do_RankedExpressionHeatmap() | Expression along components

Ranked expression heatmaps display gene expression ordered by a dimensional reduction component. Cells are ranked along a PC, UMAP dimension, or trajectory score, revealing expression patterns along continuous gradients.

Basic usage

Rank cells by the first PC component:

genes <- c("CDC25C", "KIF18B", "KIF14", "CENPE",
           "DNAAF1", "ADGB", "CFAP61", "CFAP157",
           "KCNQ5", "MEOX2", "MBP", "SNTG1",
           "S100A1", "MGP", "TNNT1", "H2AFJ")

p <- SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                        features = genes,
                                        reduction = "pca",
                                        dims = 1)
p
#> $PC_1

Multiple dimensions

Generate one heatmap per dimension:

p <- SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                        features = genes,
                                        reduction = "pca",
                                        dims = 1:2)

# Access individual plots
p$PC_1 | p$PC_2

Add metadata track

Overlay group information:

p <- SCpubr::do_RankedExpressionHeatmap(
  sample     = sample,
  features   = genes,
  reduction = "pca",
  dims       = 1,
  group.by   = c("Annotation", "subtype"),
)
p
#> $PC_1

Subsampling

Reduce cells for faster plotting:

p <- SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                        features = genes,
                                        dims = 1,
                                        subsample = 50)
p
#> $UMAPHARMONY_1

Parameter reference

Note

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

Core parameters

Parameter Description Default
features Genes to display —
dims Dimensions to rank cells by 1:2

Appearance

Parameter Description Default
main.heatmap.size Main heatmap proportion (0-1) 0.95
subsample Max cells to display 2500
interpolate Smooth heatmap FALSE

Metadata

Parameter Description Default
colors.use Named list of group colors NULL
return_object Return Seurat object FALSE

See also