plot_embedding: Plot embedding

In inferCSN: Inferring Cell-Specific Gene Regulatory Network

Plot embedding

Description

Plot embedding

Usage

plot_embedding(
  matrix,
  labels = NULL,
  method = "pca",
  colors = RColorBrewer::brewer.pal(length(unique(labels)), "Set1"),
  seed = 1,
  point_size = 1,
  cores = 1
)

Arguments

matrix	Input matrix.
labels	Input labels.
method	Method to use for dimensionality reduction.
colors	Colors to use for the plot.
seed	Seed for the random number generator.
point_size	Size of the points.
cores	Set the number of threads when setting method to umap and Rtsne.

Value

An embedding plot

Examples

data("example_matrix")
samples_use <- 1:200
plot_data <- example_matrix[samples_use, ]
labels <- sample(
  c("A", "B", "C", "D", "E"),
  nrow(plot_data),
  replace = TRUE
)

plot_embedding(
  plot_data,
  labels,
  method = "pca",
  point_size = 2
)

plot_embedding(
  plot_data,
  labels,
  method = "tsne",
  point_size = 2
)

inferCSN documentation built on Sept. 11, 2024, 9:32 p.m.