.643856 5.169925 6.643856
maple tree     tree  plantae 6.614710 6.491853 5.491853 3.906891 3.807355 5.087463 5.930737 5.426265 5.459432 6.169925
pinetree       tree  plantae 6.426265 5.491853 6.459432 1.584963 5.357552 5.523562 5.700440 5.614710 1.000000 6.643856
ginkgo         tree  plantae 4.459432 6.321928 6.149747 5.523562 6.491853 4.459432 6.554589 6.266787 4.906891 5.700440

pca_df<-prcomp(df[,-c(1,2)], scale.=TRUE)
fviz_pca_ind(pca_df,
             col.ind=df$Kingdom,
             addEllipses = TRUE,
             col.ind.sup=df$Kingdom,
             repel=TRUE)

enter image description here

Solution

  • You may use ellipse.alpha argument that can find here.

    fviz_pca_ind(pca_df,
             col.ind=df$Kingdom,
             addEllipses = TRUE,
             col.ind.sup=df$Kingdom,
             repel=TRUE, ellipse.alpha = 0)

    enter image description here

    (I forgot to set seed. Sorry...)