Seurat: BuildClusterTree – R documentation

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BuildClusterTree

Phylogenetic Analysis of Identity Classes

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,
  assay = NULL,
  features = NULL,
  dims = NULL,
  graph = NULL,
  slot = "data",
  reorder = FALSE,
  reorder.numeric = FALSE,
  verbose = TRUE
)

Arguments

`object`	Seurat object
`assay`	Assay to use for the analysis.
`features`	Genes to use for the analysis. Default is the set of variable genes (`VariableFeatures(object = object)`)
`dims`	If set, tree is calculated in PCA space; overrides `features`
`graph`	If graph is passed, build tree based on graph connectivity between clusters; overrides `dims` and `features`
`slot`	Slot(s) to use; if multiple slots are given, assumed to follow the order of 'assays' (if specified) or object's assays
`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)
`verbose`	Show progress updates

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 can be accessed with Tool

Examples

data("pbmc_small")
pbmc_small
pbmc_small <- BuildClusterTree(object = pbmc_small)
Tool(object = pbmc_small, slot = 'BuildClusterTree')

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17