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Plot UMAP by group

Source: R/plot_umap_by_group.R
plot_umap_by_group.Rd

Plot UMAP for each group separately. Accepts either a SummarizedExperiment object or a named list of them (from split_groups()).

Usage

plot_umap_by_group(
  se_obj,
  seed = 1234,
  nrow = 1,
  umap_neighbors = NULL,
  fontsize = 8,
  assay = 1,
  legend_pos = "right"
)

Arguments

se_obj

A SummarizedExperiment object, or a named list of them (e.g. from split_groups()).

seed

Random seed for UMAP (default: 1234).

nrow

Number of rows for arranging the plots (default: 1).

umap_neighbors

UMAP n_neighbors parameter (default: auto-selected based on sample count).

fontsize

Base font size (default: 8).

assay

Assay index to use, where 1 is the original data and 2 is normalised to time 0 (if available) (default: 1).

legend_pos

Legend position (default: "right").

Value

A series of UMAP plots showing the distribution of samples in each group, coloured by Time.

Examples

data(example_obj)
plot_umap_by_group(example_obj)
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 4
#> Warning: Using size for a discrete variable is not advised.


# Also accepts a list from split_groups()
example_obj_list <- split_groups(example_obj)
plot_umap_by_group(example_obj_list)
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 5
#> Warning: Using size for a discrete variable is not advised.
#> Using n_neighbors = 4
#> Warning: Using size for a discrete variable is not advised.