do_BeeSwarmPlot() | Individual cell distributions

Beeswarm plots display individual cells as ranked points, with beeswarm-style jittering to avoid overlaps. Cells are ranked by a feature (e.g., enrichment score) and colored by categorical or continuous values. Built on the ggbeeswarm package.

Basic usage

Rank cells by a feature (typically a score in metadata):

p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                             feature_to_rank = "nCount_RNA")
p

Continuous vs categorical coloring

Continuous (color by same feature)

p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                             feature_to_rank = "nCount_RNA",
                             continuous_feature = TRUE)
p

Categorical (color by group)

p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                             feature_to_rank = "nCount_RNA",
                             continuous_feature = FALSE)
p

Order groups by median

p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                             feature_to_rank = "nCount_RNA",
                             order = TRUE)
p

Remove axes

p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                             feature_to_rank = "nCount_RNA",
                             remove_x_axis = TRUE,
                             remove_y_axis = TRUE)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling, cell borders, rendering), see Shared features.

Core parameters

Parameter Description Default
feature_to_rank Feature to rank cells by —
continuous_feature Is feature continuous? FALSE

Layout

Parameter Description Default
order Order groups by median FALSE
remove_x_axis Hide X-axis FALSE
remove_y_axis Hide Y-axis FALSE

See also