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Generate an MDS plot for samples in a VISTA object

get_mds_plot.Rd

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_replicates = FALSE,
  label_size = 3,
  circle_size = 10,
  sample_colors = TRUE,
  shape_by = NULL,
  shape_values = NULL
)

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_replicates

Logical; draw sample labels when TRUE.

label_size

Numeric size of replicate labels when label_replicates = TRUE.

circle_size

Numeric size for points.

sample_colors

Logical; apply stored group colors when TRUE.

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.