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):** - Sina plots showing TXI distributions across cell types or other identities - Mean TXI values overlaid as line - Optional individual cells using geom_sina for better visualization - Flexible identity selection from metadata via additional parameters: - `primary_identity`: Character, name of metadata column for x-axis (default: current selected identities) - `secondary_identity`: Character, name of metadata column for coloring/faceting - `facet_by_secondary`: Logical, whether to facet by secondary identity (default: FALSE uses colouring)

Examples

# Basic signature plot for bulk data
p <- plot_signature(example_phyex_set)
#> 
Computing: [========================================] 100% (done)                         
#> Ran Flat Line Test
#> Significance status of signature: not significant (= no evolutionary signature in the transcriptome).