R/visualization.R
LinkedPlots.Rd
Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
Seurat object
Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
Name of the image to use in the plot
Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
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 plots into a single patchworked
ggplot object. If FALSE
, return a list of ggplot objects
Feature to visualize
Which slot to pull expression data from?
Returns final plots. If combine
, plots are stiched together
using CombinePlots
; otherwise, returns a list of ggplot objects
if (FALSE) {
LinkedDimPlot(seurat.object)
LinkedFeaturePlot(seurat.object, feature = 'Hpca')
}