Embedding plot coloured by an obs column

Usage

embedding_plot_sc(
  object,
  embedding,
  colour_by,
  label_by = NULL,
  discrete = NULL,
  embd_modality = c("rna", "adt", "wnn"),
  point_size = NULL,
  point_alpha = 0.5,
  raster = NULL,
  raster_dpi = c(512, 512),
  palette = NULL,
  label_size = 3,
  label_color = "black",
  label_font = "bold"
)

Arguments

object: A single cell class.
embedding: String. Name of the embedding (e.g. "umap").
colour_by: String. Obs column to colour by.
label_by: String. Optional obs column to label by. (default: NULL).
discrete: Optional boolean. Force a discrete scale by coercing colour_by to a factor. NULL (default) picks the scale from the column type.
embd_modality: String. Modality the embedding is pulled from. One of c("rna", "adt", "wnn"). Use "wnn" for WNN-derived embeddings.
point_size: Optional numeric. Defines the point size. If not provided, will be auto-determined.
point_alpha: Numeric. Defines the alpha.
raster: Optional boolean. Shall the plot be rasterised. If NULL and number of cells is larger than 1e5, defaults to TRUE.
raster_dpi: Two numerics. Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
palette: Optional string. Palette for the colour scale, see bx_colors(). NULL (default) resolves to "main" if colour_by is discrete and "sequential" if it is continuous.
label_size: Numeric. Size of the labels
label_color: String. Color fo the labels.
label_font: String. Font of the labels. bixverse::extract_embedding_data().

Value

A ggplot object.