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Plot gene expression distributions as boxplots

get_expression_boxplot.Rd

Displays per-sample or per-group distributions for selected genes using normalized counts. The x-axis unit is controlled by by, and faceting is controlled explicitly by facet_by.

Usage

get_expression_boxplot(
  x,
  genes = NULL,
  sample_group = NULL,
  group_column = NULL,
  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,
  by = "group",
  facet_by = "auto",
  fill_by = NULL,
  sample_order = c("input", "group", "expression")
)

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.

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. Only supported when by = "group".

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).

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". "auto" selects the most readable layout.

fill_by

When pool_genes = TRUE, either "x" (default) or "group" to force group colors even if by = "sample". When pool_genes = FALSE, either "gene" or "group".

sample_order

Ordering used when sample names are shown on the x-axis: "input", "group", or "expression".

Value

An object returned by this function.

Examples

v <- example_vista()
genes <- head(rownames(v), 3)
p <- get_expression_boxplot(v, genes = genes)
print(p)