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Plot reduced-dimensional embeddings for reference and null data

Source: R/dim_plot.R
dimPlot.Rd

Generates a UMAP (or other reduced dimension) plot comparing a reference dataset and one or multiple null datasets. Input objects can be either Seurat or SingleCellExperiment objects. All objects are internally converted to SingleCellExperiment.

Usage

dimPlot(
  ref_obj,
  null_obj,
  color_by = "seurat_clusters",
  seed = 0,
  nrow = NULL,
  ncol = NULL
)

Arguments

ref_obj

A Seurat or SingleCellExperiment object representing the reference dataset.

null_obj

A single object or a list of objects, each being either Seurat or SingleCellExperiment, representing the null datasets.

color_by

A character string specifying the cell metadata column used to color the embedding. Default: "seurat_clusters".

seed

Integer random seed for reproducibility. Default: 0.

nrow

Number of rows for faceting multiple datasets. Default: NULL.

ncol

Number of columns for faceting multiple datasets. Default: NULL.

Value

A ggplot object showing the embedded reference and null datasets.