phateR v1.0.4

Merge pull request #46 from KrishnaswamyLab/dev

phateR v1.0.4

phateR v0.4.1

Changeset:

• reinstate use.alpha parameter for Seurat compatibility.

phateR 0.4.0

Changeset:

• updated parameters k -> knn, alpha -> decay to match Python version
• better handling of load errors
• added FAQ to README

phateR v0.2.8

phateR v0.2.8 replaces the potential.method parameter with gamma to match Python PHATE v0.2.8.

Use gamma=1 (default) for the log potential, gamma=0 for the square root potential. Valid values of gamma are between -1 and 1.

phateR v0.2.7

Bugfix resolves issues with reticulate passing NA to Python as True.

PHATE 2.5 (Fast scalable PHATE, run from Python)

PHATE now calls the much faster code written in Python to perform dimensionality reduction using the reticulate package. PHATE must be installed in both Python and R in order to use the R code.

Other changes:

• precomputed distance matrices are now accepted, with phate(data=distances, knn.dist.method="precomputed")
• precomputed affinity matrices must be provided in the same way, with phate(data=affinities, knn.dist.method="precomputed"), rather than via g.kernel.
• multiprocessing is supported - call phate(..., n.jobs=5) to use 5 cores or phate(..., n.jobs = -1) to use all available.