Tutorial

To run PHATE on your dataset, create a PHATE operator and run fit_transform. Here we show an example with an artificial tree:

import phate
import scprep
tree_data, tree_clusters = phate.tree.gen_dla()
phate_operator = phate.PHATE(k=15, t=100)
tree_phate = phate_operator.fit_transform(tree_data)
scprep.plot.scatter2d(tree_phate, c=tree_clusters)
phate_operator.set_params(n_components=3)
tree_phate = phate_operator.transform()
scprep.plot.rotate_scatter3d(tree_phate, c=tree_clusters)

A demo on PHATE usage and visualization for single cell RNA-seq data can be found in this Jupyter notebook. A second tutorial is available here which works with the artificial tree shown above in more detail. You can also access interactive versions of these tutorials on Google Colaboratory: single cell RNA seq, artificial tree.