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Generate a UMAP plot for samples in a VISTA object

get_umap_plot.Rd

Runs UMAP on normalized counts, optionally restricting to selected groups or genes. UMAP is intended for exploratory sample-level structure.

Usage

get_umap_plot(
  x,
  sample_group = NULL,
  group_column = NULL,
  color_by = NULL,
  genes = NULL,
  top_n_genes = NULL,
  label = FALSE,
  label_size = 3,
  point_size = 10,
  shape_by = NULL,
  shape_values = NULL,
  n_neighbors = 15,
  min_dist = 0.1,
  metric = "euclidean",
  seed = 123,
  use_vista_colors = NULL,
  palette = NULL,
  colors = NULL,
  use_group_colors = TRUE
)

Arguments

x

A VISTA object.

sample_group

Optional character vector of groups to include (based on group_column).

group_column

Optional column name in sample_info used for filtering/grouping. Defaults to the stored grouping column.

color_by

Optional column name in sample_info used for point color. Defaults to group_column.

genes

Optional character vector of gene identifiers to restrict the matrix.

top_n_genes

Optional integer selecting top variable genes to include.

label

Logical; draw sample labels when TRUE.

label_size

Numeric label size when label = TRUE.

point_size

Numeric point size.

shape_by

Optional column name in sample_info used to map point shape.

shape_values

Optional vector passed to scale_shape_manual() when shape_by is set.

n_neighbors

UMAP n_neighbors parameter.

min_dist

UMAP min_dist parameter.

metric

UMAP distance metric.

seed

Integer random seed passed to UMAP.

use_vista_colors

Deprecated alias for use_group_colors. When supplied, it overrides use_group_colors.

palette

Optional qualitative palette name used when generating colours for non-group metadata levels.

colors

Optional named character vector of manual colours overriding both palette and stored VISTA colours.

use_group_colors

Logical; when TRUE, prefer the stored VISTA group colours when colouring by the grouping column.

Value

A ggplot object with UMAP1/UMAP2 coordinates.

Examples

if (requireNamespace("uwot", quietly = TRUE)) {
  vista <- example_vista()
  get_umap_plot(vista, top_n_genes = 50)
}
#> Warning: `n_neighbors` (15) must be smaller than sample size (6); using 5.