Animation of PCA vs. tSNE dimension reduction

diabetes-pca-tsne.R

#' ---
#' title: Animate transition from PCA <--> tsne
#' ---
# idea from: https://jef.works/genomic-data-visualization-2024/blog/2024/03/06/akwok1/

#' ## Load packages and data
library(ggplot2) 
library(gganimate) 
library(Rtsne) 
library(patchwork)

data(Diabetes, package="heplots")

#' ## PCA
diab.pca <- prcomp(Diabetes[, 1:5], scale = TRUE, rank.=2) 
df1 <- data.frame(diab.pca$x, group = Diabetes$group) 
colnames(df1) <- c("Dim1", "Dim2", "group")
df1 <- cbind(df1, method="PCA")


p1 <- ggplot(df1, aes(x=Dim1, y=Dim2, color=group, shape=group)) + 
  geom_point(size = 3) + 
  stat_ellipse(level = 0.68, linewidth=1.1) +
  geom_hline(yintercept = 0) +
  geom_vline(xintercept = 0) +
  labs(x = "Dimension 1",
       y = "Dimension 2") + 
  ggtitle("PCA") +
  theme_bw(base_size = 16) +
  theme(legend.position = "bottom") 
p1

#' ## tSNE: nonlinear dimensionality reduction 
set.seed(123) 
diab.tsne <- Rtsne(Diabetes[, 1:5], scale = TRUE)
df2 <- data.frame(diab.tsne$Y, group = Diabetes$group) 
colnames(df2) <- c("Dim1", "Dim2", "group")
df2 <- cbind(df2, method="tSNE")

p2 <- ggplot(df2, aes(x=Dim1, y=Dim2, color = group, shape=group)) + 
  geom_point(size = 3) + 
  stat_ellipse(level = 0.68, linewidth=1.1) +
  geom_hline(yintercept = 0) +
  geom_vline(xintercept = 0) +
  labs(x = "Dimension 1",
       y = "Dimension 2") + 
  ggtitle("tSNE") +
  theme_bw(base_size = 16) +
  theme(legend.position = "bottom") 
p2

p1 + p2

#' ## Make an animated plot showing transitions between the PCA representation and the tsne one

df3 <- rbind(df1, df2) 

animated_plot <- 
  ggplot(df3, aes(x=Dim1, y=Dim2, color=group, shape=group)) + 
  geom_point(size = 3) + 
  stat_ellipse(level = 0.68, linewidth=1.1) +
  geom_hline(yintercept = 0) +
  geom_vline(xintercept = 0) +
  labs(title = "PCA vs. tSNE Dimension Reduction: {closest_state}",
       subtitle = "Frame {frame} of {nframes}",
       x = "Dimension 1",
       y = "Dimension 2") + 
  transition_states( method, transition_length = 2, state_length = 3 ) + 
  view_follow() + 
  theme_bw(base_size = 16) +
  theme(legend.position = "bottom") 

animated_plot

anim_save("diabetes-pca-tsne.gif", animated_plot, path="images/")