Plot expression distributions as density curves — get_expression

Shows expression distributions pooled across the selected genes, coloured by group (or sample), with optional faceting by group or sample.

Usage

get_expression_density(
  x,
  genes = NULL,
  sample_group = NULL,
  group_column = NULL,
  log_transform = TRUE,
  facet_scales = "free",
  alpha = 0.4,
  adjust = 1,
  color_by = c("group", "sample"),
  facet_by = c("none", "group", "sample"),
  sample_order = c("input", "group", "expression"),
  palette = NULL,
  colors = NULL
)

Arguments

x: A VISTA object.
genes: Optional character vector of genes to display. 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.
facet_scales: Facet scales argument passed to facet_wrap() (default "free").
alpha: Numeric transparency for density fill.
adjust: Bandwidth adjustment factor passed to geom_density().
color_by: Either "group" (default) or "sample" to choose fill/color variable.
facet_by: One of "none" (default), "group", or "sample" to facet densities.
sample_order: Ordering for sample-level display: "input", "group", or "expression".
palette: Optional qualitative palette name used when generating colours.
colors: Optional named character vector of manual colours overriding palette.

Value

A ggplot2 object.

Examples

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