buildTree {CytoTree} | R Documentation |
buildTree
buildTree( object, method = "euclidean", dim.type = c("raw", "pca", "tsne", "dc", "umap"), dim.use = seq_len(2), verbose = FALSE )
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.use |
numeric. Number of dimensions that will be used to build the tree.
For example. If |
verbose |
logical. Whether to print calculation progress. |
A CYT object with tree
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))