ScreenUpset - Visualize cell type intersections from screened Seurat object

This function creates an UpSet plot to visualize intersections between different screening methods (e.g., scissor, scAB, scPAS, scPP) in a Seurat object metadata. It calculates all possible combinations of screening types and displays the number of cells positive for each combination.

Usage

ScreenUpset(
  screened_seurat,
  screen_type = NULL,
  order_by = c("freq", "degree"),
  show_plot = FALSE,
  n_intersections = 20,
  bar_color = "#4E79A7",
  combmatrix_point_color = "black",
  verbose = SigBridgeRUtils::getFuncOption("verbose"),
  ...
)

Arguments

screened_seurat

A Seurat object containing screening results in metadata. Must contain columns with screening types marked as "Positive".

screen_type

Character vector of screening types to analyze. Default: NULL, indicating that a self-search pattern will be used.

order_by

Character vector of columns to order the intersections by. Default: c("freq", "degree").

show_plot

Whether to show the upset plot. Default: FALSE

n_intersections

Number of intersections to display in the plot. Default: 20.

bar_color

Color for the bars in the plot. Default: "#4E79A7".

combmatrix_point_color

Color for points in the combination matrix. Default: "black".

verbose

Logical, whether to print a message

...

Additional arguments passed to ggupset::scale_x_upset(), ggupset::theme_combmatrix(), and ggplot2::theme() for customizing the plot appearance. Argumetns are auto-filtered

Value

A list containing two elements:

• plot: A ggplot object displaying the UpSet plot

• stats: A data frame with intersection statistics including:

  • intersection: Name of the intersection

  • sets: List of screening types in the intersection

  • count: Number of cells positive for all screening types in the intersection

Details

The function performs the following steps:

1. Validates input parameters and checks if specified screening types exist in metadata

2. Generates all possible combinations of screening types (from 1 to the total number of types)

3. Creates a logical matrix of positive cells for efficient computation

4. Calculates cell counts for each intersection using vectorized operations

5. Creates an UpSet plot visualization with customizable appearance

See also

Other visualization_function: ScreenFractionPlot()

Examples

if (FALSE) { # \dontrun{
# Basic usage with default parameters
result <- ScreenUpset(screened_seurat = my_seurat_obj)

# Customize screening types and appearance
result <- ScreenUpset(
  screened_seurat = my_seurat_obj,
  screen_type = c("scissor", "scAB"),
  n_intersections = 15,
  title = "Custom Title",
  bar_color = "darkred"
)
} # }