UMAP Plot — plot_umap • glyvis

Draw a UMAP scores plot. Currently supported data types:

glystats_umap_res: Result from glystats::gly_umap().
glyexp_experiment: Experiment created by glyexp::experiment(). UMAP analysis is first performed using glystats::gly_umap(), then the result is plotted.

Usage

plot_umap(x, ...)

# S3 method for class 'glystats_umap_res'
plot_umap(x, groups = NULL, group_col = NULL, ...)

# S3 method for class 'glyexp_experiment'
plot_umap(x, groups = NULL, group_col = NULL, stats_args = list(), ...)

Arguments

x: An object to be plotted.
...: Ignored.
groups: A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group.
group_col: A character string specifying where to find the group information. If you uses glystats::gly_umap() on a glyexp::experiment() to get the result, sample information has already been added to the result. In this case, you can specify the column name in the sample information tibble to be used for coloring. If not provided, this function will try "group".
stats_args: A list of keyword arguments to pass to glystats::gly_umap().

Value

A ggplot object.