Merge pull request #116 from KrishnaswamyLab/dev

MAGIC v1.1: bugfixes and CRAN release

.gitignore

@@ -5,7 +5,6 @@
 .Rhistory
 .RData
 .Ruserdata
-.Rbuildignore
 
 # R installation files
 
@@ -20,5 +19,10 @@ python/*.dll
 python/*.egg-info
 python/magic/__pycache__
 python/magic/*.pyc
-.DS_Store
 matlab/EMT.csv
+
+# Mac detritus
+
+*~
+~$*
+.DS_Store

.travis.yml

@@ -2,7 +2,6 @@
 
 language: r
 sudo: required
-cache: packages
 
 os:
   - linux
@@ -12,35 +11,29 @@ r:
   - release
   - devel
 
-cache: packages
-
 env:
   global:
     - PATH="$HOME/miniconda2/bin:$HOME/miniconda3/bin:$PATH"
     - RETICULATE_PYTHON="$HOME/miniconda2/bin/python"
 
 before_install:
-  - chmod +x travis_setup.sh
-  - ./travis_setup.sh
-  - $HOME/miniconda2/bin/pip install --user phate nose2
-  - $HOME/miniconda3/bin/pip install --user phate nose2
-  - R -e "install.packages(c('reticulate', 'devtools', 'readr', 'phateR', 'Matrix', 'ggplot2', 'viridis'))"
+  - chmod +x travis_setup.sh; ./travis_setup.sh
+  - $HOME/miniconda2/bin/pip install -q phate
+  - $HOME/miniconda3/bin/pip install -q phate
+  - R -e "install.packages(c('reticulate', 'devtools', 'readr', 'phateR', 'Matrix', 'ggplot2', 'viridis'), quiet=TRUE)"
 
 install:
-  - cd python
-  - python2 setup.py install --user
-  - python3 setup.py install --user
-  - cd ../Rmagic
-  - R CMD INSTALL .
-  - cd ..
+  - cd python; $HOME/miniconda2/bin/pip install -q .
+  - $HOME/miniconda3/bin/pip install -q .
+  - cd ../Rmagic; R CMD INSTALL .; cd ..
 
 script:
-  - cd Rmagic
-  - R CMD build .
+  - cd Rmagic; R CMD build .
   - travis_wait 30 R CMD check *tar.gz
-  - cd ../python
+  - cd ../python; $HOME/miniconda2/bin/pip install -q .[test,doc]
+  - $HOME/miniconda3/bin/pip install -q .[test,doc]
   - python2 setup.py test
   - python3 setup.py test
-  - cd ..
+  - cd doc; make html
 
 warnings_are_errors: true

README.md

@@ -1,18 +1,19 @@
 Markov Affinity-based Graph Imputation of Cells (MAGIC)
 -------------------------------------------------------
 
+[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
 [![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
 [![Read the Docs](https://img.shields.io/readthedocs/magic.svg)](https://magic.readthedocs.io/)
 [![Cell Publication DOI](https://zenodo.org/badge/DOI/10.1016/j.cell.2018.05.061.svg)](https://www.cell.com/cell/abstract/S0092-8674(18)30724-4)
 [![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/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
 
-Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising and transcript recover of single cells applied to single-cell RNA sequencing data, as described in Van Dijk D *et al.* (2018), *Recovering Gene Interactions from Single-Cell Data Using Data Diffusion*, Cell <https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
+Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising and imputation of single cells applied to single-cell RNA sequencing data, as described in Van Dijk D *et al.* (2018), *Recovering Gene Interactions from Single-Cell Data Using Data Diffusion*, Cell <https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
 
 MAGIC has been implemented in Python, Matlab, and R.
 
 <p align="center">
-<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
+<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
 <br>
 <i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
 </i>
@@ -31,11 +32,12 @@ MAGIC has been implemented in Python, Matlab, and R.
      * [Instructions for the Matlab version](#instructions-for-the-matlab-version)
   * [R](#r)
      * [Installation](#installation-1)
-        * [Installation with devtools and <code>pip</code>](#installation-with-devtools-and-pip)
+        * [Installation from CRAN](#installation-from-cran)
         * [Installation from GitHub](#installation-from-github-1)
      * [Usage](#usage-1)
         * [Quick Start](#quick-start-1)
         * [Tutorials](#tutorials-1)
+  * [Help](#help)
 
 ## Python
 
@@ -45,15 +47,15 @@ MAGIC has been implemented in Python, Matlab, and R.
 
 To install with `pip`, run the following from a terminal:
 
-        pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
+    pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 
 #### Installation from GitHub
 
 To clone the repository and install manually, run the following from a terminal:
 
-        git clone git://github.com/KrishnaswamyLab/MAGIC.git
-        cd MAGIC/python
-        python setup.py install --user
+    git clone git://github.com/KrishnaswamyLab/MAGIC.git
+    cd MAGIC/python
+    python setup.py install --user
 
 ### Usage
 
@@ -91,29 +93,30 @@ Bone Marrow data notebook: http://nbviewer.jupyter.org/github/KrishnaswamyLab/MA
 
 To use MAGIC, you will need to install both the R and Python packages.
 
-#### Installation with `devtools` and `pip`
+If `python` or `pip` are not installed, you will need to install them. We recommend
+[Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together,
+or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
 
-You can install `Rmagic` with `devtools` by running the following in R:
+#### Installation from CRAN
 
-        if (!require(devtools)) install.packages("devtools")
-        library(devtools)
-        install_github("KrishnaswamyLab/magic/Rmagic")
+In R, run this command to install MAGIC and all dependencies:
 
-You then need to install MAGIC in Python with `pip` by running the following from a terminal:
+    install.packages("Rmagic")
 
-		pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
+In a terminal, run the following command to install the Python
+repository.
 
-If `python` or `pip` are not installed, you will need to install them. We recommend [Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together, or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
+    pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 
 #### Installation from GitHub
 
 To clone the repository and install manually, run the following from a terminal:
 
-        git clone git://github.com/KrishnaswamyLab/MAGIC.git
-        cd MAGIC/python
-        python setup.py install --user
-        cd ../Rmagic
-        R CMD INSTALL .
+    git clone git://github.com/KrishnaswamyLab/MAGIC.git
+    cd MAGIC/python
+    python setup.py install --user
+    cd ../Rmagic
+    R CMD INSTALL .
 
 ### Usage
 
@@ -131,3 +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 https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.md and https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/EMT_tutorial.md or in `R/inst/examples`.
+
+## Help
+
+If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.

Rmagic/.Rbuildignore

@@ -0,0 +1,3 @@
+^data-raw$
+^tests$
+^README\.Rmd$

Rmagic/DESCRIPTION

@@ -1,12 +1,11 @@
 Package: Rmagic
 Type: Package
-Title: Markov Affinity-based Graph Imputation of Cells
+Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
 Version: 1.0.0
-Author: c(person("David van Dijk", "MSKCC", email = "davidvandijk@gmail.com", role = c("aut")),
+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')))
 Maintainer: Scott Gigante <scott.gigante@yale.edu>
-Description: MAGIC is an interactive tool to impute missing values in single-cell
-    data and restore the structure of the data.
+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:
     R (>= 3.3),
     Matrix (>= 1.2-0)
@@ -19,6 +18,6 @@ Suggests:
 	readr,
     viridis,
 	phateR
-License: MIT + file LICENSE
+License: GPL-2 | file LICENSE
 LazyData: true
 RoxygenNote: 6.0.1

Rmagic/R/magic.R

@@ -16,7 +16,8 @@
 #' If NULL, alpha decaying kernel is not used
 #' @param t int, optional, default: 'auto'
 #' power to which the diffusion operator is powered
-#' sets the level of diffusion
+#' sets the level of diffusion. If 'auto', t is selected according to the
+#' Procrustes disparity of the diffused data.'
 #' @param npca number of PCA components that should be used; default: 20.
 #' @param init magic object, optional
 #' object to use for initialization. Avoids recomputing
@@ -123,6 +124,8 @@ magic <- function(data,
     genes <- as.integer(genes - 1)
   } else if (length(genes) == 1 && genes == "all_genes") {
     gene_names <- colnames(data)
+  } else if (length(genes) == 1 && genes == "pca_only") {
+    gene_names <- paste0("PC", 1:npca)
   } else {
     # character vector
     if (!all(genes %in% colnames(data))) {

Rmagic/README.Rmd

@@ -1,6 +1,7 @@
 ---
 title : Rmagic v1.0.0
 output: github_document
+toc: true
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -14,17 +15,18 @@ knitr::opts_chunk$set(
 )
 ```
 
+[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
 [![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
 [![Read the Docs](https://img.shields.io/readthedocs/magic.svg)](https://magic.readthedocs.io/)
 [![Cell Publication DOI](https://zenodo.org/badge/DOI/10.1016/j.cell.2018.05.061.svg)](https://www.cell.com/cell/abstract/S0092-8674(18)30724-4)
 [![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/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
 
 
-Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising and transcript recover of single cells applied to single-cell RNA sequencing data, as described in Van Dijk D *et al.* (2018), *Recovering Gene Interactions from Single-Cell Data Using Data Diffusion*, Cell <https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
+Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising and imputation of single cells applied to single-cell RNA sequencing data, as described in Van Dijk D *et al.* (2018), *Recovering Gene Interactions from Single-Cell Data Using Data Diffusion*, Cell <https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
 
 <p align="center">
-<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
+<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
 <br>
 <i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
 </i>
@@ -42,11 +44,14 @@ Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for deno
 
 To use MAGIC, you will need to install both the R and Python packages.
 
-In R, run these commands to install MAGIC and all dependencies:
+If `python` or `pip` are not installed, you will need to install them. We recommend [Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together, or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
+
+#### Installation from CRAN
+
+In R, run this command to install MAGIC and all dependencies:
 
 ```{r install_Rmagic, eval=FALSE}
-if (!require(devtools)) install.packages(devtools)
-if (!require(Rmagic)) devtools::install_github("KrishnaswamyLab/magic/Rmagic")
+install.packages("Rmagic")
 ```
 
 In a terminal, run the following command to install the Python repository.
@@ -55,6 +60,20 @@ In a terminal, run the following command to install the Python repository.
 pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 ```
 
+#### Installaton from source
+
+To install the very latest version of MAGIC, you can install from GitHub with the following commands run in a terminal.
+
+```{bash install_magic_source, eval=FALSE}
+git clone https://github.com/KrishnaswamyLab/MAGIC
+cd MAGIC/python
+python setup.py install --user
+cd ../Rmagic
+R CMD INSTALL .
+```
+
+#### Extra packages for the tutorial
+
 We'll install a couple more tools for this tutorial.
 
 ```{r install_extras, eval=FALSE}
@@ -159,3 +178,6 @@ ggplot(data_PHATE) +
   labs(color="VIM")
 ```
 
+## Help
+
+If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.

Rmagic/README.md

@@ -3,6 +3,7 @@ Rmagic v1.0.0
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
+[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
 [![Travis CI
 Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
 [![Read the
@@ -13,14 +14,14 @@ Docs](https://img.shields.io/readthedocs/magic.svg)](https://magic.readthedocs.i
 Stars](https://img.shields.io/github/stars/KrishnaswamyLab/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
 
 Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm
-for denoising and transcript recover of single cells applied to
+for denoising and imputation of single cells applied to
 single-cell RNA sequencing data, as described in Van Dijk D *et al.*
 (2018), *Recovering Gene Interactions from Single-Cell Data Using Data
 Diffusion*, Cell
 <https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
 
 <p align="center">
-<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
+<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
 <br>
 <i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
 </i>
@@ -42,11 +43,16 @@ Diffusion*, Cell
 
 To use MAGIC, you will need to install both the R and Python packages.
 
-In R, run these commands to install MAGIC and all dependencies:
+If `python` or `pip` are not installed, you will need to install them. We recommend
+[Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together,
+or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
+
+#### Installation from CRAN
+
+In R, run this command to install MAGIC and all dependencies:
 
 ``` r
-if (!require(devtools)) install.packages(devtools)
-if (!require(Rmagic)) devtools::install_github("KrishnaswamyLab/magic/Rmagic")
+install.packages("Rmagic")
 ```
 
 In a terminal, run the following command to install the Python
@@ -56,6 +62,21 @@ repository.
 pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 ```
 
+#### Installaton from source
+
+To install the very latest version of MAGIC, you can install from
+GitHub with the following commands run in a terminal.
+
+``` bash
+git clone https://github.com/KrishnaswamyLab/MAGIC
+cd MAGIC/python
+python setup.py install --user
+cd ../Rmagic
+R CMD INSTALL .
+```
+
+#### Extra packages for the tutorial
+
 We’ll install a couple more tools for this tutorial.
 
 ``` r
@@ -211,3 +232,7 @@ ggplot(data_PHATE) +
 ```
 
 <img src="man/figures/README-run_phate-1.png" width="100%" />
+
+## Help
+
+If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.