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Gene expression line plot

get_expression_lineplot.Rd

Plots normalized expression for selected genes across samples or summarized groups with optional transformations and group faceting.

Usage

get_expression_lineplot(
  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 = c("sample", "group"),
  facet_by = c("auto", "group", "gene", "none"),
  fill_by = NULL,
  sample_order = c("input", "group", "expression"),
  value_transform = NULL,
  palette = NULL,
  colors = NULL,
  line_width = 1,
  point_size = 2,
  base_size = 12
)

Arguments

x

A VISTA object.

genes

Character vector of gene identifiers to plot.

sample_group

Optional character vector specifying which groups (values taken from group_column) to include.

group_column

Optional column name in sample_info defining the grouping/faceting variable.

log_transform

Logical; log2-transform expression values before plotting.

display_id

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

display_from

Optional source ID type for mapping (reserved for compatibility with other expression plotting APIs).

display_orgdb

Optional OrgDb object used for ID mapping when display_id is set but not found in rowData.

facet_scales

Scaling option passed to facet_wrap().

stats_group

Logical retained for API consistency. Statistical overlays are not currently added by get_expression_lineplot().

p.label

Label format retained for API consistency with other expression plots.

comparisons

Optional list of comparisons retained for API consistency.

pool_genes

Logical; when TRUE, average the selected genes into a single trajectory.

by

Plot unit: "sample" (default) or "group" to average replicates before plotting.

facet_by

Faceting mode: "auto" (default), "none", "group", or "gene".

fill_by

Argument retained for API consistency; ignored because line plots use colour rather than fill.

sample_order

Ordering used for sample-level plots: "input", "group", or "expression".

value_transform

Deprecated compatibility alias for transformation choice; one of "log2", "zscore", or "none".

palette

Optional qualitative palette name used for gene colours.

colors

Optional named character vector of manual gene colours.

line_width

Line width.

point_size

Point size.

base_size

Base theme size.

Value

An object returned by this function.

Examples

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