Returns final plots. If combine, plots are stiched together
using CombinePlots; otherwise, returns a list of ggplot objects
Arguments
object
A Seurat object
dims
Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
reduction
Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
image
Name of the image to use in the plot
group.by
Name of meta.data column to group the data by
alpha
Controls opacity of spots. Provide as a vector specifying the
min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
alpha value for each plot.
combine
Combine plots into a single gg object; note that if TRUE;
themeing will not work when plotting multiple features/groupings
feature
Feature to visualize
slot
If plotting a feature, which data slot to pull from (counts,
data, or scale.data)