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,
  show_plot = FALSE,
  n_intersections = 20,
  x_lab = "Screen Set Intersections",
  y_lab = "Number of Cells",
  title = "Cell Counts Across Screen Set Intersections",
  bar_color = "#4E79A7",
  combmatrix_point_color = "black",
  ...
)

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.

show_plot

Whether to show the upset plot. Default: FALSE

n_intersections

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

x_lab

Label for the x-axis. Default: "Screen Set Intersections".

y_lab

Label for the y-axis. Default: "Number of Cells".

title

Plot title. Default: "Cell Counts Across Screen Set Intersections".

bar_color

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

combmatrix_point_color

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

...

Additional arguments passed to ggplot2::theme() for customizing the plot appearance.

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"
)
} # }