Plot SHAP Beeswarm Summary for Top Driver Genes

Generates a beeswarm-style summary plot of SHAP values for the top n driver genes, as computed from FindShapKeyDriver(). This visualization helps interpret gene-level contributions to model predictions, showing both SHAP value and feature value per cell.

Usage

BeeswarmplotShap(
  seurat_obj,
  top_n = 20,
  save_plot = FALSE,
  out_dir = NULL,
  filename = "beeswarm_top_shap_DriverGenes.pdf",
  min_color = "#FFCC33",
  max_color = "#6600CC",
  width = 8,
  height = 6,
  dpi = 300
)

Arguments

seurat_obj: A Seurat object containing SHAP results from FindShapKeyDriver(), stored in seurat_obj@misc$shap.
top_n: Number of top driver genes to display (default: 20).
save_plot: Save the Beeswarmplot automatically (default: save_plot = FALSE).
out_dir: Output directory for the saved plot file. Will be created if it doesn't exist.
filename: Name of the output plot file (e.g., "beeswarm_top_shap_DriverGenes.pdf"). File format is inferred from the extension (.pdf or .png).
min_color: Color for low feature values (default: "#FFCC33").
max_color: Color for high feature values (default: "#6600CC").
width: Width of the plot in inches (default: 8).
height: Height of the plot in inches (default: 6).
dpi: Resolution in dots per inch (only used for raster outputs like PNG; default: 300).

Value

A ggplot object representing the beeswarm summary plot.

Details

The function extracts SHAP outputs from the @misc$shap slot of a Seurat object and plots per-cell SHAP values for the most important genes. The plot is saved as a PDF (with rasterized points) or PNG depending on the filename extension.

Examples

# Assuming SHAP analysis was performed using FindShapKeyDriver()
BeeswarmplotShap(seurat_obj, out_dir = "figures/", top_n = 30)
#> Error: object 'seurat_obj' not found

# To save as a raster-aware PDF
BeeswarmplotShap(seurat_obj,save_plot = TRUE,filename = "beeswarm_top_shap_DriverGenes.pdf",out_dir = out_dir)
#> Error: object 'seurat_obj' not found