lint R

KrishnaswamyLab · Mar 10, 2021 · 9f2d13a · 9f2d13a
1 parent 1130d1e
commit 9f2d13a
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Showing 2 changed files with 39 additions and 15 deletions.
diff --git a/Rmagic/R/magic.R b/Rmagic/R/magic.R
@@ -124,7 +124,8 @@ magic.default <- function(
                           k = NULL, alpha = NULL,
                           ...) {
   # check installation
-  if (!reticulate::py_module_available(module = "magic") || (is.null(pymagic))) load_pymagic()
+  if (!reticulate::py_module_available(module = "magic") || 
+      (is.null(pymagic))) load_pymagic()
   # check for deprecated arguments
   if (!is.null(k)) {
     message("Argument k is deprecated. Using knn instead.")
@@ -160,7 +161,11 @@ magic.default <- function(
   } else {
     # character vector
     if (!all(genes %in% colnames(x = data))) {
-      warning(paste0("Genes ", genes[!(genes %in% colnames(data))], " not found.", collapse = ", "))
+      warning(paste0(
+          "Genes ", 
+          genes[!(genes %in% colnames(data))], 
+          " not found.", 
+          collapse = ", "))
     }
     genes <- which(x = colnames(x = data) %in% genes)
     gene_names <- colnames(x = data)[genes]
@@ -338,10 +343,17 @@ magic.Seurat <- function(
       ...
     )
     assay_name <- paste0("MAGIC_", assay)
-    data[[assay_name]] <- Seurat::CreateAssayObject(data = t(x = as.matrix(x = results$result)))
+    data[[assay_name]] <- Seurat::CreateAssayObject(
+        data = t(x = as.matrix(x = results$result))
+    )
     print(paste0(
-      "Added MAGIC output to ", assay_name, ". To use it, pass assay='", assay_name,
-      "' to downstream methods or set DefaultAssay(seurat_object) <- '", assay_name, "'."
+      "Added MAGIC output to ", 
+        assay_name, 
+        ". To use it, pass assay='", 
+        assay_name,
+      "' to downstream methods or set DefaultAssay(seurat_object) <- '", 
+        assay_name, 
+        "'."
     ))
     Seurat::Tool(object = data) <- results[c("operator", "params")]
     return(data)

diff --git a/Rmagic/R/utils.R b/Rmagic/R/utils.R
@@ -20,16 +20,30 @@ check_pymagic_version <- function() {
   minor_version <- as.integer(rversion[2])
   if (as.integer(pyversion[1]) < major_version) {
     warning(paste0(
-      "Python MAGIC version ", pymagic$`__version__`, " is out of date (recommended: ",
-      major_version, ".", minor_version, "). Please update with pip ",
-      "(e.g. ", reticulate::py_config()$python, " -m pip install --upgrade magic-impute) or Rmagic::install.magic()."
+      "Python MAGIC version ", 
+        pymagic$`__version__`, 
+        " is out of date (recommended: ",
+      major_version, 
+        ".", 
+        minor_version, 
+        "). Please update with pip ",
+      "(e.g. ", 
+        reticulate::py_config()$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$`__version__`, " is out of date (recommended: ",
-      major_version, ".", minor_version, "). Consider updating with pip ",
-      "(e.g. ", reticulate::py_config()$python, " -m pip install --upgrade magic-impute) or Rmagic::install.magic()."
+      "Python MAGIC version ", 
+        pymagic$`__version__`, 
+        " is out of date (recommended: ",
+      major_version, 
+        ".", 
+        minor_version, 
+        "). Consider updating with pip ",
+      "(e.g. ", 
+        reticulate::py_config()$python, 
+        " -m pip install --upgrade magic-impute) or Rmagic::install.magic()."
     ))
     return(FALSE)
   }
@@ -77,8 +91,7 @@ load_pymagic <- function() {
 #'
 #' @export
 pymagic_is_available <- function() {
-  tryCatch(
-    {
+  tryCatch( {
       reticulate::import("magic")$MAGIC
       check_pymagic_version()
     },
@@ -111,8 +124,7 @@ pymagic_is_available <- function() {
 install.magic <- function(envname = "r-reticulate", method = "auto",
                           conda = "auto", pip = TRUE, ...) {
   message("Attempting to install MAGIC python package with reticulate")
-  tryCatch(
-    {
+  tryCatch( {
       reticulate::py_install("magic-impute",
         envname = envname, method = method,
         conda = conda, pip = pip, ...