myTAI (version 2.3.4)

plot_mean_var: Plot Mean-Variance Relationship

Description

Create a scatter plot showing the relationship between mean expression and variance for genes, colored by phylostratum, with optional highlighting and labeling of specific genes.

Usage

plot_mean_var(
  phyex_set,
  highlight_genes = NULL,
  colour_by = c("none", "strata")
)

Value

A ggplot2 object showing the mean-variance relationship.

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet) containing gene expression data.

highlight_genes

Optional character vector of gene IDs to highlight and label on the plot.

colour_by

Character string specifying coloring scheme: "none" (default), "strata" colors by phylostratum

Details

This function plots the mean expression versus variance for each gene, with points colored by phylostratum. Optionally, specific genes can be highlighted and labeled. This visualization helps identify expression patterns and heteroscedasticity in the data.

The function uses collapsed expression data (averaged across replicates for bulk data, or averaged across cells per cell type for single-cell data).

Examples

# Create mean-variance plot for bulk data
mv_plot <- plot_mean_var(example_phyex_set)

# Highlight and label specific genes in single-cell data
mv_plot_sc <- plot_mean_var(example_phyex_set_sc, 
  highlight_genes = example_phyex_set_sc@gene_ids[1:3])

# Color by phylostratum
mv_plot_colored <- plot_mean_var(example_phyex_set, colour_by = "strata")