Merge pull request #172 from KrishnaswamyLab/dev

MAGIC v2.0

.travis.yml

@@ -47,10 +47,10 @@ script:
   - cd Rmagic; R CMD build .
   - R CMD check *tar.gz
   - cd ../python; pip install --user -q .[test]
+  - if [ "$TRAVIS_PYTHON_VERSION" != "3.5" ]; then black . --check --diff; fi
   - python setup.py test
   - pip install --user -q .[doc]
-  - cd doc; make html
-  - cd ..
+  - cd doc; make html; cd ..
 
 deploy:
   provider: pypi

CONTRIBUTING.md

@@ -0,0 +1,39 @@
+
+Contributing to MAGIC
+============================
+
+There are many ways to contribute to `MAGIC`, with the most common ones
+being contribution of code or documentation to the project. Improving the
+documentation is no less important than improving the library itself. If you
+find a typo in the documentation, or have made improvements, do not hesitate to
+submit a GitHub pull request.
+
+But there are many other ways to help. In particular answering queries on the
+[issue tracker](https://github.com/KrishnaswamyLab/MAGIC/issues),
+investigating bugs, and [reviewing other developers' pull
+requests](https://github.com/KrishnaswamyLab/MAGIC/pulls)
+are very valuable contributions that decrease the burden on the project
+maintainers.
+
+Another way to contribute is to report issues you're facing, and give a "thumbs
+up" on issues that others reported and that are relevant to you. It also helps
+us if you spread the word: reference the project from your blog and articles,
+link to it from your website, or simply star it in GitHub to say "I use it".
+
+Code Style and Testing
+----------------------
+
+Contributors are encouraged to write tests for their code, but if you do not know how to do so, please do not feel discouraged from contributing code! Others can always help you test your contribution.
+
+Python code style is dictated by [`black`](https://pypi.org/project/black/#installation-and-usage). To automatically reformat your code when you run `git commit`, you can run `./autoblack.sh` in the root directory of this project to add a hook to your `git` repository.
+
+Code of Conduct
+---------------
+
+We abide by the principles of openness, respect, and consideration of others
+of the Python Software Foundation: https://www.python.org/psf/codeofconduct/.
+
+Attribution
+---------------
+
+This `CONTRIBUTING.md` was adapted from [scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md).

README.md

@@ -15,7 +15,7 @@ To see how MAGIC can be applied to single-cell RNA-seq, elucidating the epitheli
 
 [David van Dijk, et al. **Recovering Gene Interactions from Single-Cell Data Using Data Diffusion**. 2018. *Cell*.](https://www.cell.com/cell/abstract/S0092-8674(18)30724-4)
 
-MAGIC has been implemented in Python, Matlab, and R. Note, the current implementation of MAGIC differs compared to the algorithm described in [vanDijk18](https://www.cell.com/cell/abstract/S0092-8674(18)30724-4) in that it uses the adaptive kernel described in Moon et al, 2019 [Moon19](https://www.biorxiv.org/content/10.1101/120378v4).
+MAGIC has been implemented in Python, Matlab, and R.
 
 #### To get started immediately, check out our tutorials:  
 ##### Python  

Rmagic/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rmagic
 Type: Package
 Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
-Version: 1.5.0
+Version: 2.0.0
 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')))

Rmagic/NAMESPACE

@@ -11,5 +11,6 @@ S3method(summary,magic)
 export(install.magic)
 export(library.size.normalize)
 export(magic)
+export(pymagic_is_available)
 import(Matrix)
 importFrom(ggplot2,ggplot)

Rmagic/R/magic.R

@@ -10,8 +10,10 @@
 #' vector of column names or column indices for which to return smoothed data
 #' If 'all_genes' or NULL, the entire smoothed matrix is returned
 #' @param knn int, optional, default: 10
-#' number of nearest neighbors on which to build kernel
-#' @param decay int, optional, default: 15
+#' number of nearest neighbors on which to compute bandwidth
+#' @param knn.max int, optional, default: NULL
+#' maximum number of neighbors for each point. If NULL, defaults to 3*knn
+#' @param decay int, optional, default: 2
 #' sets decay rate of kernel tails.
 #' If NULL, alpha decaying kernel is not used
 #' @param t int, optional, default: 'auto'
@@ -107,7 +109,8 @@ magic.default <- function(
   data,
   genes = NULL,
   knn = 10,
-  decay = 15,
+  knn.max = NULL,
+  decay = 2,
   t = 'auto',
   npca = 100,
   init = NULL,
@@ -183,6 +186,7 @@ magic.default <- function(
   params <- list(
     "data" = data,
     "knn" = knn,
+    "knn.max" = knn.max,
     "decay" = decay,
     "t" = t,
     "npca" = npca,
@@ -197,6 +201,7 @@ magic.default <- function(
       operator <- init$operator
       operator$set_params(
         knn = knn,
+        knn_max = knn.max,
         decay = decay,
         t = t,
         n_pca = npca,
@@ -210,6 +215,7 @@ magic.default <- function(
   if (is.null(x = operator)) {
     operator <- pymagic$MAGIC(
       knn = knn,
+      knn_max = knn.max,
       decay = decay,
       t = t,
       n_pca = npca,
@@ -244,7 +250,8 @@ magic.seurat <- function(
   data,
   genes = NULL,
   knn = 10,
-  decay = 15,
+  knn.max = NULL,
+  decay = 2,
   t = 'auto',
   npca = 100,
   init = NULL,
@@ -260,6 +267,7 @@ magic.seurat <- function(
       data = as.matrix(x = t(x = data@data)),
       genes = genes,
       knn = knn,
+      knn.max = knn.max,
       decay = decay,
       t = t,
       npca = npca,
@@ -278,6 +286,7 @@ magic.seurat <- function(
       data,
       genes = genes,
       knn = knn,
+      knn.max = knn.max,
       decay = decay,
       t = t,
       npca = npca,
@@ -303,7 +312,8 @@ magic.Seurat <- function(
   assay = NULL,
   genes = NULL,
   knn = 10,
-  decay = 15,
+  knn.max = NULL,
+  decay = 2,
   t = 'auto',
   npca = 100,
   init = NULL,
@@ -322,6 +332,7 @@ magic.Seurat <- function(
       data = t(x = Seurat::GetAssayData(object = data, slot = 'data', assay = assay)),
       genes = genes,
       knn = knn,
+      knn.max = knn.max,
       decay = decay,
       t = t,
       npca = npca,
@@ -344,6 +355,7 @@ magic.Seurat <- function(
       data,
       genes = genes,
       knn = knn,
+      knn.max = knn.max,
       decay = decay,
       t = t,
       npca = npca,

Rmagic/README.Rmd

@@ -1,5 +1,5 @@
 ---
-title : Rmagic v1.5.0
+title : Rmagic
 output: github_document
 toc: true
 ---

Rmagic/README.md

@@ -1,4 +1,4 @@
-Rmagic v1.5.0
+Rmagic
 ================
 
 true

autoblack.sh

@@ -0,0 +1,14 @@
+cat <<EOF >> .git/hooks/pre-commit
+#!/bin/sh
+
+set -e
+
+files=\$(git diff --staged --name-only --diff-filter=d -- "*.py")
+
+for file in \$files; do
+  black -q \$file
+  git add \$file
+done
+EOF
+chmod +x .git/hooks/pre-commit
+