PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding

Documentation for package ‘phateR’ version 1.0.7

as.data.frame.phate	Convert a PHATE object to a data.frame
as.matrix.phate	Convert a PHATE object to a matrix
check_pyphate_version	Check that the current PHATE version in Python is up to date.
cluster_phate	KMeans on the PHATE potential Clustering on the PHATE operator as introduced in Moon et al. This is similar to spectral clustering.
ggplot.phate	Convert a PHATE object to a data.frame for ggplot
install.phate	Install PHATE Python Package
library.size.normalize	Performs L1 normalization on input data such that the sum of expression values for each cell sums to 1, then returns normalized matrix to the metric space using median UMI count per cell effectively scaling all cells as if they were sampled evenly.
phate	Run PHATE on an input data matrix
plot.phate	Plot a PHATE object in base R
print.phate	Print a PHATE object
summary.phate	Summarize a PHATE object
tree.data	Fake branching data for examples
tree.data.small	Fake branching data for running examples fast