Creates feature expression plots overlaid on dimensionality reductions with viridis color scales and publication-ready styling.
Usage
do_FeaturePlot(
object,
features,
reduction = "umap",
dims = c(1, 2),
slot = "data",
use_viridis = TRUE,
viridis.palette = "B",
viridis.direction = -1,
order = TRUE,
pt.size = 1,
pt.alpha = 1,
plot.axes = TRUE,
variance_digits = 1,
min.cutoff = NA,
max.cutoff = NA,
na.value = "grey90",
split.by = NULL,
plot_cell_borders = TRUE,
border.size = 2,
border.color = "black",
ncol = NULL,
nrow = NULL,
...
)Arguments
- object
Seurat object.
- features
character. Gene names or metadata columns to plot.
- reduction
character. Reduction to use (default: "umap").
- dims
numeric. Vector of 2 PC dimensions to plot (default: c(1, 2)).
- slot
character. Data slot ("data", "counts", "scale.data"). Default: "data".
- use_viridis
logical. Use viridis color scale (default: TRUE).
- viridis.palette
character. Viridis palette "A"-"H" (default: "B").
- viridis.direction
numeric. Color direction -1 or 1 (default: -1).
- order
logical. Plot high-expressing cells on top (default: TRUE).
- 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).
- min.cutoff
numeric or "q10". Minimum expression cutoff.
- max.cutoff
numeric or "q90". Maximum expression cutoff.
- na.value
character. Color for NA/zero values (default: "grey90").
- split.by
character. Metadata column for splitting (creates panels with silhouettes).
- 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").
- ncol
numeric. Number of columns for panel layout (default: NULL, auto).
- nrow
numeric. Number of rows for panel layout (default: NULL, auto).
- ...
Additional arguments (currently unused).
Examples
if (FALSE) { # \dontrun{
do_FeaturePlot(seurat_object, features = "CD3D")
do_FeaturePlot(seurat_object, features = c("CD3D", "CD8A", "CD4"))
do_FeaturePlot(seurat_object, features = "CD3D", reduction = "pca")
} # }