Calculate and Plot Sample Distances — run

This function calculates the Euclidean distance between samples based on their expression profiles and generates a heatmap visualization. It helps identify sample relationships and potential outliers.

Usage

run_distance(
  vsd,
  save_prefix = NULL,
  save_data = TRUE,
  save_plot = TRUE,
  save_dir = getwd(),
  ...
)

Arguments

vsd: A DESeq2 object containing the normalized gene expression data
save_prefix: Prefix for the save file. Default is NULL
save_data: Logical. If TRUE, saves distance matrix to TSV. Default is TRUE
save_plot: Logical. If TRUE, saves the distance heatmap to PDF. Default is TRUE
save_dir: Directory to save the results. Default is the current working directory
...: Additional arguments passed to pheatmap()

Value

A pheatmap object showing the sample distances

Examples

if (FALSE) { # \dontrun{
# Generate and display heatmap
p <- run_distance(vsd)

# Generate and save heatmap with custom parameters
p <- run_distance(vsd, save_plot = TRUE, save_dir_name = "custom_results")
} # }