dendoSeurat: Produce hierarchical clustering for a sub-cluster of a...

In basilkhuder/extendSC: Extends functionalities of scRNA-Seq workflows

Description

Produce hierarchical clustering for a sub-cluster of a downsampled Seurat object and return a dendrogram.

Usage

dendoSeurat(
  seurat.obj,
  cluster,
  annotation.name,
  down.sample,
  variable.genes = NULL,
  seed = 1,
  return.clusters = NULL
)

Arguments

seurat.obj	A seurat object.
cluster	Cluster interested in
annotation.name	Variable name given to Seurat cluster assignments
down.sample	Amount of cells to sample
variable.genes	(Optional) Subet counts data to this many variable genes for distance matrix calculation
seed	Value for the seed to set
return.clusters	(Optional) Put the height you want to cut the dendrogram at and return an object that contains cells and hierarchical clusters dendoSeurat(seurat.obj, cluster = "5", annotation.name = "seurat_clusters", down.sample = 50, seed = 1, return.clusters = 4)

basilkhuder/extendSC documentation built on July 23, 2021, 1:17 p.m.