inferCSN (version 1.2.0)

plot_embedding: 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
)

Value

An embedding plot

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 for uwot::umap and Rtsne::Rtsne.

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
)