Plot Bar Chart of Top SHAP Driver Genes

Generates a horizontal bar plot of the top n genes ranked by mean absolute SHAP value, as computed by FindShapKeyDriver(). The plot provides an interpretable summary of the most important features (genes) driving model predictions.

Usage

BarplotShap(
  seurat_obj,
  top_n = 20,
  bar_color = "steelblue",
  save_plot = FALSE,
  out_dir = NULL,
  filename = "barplot_top_shap_DriverGenes.pdf",
  width = 8,
  height = 6,
  dpi = 300
)

Arguments

seurat_obj

A Seurat object containing SHAP results from FindShapKeyDriver(), with a shap_summary table stored in seurat_obj@misc$shap.

top_n

Number of top genes to display (default: 20).

bar_color

Fill color for the bars (default: "steelblue").

save_plot

Save the Barplot automatically (default: save_plot = FALSE).

filename

Name of the plot file to save (e.g., "barplot_top_shap_DriverGenes.pdf"). File format is determined by the extension (.pdf or .png).

width

Plot width in inches (default: 8).

height

Plot height in inches (default: 6).

dpi

Resolution in dots per inch for raster formats like PNG (default: 300).

Value

A ggplot object containing the bar plot of SHAP summary values.

Details

The function pulls SHAP summary statistics from seurat_obj@misc$shap$shap_summary, creates a bar plot of the top n genes, and saves it to disk as a PNG or PDF.

Examples

# After running FindShapKeyDriver():
BarplotShap(seurat_obj, top_n = 30)
#> Error: object 'seurat_obj' not found

# Save as a PDF with a custom color
BarplotShap(seurat_obj,save_plot = TRUE,filename = "barplot_top_shap_DriverGenes.pdf", bar_color = "#F96815")
#> Error: object 'seurat_obj' not found