get_meta_dt: get_meta_dt

In jrboyd/ssvRecipes: Recipes using seqsetvis

get_meta_dt

Description

retrieves metadata data.table from Seurat object with reduction coordinates added. optional arguments all meta clustres to be specified by combining an existing cluster definition and factor level specification for arbitrary variables.

Usage

get_meta_dt(
  seurat_obj,
  combine_source = "seurat_clusters",
  to_combine = list(west_island = c(15, 6), west_projection = c(13, 4), lonely_island =
    c(11), north_archipelago = c(9, 8, 14, 12), main_continent = c(7, 0, 2, 16, 2, 1, 3,
    5, 10)),
  cluster_vars = c("seurat_clusters", "meta_cluster"),
  manual_factors = list(orig.ident = c("wt", "df4")),
  reduction = "umap"
)

Arguments

seurat_obj	an object of class Seurat to extract meta data from
to_combine
cluster_vars	cluster variables, will be made factors with levels ordered by decreasing size.
manual_factors	named list, names specify variables and entries specify factor levels to apply.
reduction	string to specify reduction, must be in seurat_obj@reductions

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.