<<<<<<< Updated upstream UMAP by group (list of objects) — plot_umap_by_group_list • TiDEomicsPlot UMAP by group (list of objects) — plot_umap_by_group_list • TiDEomics Skip to contents
<<<<<<< Updated upstream

UMAP by group (list of objects)

=======

Plot UMAP by group (list of objects)

>>>>>>> Stashed changes Source: R/plot_umap_by_group.R
plot_umap_by_group_list.Rd

Plot UMAP by group, input is a list of SummarizedExperiment objects, with each object corresponding to a group

Usage

plot_umap_by_group_list(
  se_obj_list,
  seed = 1234,
  nrow = 1,
  umap_neighbors = NULL,
  fontsize = 8,
  assay = 1
)

Arguments

se_obj_list

A list of SummarizedExperiment objects, such as output of split_groups()

seed

Random seed for UMAP (default is 1234)

nrow

Number of rows for arranging the UMAP plots (default is 1)

umap_neighbors

UMAP n_neighbors parameter (default is selected by umap_n_neighbors() function based on the number of samples)

fontsize

Font size for the plot (default is 8)

assay

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

Value

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

Examples

data("example")
example_obj_list <- split_groups(example_obj)
plot_umap_by_group_list(example_obj_list)
#> Using n_neighbors = 5
#> Using n_neighbors = 5
#> Using n_neighbors = 5
#> Using n_neighbors = 4