buildTree {flowSpy} | R Documentation |
buildTree
buildTree( object, method = "euclidean", dim.type = c("raw", "pca", "tsne", "dc", "umap"), dim.use = 1:2, verbose = FALSE )
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.use |
numeric. Number of dimensions that will be used to build the tree.
For example. If |
verbose |
logical. Whether to print calculation progress. |
An FSPY object with tree
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) }