do_DotPlot() | Marker gene expression

Dot plots visualize gene expression using two visual scales: color represents average expression, while dot size shows the percentage of cells expressing each gene. This dual encoding makes them ideal for comparing marker genes across clusters or conditions.

Basic usage

Plot marker genes across clusters:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = c("CDC25C", "KIF18B", "KIF14", "CENPE"))
p

Query multiple markers

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

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes)
p

Grouped features

Provide a named list to organize genes into categories with faceted panels:

genes <- list(
  "IPC.like"      = c("CDC25C", "KIF18B", "KIF14", "CENPE"),
  "Cilia.like" = c("DNAAF1", "ADGB", "CFAP61", "CFAP157"),
  "OPC.like" = c("KCNQ5", "MEOX2", "MBP", "SNTG1"),
  "Mesenchymal.like" = c("S100A1", "MGP", "TNNT1", "H2AFJ")
)

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes)
p

Clustering

Cluster identities

Group similar clusters together based on expression patterns:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        cluster.identities = TRUE)
p

Cluster features

Reorder genes by expression similarity:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        cluster.features = TRUE)
p

Cluster both

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        cluster.identities = TRUE,
                        cluster.features = TRUE)
p

Z-score normalization

Show relative expression across groups instead of absolute values. This highlights which group has the highest expression for each gene, but prevents cross-gene comparisons:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        zscore.data = TRUE)
p

Note

Z-scoring automatically enables enforce_symmetry = TRUE for a centered diverging color scale.

Split by condition

Create separate facets for each condition:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = c("CDC25C", "KIF18B", "KIF14", "CENPE"),
                        split.by = "subtype")
p

Warning

split.by cannot be combined with named feature lists, clustering, or z-scoring.

Filter low expression

Remove dots below a minimum percent expressed threshold:

# Only show dots where >= 50% of cells express the gene
p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        dot.min = 50)
p

Visual customization

Flip axes

Swap genes and clusters:

p <- SCpubr::do_DotPlot(sample = sample,
                        features = c("CDC25C", "KIF18B", "KIF14", "CENPE"),
                        flip = TRUE)
p

Adjust dot size

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        dot.scale = 12)
p

Control axis text angle

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        axis.text.x.angle = 90)
p

Scale limits

Clamp expression values

p <- SCpubr::do_DotPlot(sample = sample,
                        features = genes,
                        min.cutoff = 0,
                        max.cutoff = 3)
p

Parameter reference

Note

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

Core parameters

Parameter Description Default
features Genes to plot (vector or named list) —

Clustering & transformation

Parameter Description Default
cluster.identities Cluster groups by expression similarity FALSE
cluster.features Cluster genes by expression patterns FALSE
zscore.data Show Z-scores instead of average expression FALSE

Filtering

Parameter Description Default
dot.min Minimum percent expressed to show dot (0–100) 5

Appearance

Parameter Description Default
dot.scale Maximum dot size 8
axis.text.x.angle X-axis label rotation angle 45

See also