Plot gene expression distributions as boxplots — get_expression

Displays per-sample or per-group distributions for selected genes using normalized counts. When multiple genes are supplied and facet = TRUE, facets are per gene (not per group). When facet = FALSE with multiple genes, genes are shown on the x-axis and facets are per group.

Usage

get_expression_boxplot(
  x,
  genes = NULL,
  sample_group = NULL,
  group_column = NULL,
  facet = TRUE,
  log_transform = TRUE,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL,
  facet_scales = "free_y",
  stats_group = FALSE,
  p.label = "p.signif",
  comparisons = NULL,
  pool_genes = FALSE,
  x_by = "group",
  facet_by = "none",
  fill_by = NULL
)

Arguments

x: A VISTA object.
genes: Optional character vector of genes to display (≤20). Defaults to all genes.
sample_group: Optional character vector specifying which groups (as defined by group_column) to include.
group_column: Optional column name in sample_info used as the grouping variable.
facet: Logical; facet the plot when facet_by is not "none".
log_transform: Logical; apply log2(x + 1) transform before plotting.
display_id: Optional column in rowData(x) to use for gene labels (facets).
display_from: Optional source ID type for mapping (used when display_id is not found in rowData).
display_orgdb: Optional OrgDb object used for ID mapping when display_id is set but not found in rowData.
facet_scales: Facet scales argument passed to facet_wrap() (default "free_y").
stats_group: Logical; add statistical comparisons between groups when TRUE.
p.label: Label format for ggpubr::stat_compare_means().
comparisons: Optional list of specific group comparisons for stat_compare_means().
pool_genes: Logical; when TRUE, pool selected genes into one distribution per x-axis category (scenario 1).
x_by: When pool_genes = TRUE, either "group" or "sample" (x-axis and optional fill). When pool_genes = FALSE, either "group" or "gene" (x-axis for per-gene distributions).
facet_by: Faceting control: for pooled genes, "group" or "none"; for per-gene, "none" (default) or "gene".
fill_by: When pool_genes = TRUE, either "x" (default) or "group" to force group colors even if x_by = "sample". When pool_genes = FALSE, either "gene" or "group".