Plot Multiple Transcriptomic Signatures — plot_signature

Create a plot comparing multiple transcriptomic signatures on the same axes, with options for statistical testing and transformations.

Usage

plot_signature_multiple(
  phyex_sets,
  legend_title = "Phylo Expression Set",
  show_p_val = TRUE,
  conservation_test = stat_flatline_test,
  transformation = NULL,
  colours = NULL,
  ...
)

Arguments

phyex_sets: A vector of PhyloExpressionSet objects to compare (BulkPhyloExpressionSet or ScPhyloExpressionSet)
legend_title: Title for the legend (default: "Phylo Expression Set")
show_p_val: Logical indicating whether to show p-values (default: TRUE)
conservation_test: Function to use for conservation testing (default: stat_flatline_test)
transformation: Optional transformation function to apply to all datasets (default: NULL)
colours: Optional vector of colors for each dataset (default: NULL)
...: Additional arguments passed to plot_signature

Value

A ggplot2 object showing multiple transcriptomic signatures

Details

This function allows comparison of multiple transcriptomic signatures by overlaying them on the same plot. Each signature is colored differently and can be tested for conservation patterns (bulk data only). If a transformation is provided, it's applied to all datasets before plotting.

The function automatically adapts to the data type: - **Bulk data**: Line plots with optional statistical testing - **Single-cell data**: Violin plots showing distributions

All datasets must use the same axis labels (developmental stages or cell types).

Examples

# Compare multiple bulk datasets
# bulk_list <- c(bulk_phyex_set1, bulk_phyex_set2)
# p <- plot_signature_multiple(bulk_list, legend_title = "Dataset")

# Compare single-cell datasets
# sc_list <- c(sc_phyex_set1, sc_phyex_set2)
# p2 <- plot_signature_multiple(sc_list, legend_title = "Cell Type")

# With transformation
# p3 <- plot_signature_multiple(bulk_list, transformation = log1p)