do_FeaturePlot() | Continuous values on dimensional reduction

Feature plots display continuous values—gene expression, metadata scores, or dimensional reduction components—on a dimensional reduction embedding. Unlike do_DimPlot() which colors by categories, do_FeaturePlot() maps numeric values to a color gradient.

Basic usage

Plot a single feature (gene, metadata column, or PC component):

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1")
p

Multiple features

Plot several features at once:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = c("PC_1", "PC_2"),
                            ncol = 2)
p

Scale customization

Control color scale limits

Outliers often compress the color range. Use min.cutoff and max.cutoff to clamp values:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            min.cutoff = -10,
                            max.cutoff = 10)
p

Tip

Provide one value per feature: min.cutoff = c(0, 0.5, 1) for three features.

Fixed scale limits

Use scale.limits to extend the scale beyond data range (useful for comparing across samples):

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            scale.limits = c(-50, 50))
p

Note

scale.limits cannot be used with min.cutoff or max.cutoff.

Symmetrical scales

Center the color scale around zero (or another value) for diverging data:

# Absolute symmetry: scale extends equally in both directions
p1 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            enforce_symmetry = TRUE,
                            symmetry.type = "absolute")

# Centered symmetry: center around a specific value
p2 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            enforce_symmetry = TRUE,
                            symmetry.type = "centered",
                            symmetry.center = 10)

p1 | p2

Color palettes

Sequential palettes (default)

# RColorBrewer sequential palette
p1 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            use_viridis = FALSE,
                            sequential.palette = "YlOrRd",
                            sequential.direction = 1)

# Viridis palette
p2 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            use_viridis = TRUE,
                            viridis.palette = "G",
                            viridis.direction = 1)

p1 | p2

Diverging palettes

Automatically used when enforce_symmetry = TRUE:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            enforce_symmetry = TRUE,
                            diverging.palette = "RdBu",
                            diverging.direction = -1)
p

Subsetting & splitting

Highlight specific cells

# Highlight by cell barcodes
cells.use <- sample(colnames(sample), 500)
p1 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            cells.highlight = cells.use)

# Highlight by identity
p2 <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            idents.highlight = c("IPC-like"))

p1 | p2

Split by variable

Create faceted plots:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            split.by = "subtype")
p

Group overlay

Display categorical group information alongside continuous values:

Group dots

Add dots at cluster centers:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            group.by = "Annotation")
p

Group cell borders

Add a colored shadow around cells showing group membership:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            group.by = "Annotation",
                            group.by.cell_borders = TRUE,
                            group.by.cell_borders.alpha = 0.1)
p

Labels

Add identity labels to the plot:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            label = TRUE,
                            label.color = "black",
                            label.size = 4)
p

Visual enhancements

Density contours

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "PC_1",
                            plot_density_contour = TRUE,
                            contour.color = "grey50",
                            contour.position = "bottom")
p

Order by expression

Plot cells with higher expression on top:

p <- SCpubr::do_FeaturePlot(sample = sample,
                            features = "KIF14",
                            order = TRUE)
p

Parameter reference

Note

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

Core parameters

Parameter Description Default
features Features to plot (genes, metadata, PCs) —

Scale & limits (FeaturePlot-specific)

Parameter Description Default
scale.limits Fixed scale limits c(min, max) NULL
symmetry.type "absolute" or "centered" "absolute"
symmetry.center Center value for "centered" type NA

Subsetting

Parameter Description Default
idents.keep Identities to display NULL
cells.highlight Cell barcodes to highlight NULL
idents.highlight Identities to highlight NULL

Group overlay

Parameter Description Default
group.by Metadata column for group overlay NULL
group.by.colors.use Colors for groups Auto-generated
group.by.legend Legend title for groups Column name
group.by.dot.size Size of center dots 8
group.by.show.dots Show center dots TRUE
group.by.cell_borders Show colored borders FALSE
group.by.cell_borders.alpha Border transparency 0.1
colorblind Colorblind-safe group colors FALSE

Individual customization

Parameter Description Default
individual.titles Title per feature NULL
individual.subtitles Subtitle per feature NULL
individual.captions Caption per feature NULL

Appearance (FeaturePlot-specific)

Parameter Description Default
order Order cells by expression FALSE
ncol Columns for multiple features NULL
plot.axes Show axis lines FALSE
verbose Show messages TRUE

See also