Plot Gene Expression — plot_gene

This function creates boxplots showing the expression levels of selected genes across groups. It can optionally add statistical significance indicators between groups.

Usage

plot_gene_exprs(
  dds,
  res = NULL,
  group_by,
  genes,
  plot_name,
  pal = NULL,
  save_plot = T,
  save_dir = getwd()
)

Arguments

dds: DESeq2 object containing the expression data
res: Optional differential expression results data frame
group_by: Column name in colData(dds) to group by.
genes: Vector of gene names to plot
plot_name: Name for the output plot
pal: Vector of colors to use for groups. If NULL, uses default ggplot2 colors. Default is NULL
save_plot: Logical. If TRUE, saves the plot to PDF. Default is TRUE
save_dir: Directory to save the plot. Default is current working directory

Value

A ggplot object showing gene expression boxplots

Examples

if (FALSE) { # \dontrun{
# Basic expression plot
p <- plot_gene_exprs(dds, genes = c("GENE1", "GENE2"), plot_name = "my_genes")

# Expression plot with statistical significance
p <- plot_gene_exprs(dds, res = res, genes = c("GENE1", "GENE2"), plot_name = "my_genes")

# Expression plot with custom colors
p <- plot_gene_exprs(dds, genes = c("GENE1", "GENE2"), plot_name = "my_genes", pal = c("red", "blue", "green"))
} # }