Creates a PCA dimensionality reduction plot with variance explained percentages automatically added to axis labels. When split.by is used, shows each split category with a grey silhouette of all other cells.
Usage
do_PcaPlot(
object,
dims = c(1, 2),
group.by = NULL,
split.by = NULL,
colors.use = NULL,
label = TRUE,
label.size = 4,
label.color = "black",
label.fill = "white",
pt.size = 1,
pt.alpha = 1,
plot.axes = TRUE,
variance_digits = 1,
shuffle = TRUE,
plot_cell_borders = TRUE,
border.size = 2,
border.color = "black",
legend.title = NULL,
show.legend = TRUE,
ncol = NULL,
nrow = NULL,
...
)Arguments
- object
Seurat object.
- dims
numeric. Vector of 2 PC dimensions to plot (default: c(1, 2)).
- group.by
character. One or more metadata columns for grouping. If NULL (default), uses active Idents. When multiple columns are provided, each gets its own panel combined via patchwork.
- split.by
character. Metadata column for splitting (creates panels with silhouettes).
- colors.use
Named vector of colors for groups.
- label
logical. Show cluster labels (default: TRUE).
- label.size
numeric. Label font size (default: 4).
- label.color
character. Label text color (default: "black").
- label.fill
character. Label background fill (default: "white").
- pt.size
numeric. Point size (default: 1).
- pt.alpha
numeric. Point transparency (default: 1).
- plot.axes
logical. Show axes (default: TRUE).
- variance_digits
numeric. Decimal places for variance (default: 1).
- shuffle
logical. Randomize cell plotting order (default: TRUE).
- plot_cell_borders
logical. Plot black borders around cells (default: TRUE).
- border.size
numeric. Border size multiplier (default: 2).
- border.color
character. Border color (default: "black").
- legend.title
character. Custom legend title (NULL removes title).
- show.legend
logical. Show the colour legend (default: TRUE). Set to FALSE to hide the legend entirely.
- ncol
numeric. Number of columns for panel layout (default: NULL, auto). Controls layout of both split panels and multi-column group.by panels.
- nrow
numeric. Number of rows for panel layout (default: NULL, auto).
- ...
Additional arguments (currently unused).
Examples
if (FALSE) { # \dontrun{
do_PcaPlot(seurat_object, group.by = "condition")
do_PcaPlot(seurat_object, dims = c(2, 3), group.by = "cluster")
do_PcaPlot(seurat_object, split.by = "sample") # Shows silhouettes
} # }