Merge pull request #131 from KrishnaswamyLab/dev

MAGIC v1.3.0

.gitignore

@@ -20,6 +20,9 @@ python/*.egg-info
 python/magic/__pycache__
 python/magic/*.pyc
 python/tutorial_notebooks/.ipynb_checkpoints
+__pycache__
+.eggs
+
 
 matlab/EMT.csv
 

README.md

@@ -76,7 +76,7 @@ The following code runs MAGIC on test data located in the MAGIC repository.
 
 #### Tutorials
 
-We have included two tutorial notebooks on MAGIC usage and results visualization for single cell RNA-seq data.
+You can read the MAGIC documentation at https://magic.readthedocs.io/. We have included two tutorial notebooks on MAGIC usage and results visualization for single cell RNA-seq data.
 
 EMT data notebook: http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb
 
@@ -134,7 +134,7 @@ After installing the package, MAGIC can be run by loading the library and callin
 
 #### Tutorials
 
-For a working example, see the Rmarkdown tutorials at <http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html> and <http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html> or in `Rmagic/inst/examples`.
+You can read the MAGIC tutorial by running `help(Rmagic::magic)`. For a working example, see the Rmarkdown tutorials at <http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html> and <http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html> or in `Rmagic/inst/examples`.
 
 ## Help
 

Rmagic/DESCRIPTION

@@ -1,9 +1,10 @@
 Package: Rmagic
 Type: Package
 Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
-Version: 1.0.0
+Version: 1.3.0
 Authors@R: c(person(given = "David", family = "van Dijk", email = "davidvandijk@gmail.com", role = c("aut")),
-		  person(given = 'Scott', family = 'Gigante', email = 'scott.gigante@yale.edu', role = 'cre', comment = c(ORCID = '0000-0002-4544-2764')))
+		         person(given = 'Scott', family = 'Gigante', email = 'scott.gigante@yale.edu', role = 'cre', 
+		                comment = c(ORCID = '0000-0002-4544-2764')))
 Maintainer: Scott Gigante <scott.gigante@yale.edu>
 Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.
 Depends:
@@ -15,9 +16,10 @@ Imports:
     reticulate (>= 1.4),
     ggplot2
 Suggests:
-	readr,
+  	readr,
     viridis,
-	phateR
+  	phateR
 License: GPL-2 | file LICENSE
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
+Encoding: UTF-8

Rmagic/R/magic.R

@@ -39,7 +39,7 @@
 #' @param seed int or `NULL`, random state (default: `NULL`)
 #'
 #' @examples
-#' if (reticulate::py_module_available("phate")) {
+#' if (reticulate::py_module_available("magic")) {
 #'
 #' data(magic_testdata)
 #'

Rmagic/R/utils.R

@@ -10,9 +10,25 @@ null_equal <- function(x, y) {
 }
 
 load_pymagic <- function(delay_load = FALSE) {
-  result <- try(pymagic <<- reticulate::import("magic", delay_load = delay_load))
+  if (is.null(pymagic)) {
+    result <- try(pymagic <<- reticulate::import("magic", delay_load = delay_load))
+  } else {
+    result <- try(reticulate::import("magic", delay_load = delay_load))
+  }
   if (methods::is(result, "try-error")) {
-    install.magic()
+    if ((!delay_load) && length(grep("ModuleNotFoundError: No module named 'magic'", result)) > 0 ||
+        length(grep("ImportError: No module named magic", result)) > 0) {
+      if (utils::menu(c("Yes", "No"), title="Install MAGIC Python package with reticulate?") == 1) {
+        install.magic()
+      }
+    } else if (length(grep("r\\-reticulate", reticulate::py_config()$python)) > 0) {
+      message("Consider removing the 'r-reticulate' environment by running:")
+      if (grep("virtualenvs", reticulate::py_config()$python)) {
+        message("reticulate::virtualenv_remove('r-reticulate')")
+      } else {
+        message("reticulate::conda_remove('r-reticulate')")
+      }
+    }
   }
 }
 
@@ -44,6 +60,7 @@ install.magic <- function(envname = "r-reticulate", method = "auto",
       envname = envname, method = method,
       conda = conda, pip=pip, ...
     )
+    message("Install complete. Please restart R and try again.")
   },
   error = function(e) {
     stop(paste0(
@@ -57,5 +74,6 @@ install.magic <- function(envname = "r-reticulate", method = "auto",
 pymagic <- NULL
 
 .onLoad <- function(libname, pkgname) {
+  py_config <- reticulate::py_discover_config(required_module = "magic")
   load_pymagic(delay_load = TRUE)
 }

Rmagic/README.Rmd

@@ -1,5 +1,5 @@
 ---
-title : Rmagic v1.0.0
+title : Rmagic v1.3.0
 output: github_document
 toc: true
 ---
@@ -181,4 +181,4 @@ ggplot(data_PHATE) +
 
 ## Help
 
-If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.
+Please let us know of any issues at the [GitHub repo](https://github.com/KrishnaswamyLab/MAGIC/issues). If you have any questions or require assistance using MAGIC, please read the documentation by running `help(Rmagic::magic)` or contact us at <https://krishnaswamylab.org/get-help>.

Rmagic/README.md

@@ -1,4 +1,4 @@
-Rmagic v1.0.0
+Rmagic v1.3.0
 ================
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -236,4 +236,7 @@ ggplot(data_PHATE) +
 
 ## Help
 
-If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.
+Please let us know of any issues at the [GitHub
+repo](https://github.com/KrishnaswamyLab/MAGIC/issues). If you have any
+questions or require assistance using MAGIC, please read the documentation
+by running `help(Rmagic::magic)` or contact us at <https://krishnaswamylab.org/get-help>.

python/doc/source/api.rst

@@ -9,22 +9,6 @@ MAGIC
     :inherited-members:
     :show-inheritance:
 
-File Input/Output
------------------
-
-.. automodule:: magic.io
-    :members:
-    :inherited-members:
-    :show-inheritance:
-
-Data Preprocessing
-------------------
-
-.. automodule:: magic.preprocessing
-    :members:
-    :inherited-members:
-    :show-inheritance:
-
 Plotting
 --------