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Plot UMAP Dimensionality Reduction Results

plot_umap.Rd

Generates a 2D scatter plot of UMAP results to visualize sample relationships. This is a convenient wrapper function that first calls get_umap to calculate the coordinates and then plots them using ggplot2.

Usage

plot_umap(object, condition = NA, neighbors = 15, ...)

# S4 method for class 'SummarizedExperiment'
plot_umap(object, condition, neighbors)

Arguments

object

A SummarizedExperiment object. The data should be imputed.

condition

A character string specifying the column name in the condition slot to use for coloring the points. If NULL (the default), get_umap will attempt to guess groups from sample names.

neighbors

The size of the local neighborhood for the UMAP calculation.

...

Additional arguments passed on to get_umap, and in turn to the umap::umap function (e.g., min_dist, metric).

Value

A ggplot object, which can be further customized or printed.

Details

This function requires imputed, log-transformed, and normalized data for the best results, as these are the best inputs for the wrapped get_umap function.

Important: UMAP is a stochastic algorithm. For a reproducible plot, you must set a seed (e.g., set.seed(123)) before calling this function.

This function requires the umap and ggplot2 packages.

Functions

  • plot_umap(SummarizedExperiment): Method for SummarizedExperiment objects.

Examples

# This example requires the 'umap' package
if (requireNamespace("umap", quietly = TRUE)) {
  # Create a sample ProtData object
  raw_data <- data.frame(
    Gene = paste0("GENE", 1:10),
    Control_1 = rnorm(10, 10), Control_2 = rnorm(10, 10),
    Treat_A_1 = rnorm(10, 12), Treat_A_2 = rnorm(10, 12),
    Treat_B_1 = rnorm(10, 15), Treat_B_2 = rnorm(10, 15)
  )
  pd_obj <- create_protdata(dat = raw_data)

  # For reproducible UMAP results, set a seed!
  set.seed(42)

  # Generate the UMAP plot
  p <- plot_umap(pd_obj, n_neighbors = 3)

  # The plot can be printed in an interactive session
  if (interactive()) {
    print(p)
  }
}
#> Error: unable to find an inherited method for function ‘plot_umap’ for signature ‘object = "ProtData"’