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Merge pull request #116 from KrishnaswamyLab/dev
MAGIC v1.1: bugfixes and CRAN release
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‎.gitignore‎

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.Rhistory
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.RData
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# R installation files
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python/*.egg-info
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python/magic/__pycache__
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python/magic/*.pyc
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.DS_Store
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matlab/EMT.csv
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# Mac detritus
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*~
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~$*
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.DS_Store

‎.travis.yml‎

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

‎README.md‎

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Markov Affinity-based Graph Imputation of Cells (MAGIC)
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-------------------------------------------------------
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[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
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[![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
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[![Read the Docs](https://img.shields.io/readthedocs/magic.svg)](https://magic.readthedocs.io/)
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[![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)
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[![Twitter](https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow)](https://twitter.com/KrishnaswamyLab)
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[![Github Stars](https://img.shields.io/github/stars/KrishnaswamyLab/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
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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>.
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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>.
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MAGIC has been implemented in Python, Matlab, and R.
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<p align="center">
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<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
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<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
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<br>
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<i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
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</i>
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* [Instructions for the Matlab version](#instructions-for-the-matlab-version)
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* [R](#r)
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* [Installation](#installation-1)
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* [Installation with devtools and <code>pip</code>](#installation-with-devtools-and-pip)
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* [Installation from CRAN](#installation-from-cran)
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* [Installation from GitHub](#installation-from-github-1)
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* [Usage](#usage-1)
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* [Quick Start](#quick-start-1)
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* [Tutorials](#tutorials-1)
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* [Help](#help)
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## Python
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To install with `pip`, run the following from a terminal:
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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#### Installation from GitHub
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To clone the repository and install manually, run the following from a terminal:
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git clone git://github.com/KrishnaswamyLab/MAGIC.git
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cd MAGIC/python
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python setup.py install --user
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git clone git://github.com/KrishnaswamyLab/MAGIC.git
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cd MAGIC/python
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python setup.py install --user
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### Usage
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To use MAGIC, you will need to install both the R and Python packages.
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#### Installation with `devtools` and `pip`
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If `python` or `pip` are not installed, you will need to install them. We recommend
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[Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together,
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or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
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You can install `Rmagic` with `devtools` by running the following in R:
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#### Installation from CRAN
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if (!require(devtools)) install.packages("devtools")
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library(devtools)
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install_github("KrishnaswamyLab/magic/Rmagic")
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In R, run this command to install MAGIC and all dependencies:
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You then need to install MAGIC in Python with `pip` by running the following from a terminal:
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install.packages("Rmagic")
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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In a terminal, run the following command to install the Python
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repository.
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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/.
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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#### Installation from GitHub
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To clone the repository and install manually, run the following from a terminal:
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git clone git://github.com/KrishnaswamyLab/MAGIC.git
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cd MAGIC/python
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python setup.py install --user
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cd ../Rmagic
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R CMD INSTALL .
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git clone git://github.com/KrishnaswamyLab/MAGIC.git
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cd MAGIC/python
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python setup.py install --user
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cd ../Rmagic
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R CMD INSTALL .
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### Usage
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#### Tutorials
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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`.
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## Help
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If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.

‎Rmagic/.Rbuildignore‎

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^data-raw$
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^tests$
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^README\.Rmd$

‎Rmagic/DESCRIPTION‎

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Package: Rmagic
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Type: Package
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Title: Markov Affinity-based Graph Imputation of Cells
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Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
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Version: 1.0.0
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Author: c(person("David van Dijk", "MSKCC", email = "davidvandijk@gmail.com", role = c("aut")),
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Authors@R: c(person(given = "David", family = "van Dijk", email = "davidvandijk@gmail.com", role = c("aut")),
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person(given = 'Scott', family = 'Gigante', email = 'scott.gigante@yale.edu', role = 'cre', comment = c(ORCID = '0000-0002-4544-2764')))
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Maintainer: Scott Gigante <scott.gigante@yale.edu>
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Description: MAGIC is an interactive tool to impute missing values in single-cell
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data and restore the structure of the data.
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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>.
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Depends:
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Matrix (>= 1.2-0)
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readr,
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viridis,
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phateR
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License: MIT + file LICENSE
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License: GPL-2 | file LICENSE
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LazyData: true
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RoxygenNote: 6.0.1

‎Rmagic/R/magic.R‎

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

‎Rmagic/README.Rmd‎

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---
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title : Rmagic v1.0.0
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output: github_document
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toc: true
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---
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<!-- README.md is generated from README.Rmd. Please edit that file -->
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```
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[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
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[![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
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[![Read the Docs](https://img.shields.io/readthedocs/magic.svg)](https://magic.readthedocs.io/)
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[![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)
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[![Twitter](https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow)](https://twitter.com/KrishnaswamyLab)
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[![Github Stars](https://img.shields.io/github/stars/KrishnaswamyLab/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
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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>.
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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>.
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<p align="center">
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<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
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<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
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<br>
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<i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
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</i>
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To use MAGIC, you will need to install both the R and Python packages.
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In R, run these commands to install MAGIC and all dependencies:
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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/.
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#### Installation from CRAN
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In R, run this command to install MAGIC and all dependencies:
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```{r install_Rmagic, eval=FALSE}
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if (!require(devtools)) install.packages(devtools)
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if (!require(Rmagic)) devtools::install_github("KrishnaswamyLab/magic/Rmagic")
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install.packages("Rmagic")
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```
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In a terminal, run the following command to install the Python repository.
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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```
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#### Installaton from source
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To install the very latest version of MAGIC, you can install from GitHub with the following commands run in a terminal.
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```{bash install_magic_source, eval=FALSE}
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git clone https://github.com/KrishnaswamyLab/MAGIC
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cd MAGIC/python
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python setup.py install --user
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cd ../Rmagic
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R CMD INSTALL .
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```
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#### Extra packages for the tutorial
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We'll install a couple more tools for this tutorial.
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```{r install_extras, eval=FALSE}
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labs(color="VIM")
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```
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## Help
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If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.

‎Rmagic/README.md‎

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<!-- README.md is generated from README.Rmd. Please edit that file -->
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[![Latest CRAN version](https://img.shields.io/cran/v/Rmagic.svg)](https://cran.r-project.org/package=Rmagic)
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[![Travis CI
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Build](https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/MAGIC)
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[![Read the
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Stars](https://img.shields.io/github/stars/KrishnaswamyLab/MAGIC.svg?style=social&label=Stars)](https://github.com/KrishnaswamyLab/MAGIC/)
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Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm
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for denoising and transcript recover of single cells applied to
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for denoising and imputation of single cells applied to
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single-cell RNA sequencing data, as described in Van Dijk D *et al.*
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(2018), *Recovering Gene Interactions from Single-Cell Data Using Data
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Diffusion*, Cell
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<https://www.cell.com/cell/abstract/S0092-8674(18)30724-4>.
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<p align="center">
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<img src="https://github.com/KrishnaswamyLab/MAGIC/blob/master/magic.gif"/>
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<img src="https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif"/>
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<br>
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<i>Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
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</i>
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To use MAGIC, you will need to install both the R and Python packages.
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In R, run these commands to install MAGIC and all dependencies:
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If `python` or `pip` are not installed, you will need to install them. We recommend
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[Miniconda3](https://conda.io/miniconda.html) to install Python and `pip` together,
48+
or otherwise you can install `pip` from https://pip.pypa.io/en/stable/installing/.
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#### Installation from CRAN
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In R, run this command to install MAGIC and all dependencies:
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``` r
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if (!require(devtools)) install.packages(devtools)
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if (!require(Rmagic)) devtools::install_github("KrishnaswamyLab/magic/Rmagic")
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install.packages("Rmagic")
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```
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In a terminal, run the following command to install the Python
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pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
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```
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#### Installaton from source
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To install the very latest version of MAGIC, you can install from
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GitHub with the following commands run in a terminal.
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``` bash
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git clone https://github.com/KrishnaswamyLab/MAGIC
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cd MAGIC/python
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python setup.py install --user
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cd ../Rmagic
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R CMD INSTALL .
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```
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#### Extra packages for the tutorial
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We’ll install a couple more tools for this tutorial.
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``` r
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```
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<img src="man/figures/README-run_phate-1.png" width="100%" />
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## Help
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If you have any questions or require assistance using MAGIC, please contact us at <https://krishnaswamylab.org/get-help>.

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