myTAI (version 2.3.4)

plot_gene_space: Plot Gene Space Using PCA

Description

Create a PCA plot showing genes in expression space with ideal expression patterns overlaid as reference points.

Usage

plot_gene_space(
  phyex_set,
  top_p = 0.2,
  genes = NULL,
  colour_by = c("identity", "strata")
)

Value

A ggplot2 object showing the gene space PCA plot

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)

top_p

Proportion of most dynamic genes to include when genes=NULL (default: 0.2)

genes

Character vector of specific genes to plot. If NULL, uses top dynamic genes

colour_by

Character string specifying coloring scheme: "identity" (by peak expression stage/identity) or "strata" (by phylostratum) (default: "identity")

Details

This function creates a PCA visualization of genes in expression space, with ideal expression patterns (early, mid, late, reverse mid) overlaid as reference points. The analysis uses log-transformed and standardized expression values. Genes are colored either by their phylostratum or by their peak expression stage.

Examples

# Plot gene space colored by identity
p1 <- plot_gene_space(example_phyex_set, colour_by = "identity")

# Plot specific genes colored by strata
p2 <- plot_gene_space(example_phyex_set, 
                      genes = example_phyex_set@gene_ids[1:5], 
                      colour_by = "strata")