Generate an MDS plot for samples in a VISTA object

Runs classical multidimensional scaling on normalized counts, optionally restricting to groups or genes.

Usage

get_mds_plot(
  x,
  sample_group = NULL,
  group_column = NULL,
  genes = NULL,
  top_n_genes = NULL,
  label = FALSE,
  label_size = 3,
  point_size = 10,
  shape_by = NULL,
  shape_values = NULL,
  color_by = NULL,
  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 the column specified by group_column).
group_column: Optional column name in sample_info to use for grouping/filtering.
genes: Optional character vector of gene identifiers to restrict the matrix.
top_n_genes: Optional integer selecting the top variable genes to include.
label: Logical; draw sample labels when TRUE.
label_size: Numeric size of sample labels when label = TRUE.
point_size: Numeric size for points.
shape_by: Optional column name in sample_info used to map point shape. When NULL, shapes are not mapped.
shape_values: Optional vector of shapes passed to scale_shape_manual() when shape_by is set. Use a named vector to map shapes to specific levels.
color_by: Optional column name in sample_info used for point colour. Defaults to the active grouping column.
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

An object returned by this function.

Examples

v <- example_vista()
p <- get_mds_plot(v)
print(p)