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Scatter plot of a reduction, colored by a grouping variable.

plot_dr_group.Rd

The categorical counterpart of plot_dr_feature(): cells are colored by a metadata column (or by the current identities) rather than by a continuous feature. Cells are shuffled so no one group is drawn on top of the others.

Usage

plot_dr_group(
  x,
  reduction = "umap",
  group_by = NULL,
  color_scheme = NULL,
  pt_size = NULL,
  na_value = "grey50",
  file_prefix = NULL,
  file_format = c("png", "pdf"),
  width = NULL,
  height = 6
)

Arguments

x

Seurat object.

reduction

Dimensionality reduction to plot on (e.g. "umap", "tsne", "pca").

group_by

(optional) Metadata column to color by. NULL uses the current identities.

color_scheme

(optional) Vector of colors. Defaults to the "clusters" scheme.

pt_size

(optional) Point size. Defaults to get_dr_point_size(x).

na_value

Color for cells with no value in group_by.

file_prefix

(optional) Path to save to.

file_format

File formats to write when file_prefix is given.

width

(optional) Saved width in inches. NULL measures the plot's own legend and widens to fit it - see save_dr_plot().

height

Saved height in inches.

Value

A ggplot object.