
Plot Signature Across Gene Expression Quantiles
Source:R/plot_signature_gene_quantiles.R
plot_signature_gene_quantiles.Rd
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,
...
)
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.