BuildClusterTree: Phylogenetic Analysis of Identity Classes

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Constructs a phylogenetic tree relating the 'average' cell from each identity class. Tree is estimated based on a distance matrix constructed in either gene expression space or PCA space.

Usage

BuildClusterTree(object, genes.use = NULL, pcs.use = NULL, SNN.use = NULL,
  do.plot = TRUE, do.reorder = FALSE, reorder.numeric = FALSE)

Arguments

object	Seurat object
genes.use	Genes to use for the analysis. Default is the set of variable genes ([e-mail]). Assumes pcs.use=NULL (tree calculated in gene expression space)
pcs.use	If set, tree is calculated in PCA space, using the eigenvalue-weighted euclidean distance across these PC scores.
SNN.use	If SNN is passed, build tree based on SNN graph connectivity between clusters
do.plot	Plot the resulting phylogenetic tree
do.reorder	Re-order identity classes (factor ordering), according to position on the tree. This groups similar classes together which can be helpful, for example, when drawing violin plots.
reorder.numeric	Re-order identity classes according to position on the tree, assigning a numeric value ('1' is the leftmost node)

Details

Note that the tree is calculated for an 'average' cell, so gene expression or PC scores are averaged across all cells in an identity class before the tree is constructed.

Value

A Seurat object where the cluster tree is stored in [e-mail][[1]]

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.