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")
)

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.

Value

A ggplot2 object.