Plot expression distributions as ridgelines

Shows per-group (or per-sample) expression distributions pooled across the selected genes using ridge (joy) plots. Genes are pooled; no faceting to keep shapes comparable.

Usage

get_expression_joyplot(
  x,
  genes = NULL,
  sample_group = NULL,
  group_column = NULL,
  log_transform = TRUE,
  alpha = 0.7,
  scale = 1.2,
  y_by = c("group", "sample"),
  color_by = c("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.

alpha

Numeric transparency for fills.

scale

Numeric scaling factor for ridges (passed to geom_density_ridges()).

y_by

Either "group" (default) or "sample" to choose the y-axis (ridge) grouping.

color_by

Either "group" (default) or "sample" to choose fill colors.

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_joyplot(v, genes = genes)
print(p)
#> Picking joint bandwidth of 0.422