plot_reduced_dim: Plot Cells Reduced Dimensions With Feature Highlighting

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Plot Cells Reduced Dimensions With Feature Highlighting

Description

Generates a 2d plot of cells with feature highlighting

Usage

plot_reduced_dim(
  sce,
  feature_dim = "Cluster",
  reduced_dim = "UMAP",
  highlight_feature = NA,
  label_clusters = FALSE,
  size = getOption("scflow_reddimplot_pointsize", default = 0.1),
  alpha = getOption("scflow_reddimplot_alpha", default = 0.2)
)

Arguments

sce	a SingleCellExperiment object
feature_dim	the colData variable of interest
reduced_dim	the reducedDim slot for plotting
highlight_feature	highlights a feature
label_clusters	prints cluster labels
size	point size
alpha	point alpha

Value

p a ggplot object

See Also

Other plotting functions: plot_expr_by_numeric_var(), plot_reduced_dim_gene(), plot_violin()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.