myTAI (version 2.3.4)

plot_signature_gene_quantiles: Plot Signature Across Gene Expression Quantiles

Description

Create a plot showing how the transcriptomic signature changes when genes are progressively removed based on expression quantiles.

Usage

plot_signature_gene_quantiles(
  phyex_set,
  quantiles = c(1, 0.99, 0.95, 0.9, 0.8),
  selection_FUN = genes_top_mean,
  ...
)

Value

A ggplot2 object showing signatures across different quantiles

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)

quantiles

Numeric vector of quantiles to test (default: c(1.0, 0.99, 0.95, 0.90, 0.80))

selection_FUN

Function to select genes for removal (default: genes_top_mean)

...

Additional arguments passed to plot_signature_multiple

Details

This function systematically removes genes based on expression quantiles and shows how the transcriptomic signature changes. This is useful for understanding the contribution of highly expressed genes to the overall pattern and for assessing the robustness of phylotranscriptomic patterns.

The analysis works with both bulk and single-cell data, helping to determine whether phylotranscriptomic patterns are driven by a few highly expressed genes or represent broad transcriptomic trends.

Examples

# Plot signature across expression quantiles for bulk data
phyex_set <- example_phyex_set |>
    select_genes(example_phyex_set@gene_ids[1:100])
phyex_set@null_conservation_sample_size <- 500
p <- plot_signature_gene_quantiles(phyex_set, quantiles = c(0.95, 0.90))