In plofknaapje/gpowerpca: Sparse PCA using the GPower method

Load the data

knitr::opts_chunk$set(fig.width=7, fig.asp=0.618) 
library(qgraph)
library(gpowerr)
data(big5)

gpower function

power <-
  gpower(
    data = big5,
    k = 5,
    rho = 0.1,
    reg = "l1",
    center = TRUE,
    block = FALSE,
    mu = 1
  )
summary(power)
print(power, print_zero_rows = FALSE)

auto_gpower function

auto <- auto_gpower(
  data = big5,
  k = 5,
  prop_sparse = 0.2,
  reg = "l1",
  block = FALSE,
  mu = 1
)
summary(auto)
print(auto, print_zero_rows = FALSE)

auto <- auto_gpower(
  data = big5,
  k = 5,
  prop_sparse = 0.97
)

png("figures/big5smallheatmap.png", width = 600, height = 370, res=90)

row_labels = data.frame(label = substring(colnames(big5), 1, 1),
                        row.names = colnames(big5))
gpower_component_heatmap(
  data = big5,
  k = 5,
  rho = 0.3125,
  cluster_variables = TRUE,
  show_variable_names = TRUE,
  variable_highlight = row_labels,
  ignore_full_zero = TRUE
)
dev.off()

gpower_component_heatmap function

png("figures/big5fullheatmap.png", width = 600, height = 370, res=90)

row_labels = data.frame(label = substring(colnames(big5), 1, 1),
                        row.names = colnames(big5))
gpower_component_heatmap(
  data = big5,
  k = 5,
  rho = 0.1,
  cluster_variables = TRUE,
  show_variable_names = FALSE,
  variable_highlight = row_labels
)
dev.off()

png("figures/big525heatmap.png", width = 600, height = 370, res=90)

row_labels_25 = data.frame(label = substring(colnames(big5)[1:25], 1, 1),
                        row.names = colnames(big5)[1:25])

gpower_component_heatmap(
  data = big5[, 1:25],
  k = 5,
  rho = 0.1,
  cluster_variables = TRUE,
  show_variable_names = TRUE,
  variable_highlight = row_labels_25
)
dev.off()

png("figures/big5varplot.png", width = 600, height = 370, res=80)

gpower_var_plot(
  data = big5,
  k = 5,
  intervals = 40,
  reg = 'l1'
)
dev.off()

png("figures/big5compvarplot.png", width = 600, height = 370, res=80)
gpower_comp_var_plot(
  data = big5,
  k = 5,
  intervals = 40,
  reg = 'l1'
)
dev.off()