Plot your Seurat object in 3D. — TS_plot

Will be coloured according to cluster idents with a scales::hue_pal() colouring scheme. You need to have an already analysed Seurat object to be able to run the function.

Usage

TS_plot_3D(
  seurat_object = get(default_seurat_object),
  dims = 1:20,
  group.by = NULL,
  colors = NULL,
  reduction = "umap"
)

Arguments

seurat_object: The Seurat object you want to analyse. Defaults to 'default_seurat_object'
dims: What Principal Components to use for calculating the UMAP.
group.by: Variable to group cells by. Default is Seurat::Idents(), alternatives are any available metadata in the object.
colors: A vector of colors to use for the group.by parameter. Default is hue_pal()(length of unique values in your group.by parameter)
reduction: What reduction to use, defaults to "umap". Alternatively, you can use "harmony"