gpower_component_heatmap: Plots value of each column of the data for each component

In plofknaapje/gpowerr: Sparse PCA using the GPower method

Description

This plot shows the values of the components, connected to the columns of the original data. The heatmap is made using the pheatmap function from the pheatmap package.

Usage

gpower_component_heatmap(
  data,
  k,
  rho,
  reg = "l1",
  center = TRUE,
  block = FALSE,
  mu = 1,
  variable_highlight = NA,
  cluster_variables = FALSE,
  show_variable_names = TRUE,
  ignore_full_zero = TRUE
)

Arguments

data	Input matrix of size (p x n) with p < n.
k	Number of components, 0 < k < p.
rho	Relative sparsity weight factor of the optimization. Either a vector of floats of size k or float which will be repeated k times. 0 < rho < 1.
reg	regularisation type to use in the optimization. Either 'l0' or 'l1'. The default is 'l1' since it performed best in experiments.
center	Centers the data. Either TRUE or FALSE. The default is TRUE.
block	Optimization method. If FALSE, the components are calculated individually. If TRUE, all components are calculated at the same time. The default is FALSE.
mu	Mean to be applied to each component in the block. Either a vector of float of size k or a float which will be repeated k times. Only used if block is TRUE. The default is 1.
variable_highlight	Add a color coding to the variables using a matrix with of size n x 1 where the row names are the same as the column names of the data matrix.
cluster_variables	Cluster the variables using hierarchical clustering.
show_variable_names	Show the names of the variables on the right side of the graph.
ignore_full_zero	Only show variables which have at least one non-zero weight.

Examples

set.seed(360)
p <- 20
n <- 50
k <- 5
data <- scale(matrix(stats::rnorm(p * n), nrow = p, ncol = n), scale = FALSE)

gpower_component_heatmap(
  data = data,
  k = 5,
  rho = 0.1,
  reg = 'l1',
  center = TRUE,
  block = FALSE,
  mu = 1,
  variable_highlight = NA,
  cluster_variables = FALSE,
  show_variable_names = TRUE,
  ignore_full_zero = TRUE
)

plofknaapje/gpowerr documentation built on Dec. 22, 2021, 8:48 a.m.