myTAI (version 2.3.4)

plot_contribution: Plot Phylostratum Contribution to Transcriptomic Index

Description

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"))

Value

A ggplot2 object showing phylostratum contributions as a stacked area plot

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.

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(example_phyex_set)

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