Merge pull request #46 from KrishnaswamyLab/dev

phateR v1.0.4

.github/ISSUE_TEMPLATE/bug_report.md

@@ -65,5 +65,17 @@ You can do this with `R -e 'reticulate::py_discover_config(required_module = "ph
 
 </details>
 
+Output of `phateR::check_pyphate_version()`:
+
+<details>
+
+```
+Please run `phateR::check_pyphate_version()` and paste the results here.
+
+You can do this with `R -e 'phateR::check_pyphate_version()'`
+```
+
+</details>
+
 **Additional context**
 Add any other context about the problem here.

.gitignore

@@ -1,3 +1,5 @@
 .Rproj.user
 .Rhistory
 .RData
+phateR_*.tar.gz
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: phateR
 Title: PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding
-Version: 1.0.0.999
+Version: 1.0.4
 Authors@R: c(person("Krishnan", "Srinivasan", email = "[email protected]", role = c("aut")),
              person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre', comment = c(ORCID = '0000-0002-4544-2764')))
 Description: PHATE is a tool for visualizing high dimensional single-cell data
@@ -21,7 +21,8 @@ Imports:
     stats,
     graphics,
     reticulate (>= 1.8),
-    ggplot2
+    ggplot2,
+    memoise
 Suggests:
     gridGraphics,
     cowplot

NAMESPACE

@@ -13,4 +13,6 @@ export(library.size.normalize)
 export(phate)
 import(Matrix)
 importFrom(ggplot2,ggplot)
+importFrom(memoise,memoise)
+importFrom(reticulate,py_discover_config)
 importFrom(utils,packageVersion)

R/phate.R

@@ -232,7 +232,7 @@ phate <- function(data, ndim = 2, knn = 5,
     }
   }
   if (is.null(operator)) {
-    operator <- pyphate$PHATE(n_components = ndim,
+    operator <- pyphate()$PHATE(n_components = ndim,
                               knn = knn,
                               decay = decay,
                               t = t,
@@ -256,7 +256,7 @@ phate <- function(data, ndim = 2, knn = 5,
     out <- operator$von_neumann_entropy(t_max = t.max)
     t <- out[[1]]
     h <- out[[2]]
-    t.opt <- pyphate$vne$find_knee_point(h, t)
+    t.opt <- pyphate()$vne$find_knee_point(h, t)
     graphics::plot(t, h,
                    type = "l",
                    xlab = "t", ylab = "Von Neumann Entropy",

R/utils.R

@@ -54,15 +54,11 @@ failed_pyphate_import <- function(e) {
 }
 
 load_pyphate <- function() {
+  py_config <- try(reticulate::py_discover_config(required_module = "phate"))
   delay_load = list(on_load=check_pyphate_version, on_error=failed_pyphate_import)
   # load
-  if (is.null(pyphate)) {
-    # first time load
-    result <- try(pyphate <<- reticulate::import("phate", delay_load = delay_load))
-  } else {
-    # already loaded
-    result <- try(reticulate::import("phate", delay_load = delay_load))
-  }
+  pyphate <- try(reticulate::import("phate", delay_load = delay_load))
+  pyphate
 }
 
 #' Install PHATE Python Package
@@ -106,7 +102,8 @@ install.phate <- function(envname = "r-reticulate", method = "auto",
 
 pyphate <- NULL
 
+#' @importFrom reticulate py_discover_config
+#' @importFrom memoise memoise
 .onLoad <- function(libname, pkgname) {
-  py_config <- reticulate::py_discover_config(required_module = "phate")
-  load_pyphate()
+  pyphate <<- memoise::memoise(load_pyphate)
 }

README.Rmd

@@ -22,10 +22,9 @@ knitr::opts_chunk$set(
 [![Twitter](https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow)](https://twitter.com/KrishnaswamyLab)
 [![Github Stars](https://img.shields.io/github/stars/KrishnaswamyLab/PHATE.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/PHATE/)
 
-This R package provides an implementation of the
-[PHATE dimensionality reduction and visualization method](https://www.biorxiv.org/content/early/2017/12/01/120378).
+This R package provides an implementation of the [PHATE dimensionality reduction and visualization method](https://www.nature.com/articles/s41587-019-0336-3).
 
-For a thorough overview of the PHATE visualization method, please see the [bioRxiv preprint](https://www.biorxiv.org/content/early/2017/12/01/120378)
+For a thorough overview of the PHATE visualization method, please see the [Nature Biotechnology publication](https://www.nature.com/articles/s41587-019-0336-3).
 
 For our Python and Matlab implementations, please see [KrishnaswamyLab/PHATE](https://github.com/KrishnaswamyLab/PHATE).
 
@@ -165,6 +164,10 @@ ggplot(tree.phate, aes(x=PHATE1, y=PHATE2, color=tree.data$branches)) +
 
 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 data.
 
+  - **Can I run PHATE with Seurat?**
+
+PHATE was removed from Seurat in version 3. You can install a version of Seurat with `RunPHATE` included by following the instructions at <https://github.com/satijalab/seurat/pull/1172#issuecomment-564782167>.
+
 * **I have installed PHATE in Python, but phateR says it is not installed!**
 
 Check your `reticulate::py_discover_config("phate")` and compare it to the version of Python in which you installed PHATE (run `which python` and `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 to your `~/.Renviron`:
@@ -175,5 +178,5 @@ You can read more about `Renviron` at <https://CRAN.R-project.org/package=startu
 
 ### Help
 
-Please let us know of any issues at the [GitHub repository](https://github.com/KrishnaswamyLab/phateR/issues). If you have any questions or require assistance using PHATE, please read the documentation by running `help(phateR::phate)` or contact us at <https://krishnaswamylab.org/get-help>.
+Please let us know of any issues at the [GitHub repository](https://github.com/KrishnaswamyLab/phateR/issues). If you have any questions or require assistance using PHATE, please read the documentation at <https://CRAN.R-project.org/package=phateR/phateR.pdf> or by running `help(phateR::phate)` or contact us at <https://krishnaswamylab.org/get-help>.
 

README.md

@@ -18,11 +18,10 @@ Stars](https://img.shields.io/github/stars/KrishnaswamyLab/PHATE.svg?style=socia
 
 This R package provides an implementation of the [PHATE dimensionality
 reduction and visualization
-method](https://www.biorxiv.org/content/early/2017/12/01/120378).
+method](https://www.nature.com/articles/s41587-019-0336-3).
 
 For a thorough overview of the PHATE visualization method, please see
-the [bioRxiv
-preprint](https://www.biorxiv.org/content/early/2017/12/01/120378)
+the [Nature Biotechnology publication](https://www.nature.com/articles/s41587-019-0336-3).
 
 For our Python and Matlab implementations, please see
 [KrishnaswamyLab/PHATE](https://github.com/KrishnaswamyLab/PHATE).
@@ -203,6 +202,10 @@ To be consistent with common dimensionality reductions such as PCA
 (observations) be rows and genes (features) be columns of your input
 data.
 
+  - **Can I run PHATE with Seurat?**
+
+PHATE was removed from Seurat in version 3. You can install a version of Seurat with `RunPHATE` included by following the instructions at <https://github.com/satijalab/seurat/pull/1172#issuecomment-564782167>.
+
   - **I have installed PHATE in Python, but phateR says it is not
     installed\!**
 
@@ -222,5 +225,6 @@ You can read more about `Renviron` at
 Please let us know of any issues at the [GitHub
 repository](https://github.com/KrishnaswamyLab/phateR/issues). If you
 have any questions or require assistance using PHATE, please read the
-documentation by running `help(phateR::phate)` or contact us at
+documentation at <https://CRAN.R-project.org/package=phateR/phateR.pdf>
+or by running `help(phateR::phate)` or contact us at
 <https://krishnaswamylab.org/get-help>.