The plot from n_factors not working : plot the number of factors with percentage of variance explained and eigenvalues

[DominiqueMakowski]

Because the n_factors function got moved (and improved) to the parameters package, some of you realized that the figure featured here, showing the eigenvalues, the percentage of variance explained etc. was not available.

It turns out that this plot wasn't the best way to represent the results of n_factors; as the explained variance and the eigenvalues that is shows are extracted from one particular "dimension-reduction technique" (such as PCA or FA). But n_factors actually tries to estimate the optimal number of factors across different dimension reduction methods, so the two aren't really part of the same "step".

That said, here's a way of plotting them together with ggplot with multiple y axes:

library(dplyr)
library(ggplot2)
library(parameters)
library(effectsize)
library(see)

data <- summary(parameters::n_factors(attitude))
rez_pca <- summary(parameters::principal_components(attitude, n=4))

data$Eigenvalues <- as.numeric(rez_pca[1, -1]) # First row
data$VarianceExplained <- as.numeric(rez_pca[3, -1]) # Third row

# Rescale everything to eigenvalue scale - as this will our principal y-axis
newrange <- c(min(data$Eigenvalues), max(data$Eigenvalues))
data$Z_VarianceExplained <- effectsize::change_scale(data$VarianceExplained, to=newrange, range = c(0, 1))
data$Z_n_Methods <- effectsize::change_scale(data$n_Methods, to=newrange) 

# Plot
data %>% 
  ggplot(aes(x=n_Factors, y=Eigenvalues)) +
  geom_area(aes(y=Z_n_Methods), fill="orange", alpha=0.5) + 
  geom_line(aes(y=Z_VarianceExplained), color="red") +
  geom_line(aes(y=Eigenvalues), color="blue") +
  geom_hline(aes(yintercept = 1), linetype="dotted") +
  scale_y_continuous("Eingenvalue (blue)", 
                     sec.axis = sec_axis(~ . / max(data$Eigenvalues), 
                                         name = "Proportion of Explained Variance (red)", 
                                         labels=scales::percent,)) +
  see::theme_modern()

^{Created on 2021-02-21 by the reprex package (v0.3.0)}