buildTree: buildTree

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

buildTree

Usage

buildTree(
  object,
  method = "euclidean",
  dim.type = c("raw", "pca", "tsne", "dc", "umap"),
  dim.use = seq_len(2),
  verbose = FALSE
)

Arguments

object	a CYT object
method	character. Mehtod to build MST.
dim.type	character. Type of dimensions that will be used to build the tree. Five dim.type are provided, 'raw', 'pca', 'tsne', 'dc' and 'umap'. By default is 'raw'.
dim.use	numeric. Number of dimensions that will be used to build the tree. For example. If dim.use is 'raw', there is no limit for dim.type. And if the dim.use is 'tsne' or 'umap', the default dim.use is seq_len(2).
verbose	logical. Whether to print calculation progress.

Value

A CYT object with tree

Examples

cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- buildTree(cyt, dim.type = "raw")

# build minimum spanning tree (MST) based on tsne
cyt <- buildTree(cyt, dim.type = "tsne", dim.use = seq_len(2))

# Using PCA
cyt <- buildTree(cyt, dim.type = "pca", dim.use =seq_len(4))

# Using UMAP
cyt <- buildTree(cyt, dim.type = "umap", dim.use = seq_len(2))

# Using Diffusion Maps
cyt <- buildTree(cyt, dim.type = "dc", dim.use = seq_len(3))

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.