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

## Documentation for package ‘phateR’ version 0.2.9

- 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
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