Merge pull request #165 from KrishnaswamyLab/dev

MAGIC v1.5.6
KrishnaswamyLab · Oct 10, 2019 · 32724af · 32724af
2 parents 84c052d + 0a51509
commit 32724af
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Showing 9 changed files with 117 additions and 63 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -16,8 +16,11 @@ r:
 
 addons:
   apt:
+    sources:
+      - deadsnakes
     packages:
       - libhdf5-dev
+      - python3.6
 
 cache:
   - packages
@@ -27,18 +30,16 @@ cache:
 
 before_install:
   - curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
-  - sudo python3 get-pip.py
+  - sudo python3.6 get-pip.py
   - mkdir -p ~/bin && export PATH=~/bin/:$PATH
-  - ln -s $(which python3) ~/bin/python
-  - ln -s $(which pip3) ~/bin/pip
+  - ln -s $(which python3.6) ~/bin/python
+  - ln -s $(which pip3.6) ~/bin/pip
   - sudo pip install --upgrade pip
   - pip install --user -q phate
 
 install:
   - cd python; pip install --user -q .
   - cd ../Rmagic; R -e 'install.packages("devtools", repos="http://cloud.r-project.org")'
-  - R_VERSION=$(R -e "message(R.version[['minor']])" 2>&1 1>/dev/null | head -c 1)
-  - if [ $R_VERSION -lt 5 ]; then export _R_CHECK_FORCE_SUGGESTS_="FALSE"; else R -e "devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')"; fi
   - R -e 'devtools::install_deps(dep = T, upgrade="always")'
   - cd ..
 

diff --git a/Rmagic/R/magic.R b/Rmagic/R/magic.R
@@ -47,7 +47,7 @@
 #'  * **params**: Parameters passed to magic
 #'
 #' @examples
-#' if (reticulate::py_module_available("magic")) {
+#' if (pymagic_is_available()) {
 #'
 #' data(magic_testdata)
 #'
@@ -76,7 +76,7 @@
 #'
 #' }
 #'
-#' if (reticulate::py_module_available("magic") && require(Seurat)) {
+#' if (pymagic_is_available() && require(Seurat)) {
 #'
 #' data(magic_testdata)
 #'
@@ -255,22 +255,41 @@ magic.seurat <- function(
   seed = NULL,
   ...
 ) {
-  results <- magic(
-    data = as.matrix(x = t(x = data@data)),
-    genes = genes,
-    knn = knn,
-    decay = decay,
-    t = t,
-    npca = npca,
-    init = init,
-    t.max = t.max,
-    knn.dist.method = knn.dist.method,
-    verbose = verbose,
-    n.jobs = n.jobs,
-    seed = seed
-  )
-  data@data <- t(x = as.matrix(x = results$result))
-  return(data)
+  if (requireNamespace("Seurat", quietly = TRUE)) {
+    results <- magic(
+      data = as.matrix(x = t(x = data@data)),
+      genes = genes,
+      knn = knn,
+      decay = decay,
+      t = t,
+      npca = npca,
+      init = init,
+      t.max = t.max,
+      knn.dist.method = knn.dist.method,
+      verbose = verbose,
+      n.jobs = n.jobs,
+      seed = seed
+    )
+    data@data <- t(x = as.matrix(x = results$result))
+    return(data)
+  } else {
+    message("Seurat package not available. Running default MAGIC implementation.")
+    return(magic(
+      data,
+      genes = genes,
+      knn = knn,
+      decay = decay,
+      t = t,
+      npca = npca,
+      init = init,
+      t.max = t.max,
+      knn.dist.method = knn.dist.method,
+      verbose = verbose,
+      n.jobs = n.jobs,
+      seed = seed,
+      ...
+    ))
+  }
 }
 
 #' @param assay Assay to use for imputation, defaults to the default assay
@@ -295,32 +314,48 @@ magic.Seurat <- function(
   seed = NULL,
   ...
 ) {
-  if (!requireNamespace(package = 'Seurat', quietly = TRUE)) {
-    stop("Please install Seurat v3 to run MAGIC on new Seurat objects")
-  }
-  if (is.null(x = assay)) {
-    assay <- Seurat::DefaultAssay(object = data)
+  if (requireNamespace("Seurat", quietly = TRUE)) {
+    if (is.null(x = assay)) {
+      assay <- Seurat::DefaultAssay(object = data)
+    }
+    results <- magic(
+      data = t(x = Seurat::GetAssayData(object = data, slot = 'data', assay = assay)),
+      genes = genes,
+      knn = knn,
+      decay = decay,
+      t = t,
+      npca = npca,
+      init = init,
+      t.max = t.max,
+      knn.dist.method = knn.dist.method,
+      verbose = verbose,
+      n.jobs = n.jobs,
+      seed = seed
+    )
+    assay_name <- paste0('MAGIC_', assay)
+    data[[assay_name]] <- Seurat::CreateAssayObject(data = t(x = as.matrix(x = results$result)))
+    print(paste0("Added MAGIC output to ", assay_name, ". To use it, pass assay='", assay_name,
+                 "' to downstream methods or set seurat_object@active.assay <- '", assay_name, "'."))
+    Seurat::Tool(object = data) <- results[c('operator', 'params')]
+    return(data)
+  } else {
+    message("Seurat package not available. Running default MAGIC implementation.")
+    return(magic(
+      data,
+      genes = genes,
+      knn = knn,
+      decay = decay,
+      t = t,
+      npca = npca,
+      init = init,
+      t.max = t.max,
+      knn.dist.method = knn.dist.method,
+      verbose = verbose,
+      n.jobs = n.jobs,
+      seed = seed,
+      ...
+    ))
   }
-  results <- magic(
-    data = t(x = Seurat::GetAssayData(object = data, slot = 'data', assay = assay)),
-    genes = genes,
-    knn = knn,
-    decay = decay,
-    t = t,
-    npca = npca,
-    init = init,
-    t.max = t.max,
-    knn.dist.method = knn.dist.method,
-    verbose = verbose,
-    n.jobs = n.jobs,
-    seed = seed
-  )
-  assay_name <- paste0('MAGIC_', assay)
-  data[[assay_name]] <- Seurat::CreateAssayObject(data = t(x = as.matrix(x = results$result)))
-  print(paste0("Added MAGIC output to ", assay_name, ". To use it, pass assay='", assay_name,
-    "' to downstream methods or set seurat_object@active.assay <- '", assay_name, "'."))
-  Seurat::Tool(object = data) <- results[c('operator', 'params')]
-  return(data)
 }
 
 #' Print a MAGIC object
@@ -330,7 +365,7 @@ magic.Seurat <- function(
 #' @param x A fitted MAGIC object
 #' @param ... Arguments for print()
 #' @examples
-#' if (reticulate::py_module_available("magic")) {
+#' if (pymagic_is_available()) {
 #'
 #' data(magic_testdata)
 #' data_magic <- magic(magic_testdata)
@@ -359,7 +394,7 @@ print.magic <- function(x, ...) {
 #' @param object A fitted MAGIC object
 #' @param ... Arguments for summary()
 #' @examples
-#' if (reticulate::py_module_available("magic")) {
+#' if (pymagic_is_available()) {
 #'
 #' data(magic_testdata)
 #' data_magic <- magic(magic_testdata)
@@ -413,7 +448,7 @@ as.data.frame.magic <- function(x, ...) {
 #' @param data A fitted MAGIC object
 #' @param ... Arguments for ggplot()
 #' @examples
-#' if (reticulate::py_module_available("magic") && require(ggplot2)) {
+#' if (pymagic_is_available() && require(ggplot2)) {
 #'
 #' data(magic_testdata)
 #' data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))

diff --git a/Rmagic/R/utils.R b/Rmagic/R/utils.R
@@ -57,6 +57,23 @@ load_pymagic <- function() {
   }
 }
 
+#' Check whether MAGIC Python package is available and can be loaded
+#' 
+#' This is used primarily to avoid running tests on CRAN
+#' and elsewhere where the Python package should not be
+#' installed.
+#' 
+#' @export
+pymagic_is_available <- function() {
+  tryCatch({
+    reticulate::py_module_available("magic")$MAGIC
+  },
+  error = function(e) {
+    FALSE
+  }
+  )
+}
+
 #' Install MAGIC Python Package
 #'
 #' Install MAGIC Python package into a virtualenv or conda env.

diff --git a/python/doc/source/requirements.txt b/python/doc/source/requirements.txt
@@ -1,10 +1,10 @@
 scikit-learn>=0.19.1
 numpy>=1.14.0
-pandas>=0.21.0
+pandas>=0.25
+scprep>=1.0
 scipy>=1.1.0
 matplotlib>=2.0.1
 future
 graphtools>=1.0.0
-scprep>=0.10.0
 sphinx
 sphinxcontrib-napoleon
diff --git a/python/magic/magic.py b/python/magic/magic.py
@@ -668,7 +668,8 @@ def _impute(self, data, t_max=20, plot=False, ax=None,
         # than those of the data matrix. (M^t) * D
         if (t_opt is not None) and \
                 (self.diff_op.shape[1] < data_imputed.shape[1]):
-            diff_op_t = np.linalg.matrix_power(self.diff_op, t_opt)
+            diff_op_t = np.linalg.matrix_power(
+                scprep.utils.toarray(self.diff_op), t_opt)
             data_imputed = diff_op_t.dot(data_imputed)
 
         # fast magic

diff --git a/python/magic/version.py b/python/magic/version.py
@@ -1 +1 @@
-__version__ = "1.5.5"
+__version__ = "1.5.6"
diff --git a/python/requirements.txt b/python/requirements.txt
@@ -1,9 +1,9 @@
 numpy>=1.14.0
-pandas>=0.21.0,<0.24
 scipy>=1.1.0
+pandas>=0.25
+scprep>=1.0
 matplotlib
 scikit-learn>=0.19.1
 future
 tasklogger>=0.4.0
 graphtools>=1.0.0
-scprep>=0.11.1
diff --git a/python/setup.py b/python/setup.py
@@ -4,14 +4,14 @@
 
 install_requires = [
     'numpy>=1.14.0',
-    'pandas>=0.21.0,<0.24',
     'scipy>=1.1.0',
     'matplotlib',
     'scikit-learn>=0.19.1',
     'future',
     'tasklogger>=0.4.0',
     'graphtools>=1.0.0',
-    'scprep>=0.11.1'
+    'pandas>=0.25',
+    'scprep>=1.0',
 ]
 
 test_requires = [

diff --git a/python/test/test.py b/python/test/test.py
@@ -15,9 +15,9 @@
 
 
 def test_scdata():
-    scdata = scprep.io.load_csv("../data/test_data.csv")
-    scdata = scprep.filter.remove_empty_cells(scdata)
-    scdata = scprep.filter.remove_empty_genes(scdata)
+    scdata = scprep.io.load_csv("../data/test_data.csv", cell_names=False)
+    scdata = scprep.filter.filter_empty_cells(scdata)
+    scdata = scprep.filter.filter_empty_genes(scdata)
     scdata_norm = scprep.normalize.library_size_normalize(scdata)
     scdata_norm = scprep.transform.sqrt(scdata_norm)
     assert scdata.shape == scdata_norm.shape
@@ -37,7 +37,7 @@ def test_scdata():
                                              genes="all_genes")
     assert scdata_norm.shape == magic_all_genes.shape
     dremi = magic_op.knnDREMI("VIM", "ZEB1", plot=True)
-    np.testing.assert_allclose(dremi, 1.5687165, atol=0.0000005)
+    np.testing.assert_allclose(dremi, 1.573619, atol=0.0000005)
 
 
 def test_anndata():