buildTree: buildTree

In JhuangLab/flowSpy: 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 = 1:2,
  verbose = FALSE
)

Arguments

object	an FSPY 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 1:2.
verbose	logical. Whether to print calculation progress.

Value

An FSPY object with tree

Examples

if (FALSE) {
# build minimum spanning tree (MST) based on raw expression matrix
fspy <- buildTree(fspy, dim.type = "raw")

# build minimum spanning tree (MST) based on tsne
fspy <- buildTree(fspy, dim.type = "tsne", dim.use = 1:2)

# Using PCA
fspy <- buildTree(fspy, dim.type = "pca", dim.use = 1:4)

# Using UMAP
fspy <- buildTree(fspy, dim.type = "umap", dim.use = 1:2)

# Using Diffusion Maps
fspy <- buildTree(fspy, dim.type = "dc", dim.use = 1:3)
}

JhuangLab/flowSpy documentation built on July 15, 2020, 8:31 a.m.