使用tidydr快速可视化各种降维结果

install.packages("tidydr")

devtools::install_github("YuLab-SMU/tidydr")

library(tidydr)

# 查看支持的方法
available_methods()
## The `dr()` function works for the following methods that
## require data matrix (or data frame) as input:
##   +  stats::prcomp()
##   +  Rtsne::Rtsne()
##   +  uwot::umap()
##   +  uwot::tumap()
##   +  uwot::lvish()
## The `dr()` function works for the following methods that
## require distance matrix (or distance object) as input:
##   +  stats::cmdscale()
##   +  MASS::sammon()
##   +  vegan::metaMDS()
##   +  ape::pcoa()
##   +  smacof::mds()
##   +  vegan::wcmdscale()
##   +  ecodist::pco()
##   +  labdsv::pco()
##   +  ade4::dudi.pco()

# 首先选择方法
x <- dr(data = iris[,1:4], fun = prcomp)

# 然后用ggplot2画图，就是这么简单！
library(ggplot2)
## metadata as a vector
ggplot(x, aes(Dim1, Dim2), metadata=iris$Species) + 
  geom_point(aes(color=.group))+theme_minimal()

autoplot(x, aes(color=Species), metadata = iris[, 5, drop=FALSE]) +
  theme_dr()