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Violin plot of expression values

get_expression_violinplot.Rd

Mirrors the main user-facing arguments of get_expression_boxplot() so the two geoms can be swapped with minimal code changes. Violin plots currently keep group-based semantics (by = "group") because a violin requires replicate-level distributions within groups rather than one value per sample.

Usage

get_expression_violinplot(
  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 = c("auto", "gene", "none"),
  fill_by = NULL,
  sample_order = c("input", "group", "expression"),
  value_transform = NULL,
  summarise = FALSE
)

Arguments

x

A VISTA object.

genes

Optional character vector of gene IDs to include; defaults to all genes selected by the plotting mode.

sample_group

Optional subset of groups (values of group_column) to keep.

group_column

Grouping column in sample_info; defaults to the stored grouping.

log_transform

Logical; log2-transform expression values before plotting.

display_id

Optional ID/column name to use for labels/facets. If supplied and present in rowData(x), those values are used.

display_from

Optional source ID type for mapping (reserved for compatibility with get_expression_boxplot()).

display_orgdb

Optional OrgDb object used for ID mapping when display_id is set but not found in rowData (reserved for compatibility with get_expression_boxplot()).

facet_scales

Scaling option passed to facet_wrap().

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; pool all selected genes into one violin per group.

by

Plot unit. Violin plots currently support only "group".

facet_by

Faceting mode. Uses the same argument pattern as get_expression_boxplot(), but pool_genes = TRUE falls back to "none" because pooled violins already aggregate across genes.

fill_by

Fill strategy. Uses the same values as get_expression_boxplot().

sample_order

Ordering for sample-level display before values are grouped into violins.

value_transform

Deprecated compatibility alias. "log2" maps to log_transform = TRUE, "none" maps to FALSE, and "zscore" applies a per-gene z-score transform.

summarise

Logical retained for compatibility. Violin plots always use replicate-level values, so summarise = TRUE is ignored with a warning.

Value

A ggplot2 object.

Examples

v <- example_vista()
genes <- head(rownames(v), 4)
p <- get_expression_violinplot(v, genes = genes)
print(p)