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

## Documentation for package ‘phateR’ version 1.0.4

- DESCRIPTION file.

## Help Pages

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