buildTree {flowSpy}R Documentation

buildTree

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)
}


[Package flowSpy version 1.0.4 Index]