UMAP — plot_umap • TiDEomics

Plot UMAP of samples, using features without missing values

The UMAP plots are labelled by Group, Time, Replicate (if more than 1), Batch (if more than 1), and number of identified features (non-missing values).

Usage

plot_umap(
  se_obj,
  seed = 1234,
  plot = TRUE,
  plot_ID = FALSE,
  circle = FALSE,
  xlim_min = NULL,
  xlim_max = NULL,
  ylim_min = NULL,
  ylim_max = NULL,
  umap_neighbors = NULL,
  fontsize = 8,
  assay = 1,
  ...
)

Arguments

se_obj: A SummarizedExperiment object created by create_input()
seed: Random seed for UMAP (default is 1234)
plot: Whether to plot the figures (default is TRUE)
plot_ID: Whether to include a UMAP plot coloured by number of identified features (default is FALSE)
circle: Logical, whether to draw circles (ellipses) around samples of each group (default is FALSE)
xlim_min: Minimum x-axis limit when drawing ellipses (default 1.5*min UMAP x)
xlim_max: Maximum x-axis limit when drawing ellipses (default 1.5*max UMAP x)
ylim_min: Minimum y-axis limit when drawing ellipses (default 1.5*min UMAP y)
ylim_max: Maximum y-axis limit when drawing ellipses (default 1.5*max UMAP y)
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)
...: Additional arguments passed to ggforce::geom_mark_ellipse() for customizing the ellipses

Value

A UMAP plot showing the distribution of samples. And a data frame containing UMAP coordinates and sample annotations for custom plotting.

Examples

data("example")
umap_layout <- plot_umap(example_obj)
#> Using n_neighbors = 8

#> Warning: Using size for a discrete variable is not advised.