How to add density plot per component in PCA plot in R?

user_14010653 0
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I would like to know how add density to PCA plot .

This is my basic example which i would like to begin

x <- iris[1:4]
pc <- prcomp(x)
df <- cbind(pc$x[,1:2], iris[,5]) %>% as.data.frame()
df$PC1 <- as.numeric(df$PC1) / (pc$sdev[1] * sqrt(nrow(iris)))
df$PC2 <- as.numeric(df$PC2) / (pc$sdev[2] * sqrt(nrow(iris)))
df$V3 <- as.factor(df$V3)

#ggplot method
p1 <- ggplot(df, aes(PC1, PC2, colour = V3)) +
  geom_point(size = 3, aes(shape = V3)) +
  stat_ellipse(geom = "polygon", aes(fill = after_scale(alpha(colour, 0))),
               data = df[df$V3 == "1" | df$V3 == "2",], size = 1) 
p1

Now PCA with density figure(E)

I would like to add similar to my plot too how to do that? Any suggestion or help would be really appreciated.

pca ggplot2 r
1 Answers

You could use the package cowplot by using insert_*axis_grob to insert two geom_density plots at the top x-axis and right y-axis. For the top x-axis density curve you can use the values of PC1 and for the right y-axis density curve you can use the values of PC2 and both color and fill them with V3. Make sure to specify the right axis for both graphs. Here is a reproducible example:

library(cowplot)
library(dplyr)
library(ggplot2)
x <- iris[1:4]
pc <- prcomp(x)
df <- cbind(pc$x[,1:2], iris[,5]) %>% as.data.frame()
df$PC1 <- as.numeric(df$PC1) / (pc$sdev[1] * sqrt(nrow(iris)))
df$PC2 <- as.numeric(df$PC2) / (pc$sdev[2] * sqrt(nrow(iris)))
df$V3 <- as.factor(df$V3)

# plot
p1 <- ggplot(df, aes(PC1, PC2, colour = V3)) +
  geom_point(size = 3, aes(shape = V3)) +
  stat_ellipse(geom = "polygon", aes(fill = after_scale(alpha(colour, 0))),
               data = df[df$V3 == "1" | df$V3 == "2",], size = 1)

# Add density curves to y and x axis
xdens <- 
  axis_canvas(p1, axis = "x") + 
  geom_density(data = df, aes(x = PC1, fill = V3, colour = V3), alpha = 0.3)
ydens <-
  axis_canvas(p1, axis = "y", coord_flip = TRUE) + 
  geom_density(data = df, aes(x = PC2, fill = V3, colour = V3), alpha = 0.3) +
  coord_flip()
p1 %>%
  insert_xaxis_grob(xdens, grid::unit(1, "in"), position = "top") %>%
  insert_yaxis_grob(ydens, grid::unit(1, "in"), position = "right") %>%
  ggdraw()

Created on 2022-08-31 with reprex v2.0.2

user_142827140
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