PHATE is a tool for visualizing high dimensional single-cell data with natural progressions or trajectories. PHATE uses a novel conceptual framework for learning and visualizing the manifold inherent to biological systems in which smooth transitions mark the progressions of cells from one state to another. To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic stem cells, human embryonic stem cells, and bone marrow samples, check out our preprint on bioRxiv at < http://biorxiv.org/content/early/2017/03/24/120378>.
This R package provides an implementation of the PHATE dimensionality reduction and visualization method.
For a thorough overview of the PHATE visualization method, please see the bioRxiv preprint
For our Python and Matlab implementations, please see KrishnaswamyLab/PHATE.
In order to use PHATE in R, you must also install the Python package.
pip are not installed, you will need to install them.
We recommend Miniconda3 to install
pip together, or otherwise you can install
phate in Python by running the following code from a
pip install --user phate
phateR from CRAN by running the following code in R:
The development version of PHATE can be installed directly from R with
if (!suppressWarnings(require(devtools))) install.packages("devtools")reticulate::py_install("phate", pip=TRUE)devtools::install_github("KrishnaswamyLab/phateR")
The latest source version of PHATE can be accessed by running the following in a terminal:
git clone --recursive git://github.com/KrishnaswamyLab/PHATE.gitcd PHATE/Pythonpython setup.py install --usercd ../phateRR CMD INSTALL
phateR folder is empty, you have may forgotten to use the
--recursive option for
git clone. You can rectify this by running
the following in a terminal:
cd PHATEgit submodule initgit submodule updatecd Pythonpython setup.py install --usercd ../phateRR CMD INSTALL
If you have loaded a data matrix
data in R (cells on rows, genes on
columns) you can run PHATE as follows:
library(phateR)data_phate <- phate(data)
phateR accepts R matrices,
Matrix sparse matrices,
any other data type that can be converted to a matrix with the function
This is a basic example running
phate on a highly branched example
dataset that is included with the package. You can read a tutorial on
running PHATE on single-cell RNA-seq at
inst/examples. Running this tutorial from start to finish should
take approximately 3 minutes.
First, let’s load the tree data and examine it with PCA.
library(phateR)#> Loading required package: Matrixdata(tree.data)plot(prcomp(tree.data$data)$x, col=tree.data$branches)
Now we run PHATE on the data. We’ll just go ahead and try with the default parameters.
# runs phatetree.phate <- phate(tree.data$data)summary(tree.phate)#> PHATE embedding#> k = 5, alpha = 40, t = auto#> Data: (3000, 100)#> Embedding: (3000, 2)
Let’s plot the results.
# plot embeddingpalette(rainbow(10))plot(tree.phate, col = tree.data$branches)
Good news! Our branches separate nicely. However, most of the
interesting activity seems to be concentrated into one region of the
plot - in this case we should try the square root potential instead by
gamma=0. We can also try increasing
t to make the structure a
little clearer - in this case, because synthetic data in unusually
structured, we can use a very large value, like 120, but in biological
data the automatic
t selection is generally very close to ideal. Note
here that if we pass our previous result in with the argument
won’t have to recompute the diffusion operator.
# runs phate with different parameterstree.phate <- phate(tree.data$data, gamma=0, t=120, init=tree.phate)# plot embeddingpalette(rainbow(10))plot(tree.phate, col = tree.data$branches)
We can also pass the PHATE object directly to
ggplot, if it is
library(ggplot2)#> Warning: package 'ggplot2' was built under R version 3.5.3ggplot(tree.phate, aes(x=PHATE1, y=PHATE2, color=tree.data$branches)) +geom_point()
To be consistent with common dimensionality reductions such as PCA
stats::prcomp) and t-SNE (
Rtsne::Rtsne), we require that cells
(observations) be rows and genes (features) be columns of your input
reticulate::py_discover_config("phate") and compare it to
the version of Python in which you installed PHATE (run
which pip in a terminal.) Chances are
reticulate can’t find the
right version of Python; you can fix this by adding the following line
You can read more about
Please let us know of any issues at the GitHub
repository. If you
have any questions or require assistance using PHATE, please read the
documentation by running
help(phateR::phate) or contact us at