Plot Phylostratum Contribution to Transcriptomic Index

Create a stacked area plot showing the contribution of each phylostratum to the overall transcriptomic index across developmental stages or cell types.

Usage

plot_contribution(phyex_set, type = c("stacked", "line"))

Arguments

phyex_set: A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)
type: One of "stacked" or "line". If stacked, will show the lines stacked in a cumulative area plot, otherwise they will not be stacked.

Value

A ggplot2 object showing phylostratum contributions as a stacked area plot

Details

This function visualizes how different phylostrata contribute to the overall transcriptomic index pattern across developmental stages (bulk data) or cell types (single-cell data). Each area represents the contribution of a specific phylostratum, with older strata typically shown in darker colors and younger strata in lighter colors.

The plot uses the PS_colours function to create a consistent color scheme that matches other myTAI visualizations.

Examples

# Create contribution plot for bulk data
# contrib_plot <- plot_contribution(bulk_phyex_set)

# Create contribution plot for single-cell data
# contrib_plot_sc <- plot_contribution(sc_phyex_set)