Generate UpSet Plot for Gene Set Intersections

Visualizes intersections among multiple gene sets using the classic UpSetR package. Uses grid graphics capture to ensure plot generation in all environments.

Usage

draw_upset_intersections(
  gene_lists,
  project_name,
  filename,
  group_colors = NULL
)

Arguments

gene_lists

A named list of character vectors of gene identifiers.

project_name

Character. Used for the file title.

filename

Character. Output file path (must end in .pdf or .png).

group_colors

Optional named character vector. Not used in this version.

Value

Invisibly returns NULL. Saves the plot to filename.

Examples

gene_sets <- list(
  Upregulated = c("A", "B", "C", "D"),
  Downregulated = c("C", "D", "E", "F"),
  Bound_by_TF = c("B", "D", "F", "G")
)

tf <- tempfile(fileext = ".pdf")

if (requireNamespace("UpSetR", quietly = TRUE)) {
  draw_upset_intersections(
    gene_lists = gene_sets,
    project_name = "Transcriptional Regulation",
    filename = tf
  )
}
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#>   Please report the issue to the authors.
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#>   Please report the issue to the authors.