Separate boxplots for multiple violin plot
The vioplot package comes built in with boxplots. You can download it from CRAN or there are more features (including formula input and separate colours) in the development version on GitHub: https://github.com/TomKellyGenetics/vioplot

devtools::install_github(“TomKellyGenetics/vioplot”)
library(“vioplot”)
vioplot(pbmc_small@dr@pca[,1]~pbmc_small@meta.data$ident)


To plot several PCs:

library(“RColorBrewer”)
colours &lt;- brewer.pal(length(unique(pbmc_small@meta.data$ident)), “Set3”)
par(mfrow = c(1, 2))
vioplot(pbmc_small@dr@pca[,1]~pbmc_small@meta.data$ident, main = “PC1”, xlab = “Identity”, col = colours)
vioplot(pbmc_small@dr@pca[,2]~pbmc_small@meta.data$ident , main = “PC2”, xlab = “Identity”, col = colours)
par(mfrow = c(1, 1))