Shared features across functions

Most SCpubr functions share a common set of parameters. This reference guide organizes them by category for quick lookup.

Data & grouping

Parameter	Description
`sample`	Seurat object to use for plotting
`group.by`	Metadata variable to group values by
`split.by`	Metadata variable to split plots by
`features`	Genes, metadata columns, or dimensional reduction components
`input_gene_list`	Named list of gene sets
`assay`	Assay name to pull data from
`slot`	Slot within assay (`data`, `counts`, `scale.data`)
`reduction`	Dimensional reduction to use (e.g., `"umap"`, `"pca"`)
`dims`	Which dimensions of the reduction to use

Color scales

Categorical variables

Use colors.use to define custom colors for categorical variables:

Named vector
Named list

# One color per identity
colors <- c("0" = "#001219", "1" = "#005f73", "2" = "#0a9396",
            "3" = "#94d2bd", "4" = "#e9d8a6", "5" = "#ee9b00")

SCpubr::do_DimPlot(sample, colors.use = colors)

# Multiple metadata variables (for heatmaps)
colors <- list(
  "seurat_clusters" = c("0" = "#001219", "1" = "#005f73", "2" = "#0a9396"),
  "cell_type"       = c("A" = "#ca6702", "B" = "#0a9396")
)

SCpubr::do_SCExpressionHeatmap(sample, features = genes, 
                                metadata = names(colors),
                                metadata.colors = colors)

Continuous variables

Parameter	Description	Values
`use_viridis`	Use viridis palette	`TRUE` / `FALSE`
`viridis.palette`	Viridis palette name	`"A"` (magma), `"B"` (inferno), `"C"` (plasma), `"D"` (viridis), `"E"` (cividis), `"F"` (rocket), `"G"` (mako), `"H"` (turbo)
`viridis.direction`	Color mapping direction	`1` (dark→low) or `-1` (dark→high)
`sequential.palette`	RColorBrewer sequential palette	`"YlOrRd"`, `"YlOrBr"`, `"YlGnBu"`, `"YlGn"`, `"Reds"`, `"RdPu"`, `"Purples"`, `"PuRd"`, `"PuBuGn"`, `"PuBu"`, `"OrRd"`, `"Oranges"`, `"Greys"`, `"Greens"`, `"GnBu"`, `"BuPu"`, `"BuGn"`, `"Blues"`
`sequential.direction`	Color mapping direction	`1` or `-1` (note: inverted from viridis)
`diverging.palette`	RColorBrewer diverging palette	`"Spectral"`, `"RdYlGn"`, `"RdGy"`, `"RdBu"`, `"PuOr"`, `"PRGn"`, `"PiYG"`, `"BrBG"`

Scale limits & symmetry

Parameter	Description
`min.cutoff`	Minimum value for color scale (values below are clamped)
`max.cutoff`	Maximum value for color scale (values above are clamped)
`enforce_symmetry`	Center scale around middle value; use diverging palette

Titles & labels

Parameter	Description
`plot.title`	Main title
`plot.subtitle`	Subtitle
`plot.caption`	Caption (bottom)
`xlab`	X-axis label
`ylab`	Y-axis label
`legend.title`	Legend title

Typography

Parameter	Description	Values
`font.size`	Base font size (other elements scale proportionally)	Numeric
`font.type`	Font family	`"sans"`, `"serif"`, `"mono"`
`plot.title.face`	Title font style	`"plain"`, `"italic"`, `"bold"`, `"bold.italic"`
`plot.subtitle.face`	Subtitle font style	Same as above
`plot.caption.face`	Caption font style	Same as above
`axis.title.face`	Axis titles font style	Same as above
`axis.text.face`	Axis tick labels font style	Same as above
`legend.title.face`	Legend title font style	Same as above
`legend.text.face`	Legend text font style	Same as above
`strip.text.face`	Facet strip labels font style	Same as above

Legend

Position & layout

Parameter	Description	Values
`legend.position`	Legend placement	`"right"`, `"left"`, `"top"`, `"bottom"`, `"none"`
`legend.title.position`	Title position within legend	`"top"`, `"bottom"`, `"left"`, `"right"`
`legend.ncol` / `legend.nrow`	Layout dimensions	Numeric
`legend.byrow`	Fill by rows	`TRUE` / `FALSE`
`legend.icon.size`	Icon size (categorical)	Numeric

Colorbar (continuous)

Parameter	Description
`legend.type`	`"normal"` or `"colorbar"`
`legend.length` / `legend.width`	Colorbar dimensions
`legend.framecolor` / `legend.framewidth`	Border styling
`legend.tickcolor` / `legend.tickwidth`	Tick styling
`number.breaks`	Number of legend breaks

Grid

Parameter	Description	Values
`plot.grid`	Show grid lines	`TRUE` / `FALSE`
`grid.color`	Grid line color	Color string
`grid.type`	Line type	`"blank"`, `"solid"`, `"dashed"`, `"dotted"`, `"dotdash"`, `"longdash"`, `"twodash"`

Axes

Parameter	Description
`flip`	Swap X and Y axes

Rendering

Parameter	Description
`na.value`	Color for `NA` values
`raster`	Rasterize plot (reduces file size for large datasets)
`raster.dpi`	Rasterization resolution

Dimensional reduction enhancements

These parameters apply to do_DimPlot, do_FeaturePlot, do_NebulosaPlot, and similar functions.

Cell borders

Adds a shadow layer behind cells to create an outline effect. Increases file size but improves publication figures.

Parameter	Description	Default
`plot_cell_borders`	Enable cell borders	`FALSE`
`border.size`	Border dot size	`2`
`border.color`	Border color	`"black"`
`border.density`	Proportion of cells used (0–1); lower = lighter file	`1`

Density contours

Parameter	Description	Values
`plot_density_contour`	Show density contour lines	`TRUE` / `FALSE`
`contour.position`	Layer position	`"top"`, `"bottom"`
`contour.color`	Contour line color	Color string
`contour_expand_axes`	Expand axes to fit contours (0–1 proportion)	Numeric

Marginal distributions

Parameter	Description	Values
`plot_marginal_distributions`	Show marginal plots	`TRUE` / `FALSE`
`marginal.type`	Distribution type	`"density"`, `"histogram"`, `"boxplot"`, `"violin"`, `"densigram"`
`marginal.size`	Size ratio (main:marginal)	Numeric
`marginal.group`	Split by identity	`TRUE` / `FALSE`

Note

Marginal distributions are incompatible with split.by, plot_cell_borders, and cells.highlight.