Plot mean expression per group as a lollipop chart — get_expression

Summarizes expression per group for a handful of genes using a stem-and-dot (lollipop) plot. Values are averaged across replicates in each group; this function does not show individual replicates. For per-sample display or pairwise tests, use get_expression_barplot().

Usage

get_expression_lollipop(
  x,
  genes,
  sample_group = NULL,
  group_column = NULL,
  log_transform = TRUE,
  facet_scale = "free_y",
  point_size = 6,
  line_size = 1.2,
  label = TRUE,
  label_digits = 1,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL
)

Arguments

x: A VISTA object.
genes: Character vector (≤15 genes) to plot.
sample_group: Optional character vector of groups (from group_column) to include.
group_column: Optional column name in sample_info to use for grouping samples.
log_transform: Logical; log2-transform expression before plotting.
facet_scale: Scaling option passed to facet_wrap() when plotting multiple genes.
point_size: Numeric size of the dots.
line_size: Numeric size of the stems.
label: Logical; draw numeric labels above the dots.
label_digits: Integer; digits to show in labels when label = TRUE.
display_id: Optional ID/column name to use for labels/facets. If supplied and present in rowData(x), those values are used; otherwise falls back to ID mapping.
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.