myTAI (version 2.3.4)

plot_signature_multiple: Plot Multiple Transcriptomic Signatures

Description

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,
  ...
)

Value

A ggplot2 object showing multiple transcriptomic signatures

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

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
phyex_set <- example_phyex_set

bulk_list <- c(phyex_set, 
  phyex_set |> remove_genes(phyex_set@gene_ids[1:5]))
p <- plot_signature_multiple(bulk_list, legend_title = "Dataset")