| 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)
}