R: buildTree

buildTree {CytoTree}

R Documentation

buildTree

Description

buildTree

Usage

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

Arguments

`object`	an 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

An 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))

[Package CytoTree version 1.2.0 Index]