Merge pull request #191 from KrishnaswamyLab/dev

MAGIC v2.0.4

.github/ISSUE_TEMPLATE/bug_report.md

@@ -65,5 +65,17 @@ You can do this with `R -e 'reticulate::py_discover_config(required_module = "ma
 
 </details>
 
+Output of `Rmagic::check_pymagic_version()`:
+
+<details>
+
+```
+If you are running MAGIC in R, please run `Rmagic::check_pymagic_version()` and paste the results here.
+
+You can do this with `R -e 'Rmagic::check_pymagic_version()'`
+```
+
+</details>
+
 **Additional context**
 Add any other context about the problem here.

.travis.yml

@@ -20,7 +20,7 @@ addons:
       - deadsnakes
     packages:
       - libhdf5-dev
-      - python3.6
+      - python3.6-dev
 
 cache:
   - packages
@@ -40,6 +40,7 @@ before_install:
 install:
   - cd python; pip install --user -q .
   - cd ../Rmagic; R -e 'install.packages("devtools", repos="http://cloud.r-project.org")'
+  - R -e 'install.packages("BiocManager", repos="http://cloud.r-project.org"); BiocManager::install("multtest")'
   - R -e 'devtools::install_deps(dep = T, upgrade="always")'
   - cd ..
 
@@ -48,7 +49,7 @@ script:
   - cd Rmagic; R CMD build .
   - R CMD check *tar.gz
   - cd ../python; pip install --user -q .[test]
-  - if [ "$TRAVIS_PYTHON_VERSION" != "3.5" ]; then black . --check --diff; fi
+  - if [ "$TRAVIS_PYTHON_VERSION" != "3.5" ]; then black . --check --diff -t py35; fi
   - python setup.py test
   - pip install --user -q .[doc]
   - cd doc; make html; cd ..

Rmagic/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rmagic
 Type: Package
 Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
-Version: 2.0.3
+Version: 2.0.3.999
 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')))
@@ -22,5 +22,5 @@ Suggests:
     phateR
 License: GPL-2 | file LICENSE
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Encoding: UTF-8

Rmagic/NAMESPACE

@@ -8,9 +8,11 @@ S3method(magic,default)
 S3method(magic,seurat)
 S3method(print,magic)
 S3method(summary,magic)
+export(check_pymagic_version)
 export(install.magic)
 export(library.size.normalize)
 export(magic)
 export(pymagic_is_available)
 import(Matrix)
 importFrom(ggplot2,ggplot)
+importFrom(utils,packageVersion)

Rmagic/R/magic.R

@@ -21,6 +21,11 @@
 #' 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: 100.
+#' @param solver str, optional, default: 'exact'
+#' Which solver to use. "exact" uses the implementation described
+#' in van Dijk et al. (2018). "approximate" uses a faster implementation
+#' that performs imputation in the PCA space and then projects back to the
+#' gene space. Note, the "approximate" solver may return negative values.
 #' @param init magic object, optional
 #' object to use for initialization. Avoids recomputing
 #' intermediate steps if parameters are the same.
@@ -113,6 +118,7 @@ magic.default <- function(
   decay = 1,
   t = 3,
   npca = 100,
+  solver = 'exact',
   init = NULL,
   t.max = 20,
   knn.dist.method = 'euclidean',
@@ -134,32 +140,16 @@ magic.default <- function(
     message("Argument alpha is deprecated. Using decay instead.")
     decay <- alpha
   }
-  knn <- as.integer(x = knn)
-  t.max <- as.integer(x = t.max)
-  n.jobs <- as.integer(x = n.jobs)
-  if (is.numeric(x = npca)) {
-    npca <- as.integer(x = npca)
-  } else if (!is.null(x = npca) && is.na(x = npca)) {
-    npca <- NULL
-  }
-  if (is.numeric(x = decay)) {
-    decay <- as.double(x = decay)
-  } else if (!is.null(x = decay) && is.na(x = decay)) {
-    decay <- NULL
-  }
-  if (is.numeric(x = t)) {
-    t <- as.integer(x = t)
-  } else if (is.null(x = t) || is.na(x = t)) {
-    t <- 'auto'
-  }
-  if (is.numeric(x = seed)) {
-    seed <- as.integer(x = seed)
-  } else if (!is.null(x = seed) && is.na(x = seed)) {
-    seed <- NULL
-  }
-  if (is.numeric(x = verbose)) {
-    verbose <- as.integer(x = verbose)
-  }
+  # validate parameters
+  knn <- check.int(x = knn)
+  t.max <- check.int(x = t.max)
+  n.jobs <- check.int(x = n.jobs)
+  npca <- check.int.or.null(npca)
+  knn.max <- check.int.or.null(knn.max)
+  seed <- check.int.or.null(seed)
+  verbose <- check.int.or.null(verbose)
+  decay <- check.double.or.null(decay)
+  t <- check.int.or.string(t, 'auto')
   if (!methods::is(object = data, "Matrix")) {
     data <- as.matrix(x = data)
   }
@@ -190,6 +180,7 @@ magic.default <- function(
     "decay" = decay,
     "t" = t,
     "npca" = npca,
+    "solver" = solver,
     "knn.dist.method" = knn.dist.method
   )
   # use pre-initialized values if given
@@ -205,10 +196,12 @@ magic.default <- function(
         decay = decay,
         t = t,
         n_pca = npca,
+        solver = solver,
         knn_dist = knn.dist.method,
         n_jobs = n.jobs,
         random_state = seed,
-        verbose = verbose
+        verbose = verbose,
+        ...
       )
     }
   }
@@ -219,10 +212,12 @@ magic.default <- function(
       decay = decay,
       t = t,
       n_pca = npca,
+      solver = solver,
       knn_dist = knn.dist.method,
       n_jobs = n.jobs,
       random_state = seed,
-      verbose = verbose
+      verbose = verbose,
+      ...
     )
   }
   result <- operator$fit_transform(
@@ -254,6 +249,7 @@ magic.seurat <- function(
   decay = 1,
   t = 3,
   npca = 100,
+  solver = "exact",
   init = NULL,
   t.max = 20,
   knn.dist.method = 'euclidean',
@@ -271,12 +267,14 @@ magic.seurat <- function(
       decay = decay,
       t = t,
       npca = npca,
+      solver = solver,
       init = init,
       t.max = t.max,
       knn.dist.method = knn.dist.method,
       verbose = verbose,
       n.jobs = n.jobs,
-      seed = seed
+      seed = seed,
+      ...
     )
     data@data <- t(x = as.matrix(x = results$result))
     return(data)
@@ -290,6 +288,7 @@ magic.seurat <- function(
       decay = decay,
       t = t,
       npca = npca,
+      solver = solver,
       init = init,
       t.max = t.max,
       knn.dist.method = knn.dist.method,
@@ -316,6 +315,7 @@ magic.Seurat <- function(
   decay = 1,
   t = 3,
   npca = 100,
+  solver = 'exact',
   init = NULL,
   t.max = 20,
   knn.dist.method = 'euclidean',
@@ -336,17 +336,19 @@ magic.Seurat <- function(
       decay = decay,
       t = t,
       npca = npca,
+      solver = solver,
       init = init,
       t.max = t.max,
       knn.dist.method = knn.dist.method,
       verbose = verbose,
       n.jobs = n.jobs,
-      seed = seed
+      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, "'."))
+                 "' to downstream methods or set DefaultAssay(seurat_object) <- '", assay_name, "'."))
     Seurat::Tool(object = data) <- results[c('operator', 'params')]
     return(data)
   } else {

Rmagic/R/utils.R

@@ -9,6 +9,10 @@ null_equal <- function(x, y) {
   }
 }
 
+#' Check that the current MAGIC version in Python is up to date.
+#'
+#' @importFrom utils packageVersion
+#' @export
 check_pymagic_version <- function() {
   pyversion <- strsplit(pymagic$`__version__`, '\\.')[[1]]
   rversion <- strsplit(as.character(packageVersion("Rmagic")), '\\.')[[1]]
@@ -17,12 +21,12 @@ check_pymagic_version <- function() {
   if (as.integer(pyversion[1]) < major_version) {
     warning(paste0("Python MAGIC version ", pymagic$`__version__`, " is out of date (recommended: ",
                    major_version, ".", minor_version, "). Please update with pip ",
-                   "(e.g. pip install --upgrade magic-impute) or Rmagic::install.magic()."))
+                   "(e.g. ", reticulate::py_config()$python, " -m pip install --upgrade magic-impute) or Rmagic::install.magic()."))
     return(FALSE)
   } else if (as.integer(pyversion[2]) < minor_version) {
     warning(paste0("Python MAGIC version ", pymagic$`__version__`, " is out of date (recommended: ",
                    major_version, ".", minor_version, "). Consider updating with pip ",
-                   "(e.g. pip install --upgrade magic-impute) or Rmagic::install.magic()."))
+                   "(e.g. ", reticulate::py_config()$python, " -m pip install --upgrade magic-impute) or Rmagic::install.magic()."))
     return(FALSE)
   }
   return(TRUE)
@@ -112,7 +116,7 @@ install.magic <- function(envname = "r-reticulate", method = "auto",
   error = function(e) {
     stop(paste0(
       "Cannot locate MAGIC Python package, please install through pip ",
-      "(e.g. pip install magic-impute) and then restart R."
+      "(e.g. ", reticulate::py_config()$python, " -m pip install magic-impute) and then restart R."
     ))
   }
   )
@@ -124,3 +128,38 @@ pymagic <- NULL
   py_config <- reticulate::py_discover_config(required_module = "magic")
   load_pymagic()
 }
+
+######
+# Parameter validation
+######
+
+check.int <- function(x) {
+    as.integer(x)
+}
+
+check.int.or.null <- function(x) {
+  if (is.numeric(x = x)) {
+    x <- as.integer(x = x)
+  } else if (!is.null(x = x) && is.na(x = x)) {
+    x <- NULL
+  }
+  x
+}
+
+check.double.or.null <- function(x) {
+  if (is.numeric(x = x)) {
+    x <- as.integer(x = x)
+  } else if (!is.null(x = x) && is.na(x = x)) {
+    x <- NULL
+  }
+  x
+}
+
+check.int.or.string <- function(x, str) {
+  if (is.numeric(x = x)) {
+    x <- as.integer(x = x)
+  } else if (is.null(x = x) || is.na(x = x)) {
+    x <- str
+  }
+  x
+}