Plot Cells Reduced Dimensions With Feature Highlighting

Generates a 2d plot of cells with feature highlighting

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()