[英]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?有谁知道如何更改椭圆中颜色的透明度(或 alpha)?
I want to remain only the line of boundary in the plot.我只想保留 plot 中的边界线。
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我试图模仿这个站点中的代码: 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.但我找不到关于椭圆颜色的 alpha 值的选项。
#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)
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