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 1.4.0 Index]