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Plot Individual Gene Expression Profiles

Source: R/plot_gene_profiles.R
plot_gene_profiles.Rd

Create a plot showing expression profiles for individual genes across developmental stages or cell types, with various visualization options.

Usage

plot_gene_profiles(
  phyex_set,
  genes = NULL,
  show_set_mean = FALSE,
  show_reps = FALSE,
  transformation = c("log", "std_log", "none"),
  colour_by = c("manual", "strata", "stage"),
  colours = NULL,
  max_genes = 100,
  show_labels = TRUE,
  label_size = 1.75,
  show_legend = TRUE,
  facet_by_strata = FALSE
)

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)

genes

Character vector of gene IDs to plot. If NULL, top expressing genes are selected

show_set_mean

Logical indicating whether to show the mean expression across all genes (default: FALSE)

show_reps

Logical indicating whether to show individual replicates (bulk) or cells (single-cell) (default: FALSE)

transformation

Character string specifying expression transformation: "log" (log1p), "std_log" (standardized log1p), or "none" (default: "log")

colour_by

Character string specifying coloring scheme: "strata" (by phylostratum), "stage" (by developmental stage/cell type), or "manual" (default: "manual")

colours

Optional vector of colors for manual coloring (default: NULL)

max_genes

Maximum number of genes to plot when genes=NULL (default: 100)

show_labels

Logical indicating whether to show gene labels (default: TRUE)

label_size

Font size of gene id labels if shown (default: 0.5).

show_legend

Logical indicating whether to show legend (default: TRUE)

facet_by_strata

Logical indicating whether to facet by phylostratum (default: FALSE)

Value

A ggplot2 object showing gene expression profiles

Details

This function creates detailed visualizations of individual gene expression patterns across development (bulk data) or cell types (single-cell data). Genes can be colored by phylostratum or developmental stage, and various transformations can be applied to highlight different aspects of the data.

Author

Filipa Martins Costa, Stefan Manolache, Hajk-Georg Drost

Examples

# Plot specific genes for bulk data
# p1 <- plot_gene_profiles(bulk_phyex_set, genes = c("gene1", "gene2", "gene3"))

# Plot for single-cell data with faceting by strata
# p2 <- plot_gene_profiles(sc_phyex_set, facet_by_strata = TRUE)
# p2 <- plot_gene_profiles(phyex_set, facet_by_strata = TRUE)