How to plot a PCA bubbleplot in r?-CodePudding

I have done a PCA, but I tried to plot the points in bubbleplot format, with different sizes depending on a variable value:

Here is my code:

library("FactoMineR")
library("factoextra")

ulva<-c(1,1,0,2,3,2)
sediment<-c(1,1,1,3,3,4)
deep<-c(3,3,2,1,1,1)
site<-c("CH","CH","CH","AA","AA","AA")
ulva2<-c("1","1","0","2","3","2")
data<-data.frame(site,sediment,deep,ulva2)
#Then I perform the PCA
s.pca <- PCA(data[,2:3], graph = FALSE)
#And I plot it:
a<-fviz_pca_biplot(s.pca, repel = TRUE, # Variables color
                col.ind = "#00FF00",  # Individuals color
                pointsize=ulva2,fill.ind = "#00FF00",
                pointshape = 21, 
                )
a

The problem is that I cannot change the "sizepoint" title, I would like to write "Ulva" instead of "sizepoint". Furthermore, I would like to write the site (CH or AA) in the point and not the number of the sample.

I would appreciate any help, please.

Thank you in advance.

CodePudding user response：

Since factoextra as a plotting library wraps ggplot2, we can use standard additional plot components to add the labels you want and change the legend.

First, make sure when plotting that you set label = "none" in fviz_pca_biplot() to ensure that the sample number isn't plotted next to the points.

a<-fviz_pca_biplot(s.pca, repel = TRUE, # Variables color
                   col.ind = "#00FF00",  # Individuals color
                   pointsize=ulva2,fill.ind = "#00FF00",
                   pointshape = 21,
                   label = "none"
)

Now, we want to get a data frame plotting the labels, so let's pull out the new coordinate system and attach the old labels to it.

# get label per point
df_label <- as.data.frame(s.pca$ind$coord)
names(df_label) <- c("x", "y")
df_label$label <- site
df_label
#>            x          y label
#> 1 -1.5990451  0.2392449    CH
#> 2 -1.5990451  0.2392449    CH
#> 3 -0.8112065 -0.5485937    CH
#> 4  1.1421751 -0.1708892    AA
#> 5  1.1421751 -0.1708892    AA
#> 6  1.7249466  0.4118823    AA

Now with this, we can use geom_text() to plot those points, at the same time using labs() to change the legend to say "Ulva".

a  
  geom_text(
    data = df_label,
    aes(label = label),
    check_overlap = TRUE
  )  
  labs(
    size = "Ulva"
  )

If overlapping points might have multiple sites, so that you would want to show them individually, use ggrepel::geom_text_repel() instead of ggplot2::geom_text().