Plot Transcriptomic Signature — plot

Create a plot of the transcriptomic index signature across developmental stages or cell types, with options for showing individual samples/cells and statistical testing.

Usage

plot_signature(
  phyex_set,
  show_reps = TRUE,
  show_p_val = TRUE,
  conservation_test = stat_flatline_test,
  colour = NULL,
  ...
)

Arguments

phyex_set: A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)
show_reps: Logical, whether to show individual replicates
show_p_val: Logical, whether to show conservation test p-value
conservation_test: Function, conservation test to use for p-value calculation
colour: Character, custom color for the plot elements
...: Additional arguments passed to specific methods

Value

A ggplot2 object showing the transcriptomic signature

Details

This function creates visualizations appropriate for the data type:

**Bulk data (BulkPhyloExpressionSet):** - Line plots showing TXI trends across developmental stages - Optional individual biological replicates as jittered points - Optional conservation test p-values

**Single-cell data (ScPhyloExpressionSet):** - Violin plots showing TXI distributions across cell types - Mean TXI values overlaid as line - Optional individual cells using geom_sina for better visualization

Examples

# Basic signature plot for bulk data
# p1 <- plot_signature(bulk_phyex_set)

# Bulk plot with replicates and p-value
# p2 <- plot_signature(bulk_phyex_set, show_reps = TRUE, show_p_val = TRUE)

# Single-cell plot with individual cells
# p3 <- plot_signature(sc_phyex_set, show_reps = TRUE)