Core function that builds dimensionality reduction plots using native ggplot2. When split.by is used, shows the split population in color with a grey silhouette of all other cells in the background (SCpubr-style).
Usage
.do_DimPlot_internal(
object,
reduction = "umap",
dims = c(1, 2),
group.by = NULL,
split.by = NULL,
colors.use = NULL,
label = TRUE,
label.size = 4,
label.color = "black",
label.fill = "white",
label.box = TRUE,
pt.size = 1,
pt.alpha = 1,
plot.axes = TRUE,
shuffle = TRUE,
raster = NULL,
raster.dpi = 300,
na.value = "grey75",
plot_cell_borders = TRUE,
border.size = 2,
border.color = "black",
legend.title = NULL,
show.legend = TRUE,
ncol = NULL,
nrow = NULL
)Arguments
- object
Seurat object.
- reduction
character. Name of reduction to use.
- dims
numeric. Vector of 2 dimensions to plot.
- group.by
character. Metadata column for grouping.
- split.by
character. Metadata column for splitting (creates separate panels with silhouettes of other cells).
- colors.use
Named vector of colors.
- label
logical. Show cluster labels.
- label.size
numeric. Label font size.
- label.color
character. Label text color.
- label.fill
character. Label background fill.
- label.box
logical. Use boxed labels.
- pt.size
numeric. Point size.
- pt.alpha
numeric. Point transparency.
- plot.axes
logical. Show axes.
- shuffle
logical. Randomize cell plotting order.
- raster
logical. Rasterize points for large datasets.
- raster.dpi
numeric. DPI for rasterization.
- na.value
character. Color for NA/silhouette cells.
- plot_cell_borders
logical. Plot black borders around cells.
- border.size
numeric. Border size multiplier (default: 2).
- border.color
character. Border color (default: "black").
- legend.title
character. Custom legend title (NULL for default).
- show.legend
logical. Show the colour legend (default: TRUE).
- ncol
numeric. Number of columns for panel layout (default: NULL, auto).
- nrow
numeric. Number of rows for panel layout (default: NULL, auto).