20 Velocity latent time

plot_velocity_latent_time(sce, reduction = “UMAP”)

### Program and Regulon Activity

Gene set scores and regulons share a unified visualization layer. The `source` parameter lets you switch between "geneset_scoring" and "scenic" without changing the plot call.


``` r
# Single program on embedding
plot_program_activity(sce, program = "T_cell", source = "geneset_scoring")

# Multi-program heatmap across groups
plot_program_heatmap(sce, programs = c("T_cell", "B_cell", "Myeloid"))

# Program dotplot (size = percent expressed, color = mean activity)
plot_program_dotplot(sce, programs = c("T_cell", "B_cell", "Myeloid"), group.by = "colLabels")

# SCENIC regulon on embedding
plot_scenic_activity(sce, regulon = "STAT1(+)")

20.0.1 Perturbation Priority

# Ranked bar chart of perturbation AUC per cell type
plot_perturbation_ranking(sce)

20.0.2 Spatial Analysis

# Deconvolution composition bar chart
plot_spatial_deconvolution(sce)

# Cell type × spot proportion heatmap
plot_spatial_composition(sce, n = 10)

20.0.3 Cell-Cell Communication

plot_cci_bubble(sce, type = "interaction")
plot_cci_sigmoid(sce)
plot_cci_network(sce)

20.0.4 Reference Mapping

# Label transfer summary heatmap
plot_reference_label_transfer_heatmap(sce, group.by = "colLabels")

# Per-label confidence distribution
plot_reference_label_confidence(sce)