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Plot Gene Space Using PCA

Source: R/plot_gene_space.R
plot_gene_space.Rd

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")
)

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")

Value

A ggplot2 object showing the gene space PCA plot

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(phyex_set, colour_by = "identity")

# Plot specific genes colored by strata
# p2 <- plot_gene_space(phyex_set, genes = c("gene1", "gene2"), colour_by = "strata")