1. singleCellTK
  2. R
  3. exportSCEtoAnndata.R
Browse code

Fix bugs in exportSCEtoSeurat. Add parallel param to scDblFinder. Fix typo in warning message in exportSCEtoAnndata

rz2333 authored on 13/04/2022 15:19:13
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @efd833037
... ... 
@@ -44,7 +44,7 @@ exportSCEtoAnnData <- function(sce,
44 44 
             "If one of these have been previously run to install the modules,",
45 45 
             "make sure to run selectSCTKConda() or selectSCTKVirtualEnvironment(),",
46 46 
             " respectively, if R has been restarted since the module installation.",
47 
-            " Alternatively, Scrublet can be installed on the local machine",
47 
+            " Alternatively, 'scanpy' can be installed on the local machine",
48 48 
             "with pip (e.g. pip install --user scanpy) and then the 'use_python()'",
49 49 
             " function from the 'reticulate' package can be used to select the",
50 50 
             " correct Python environment.")
Browse code

Minor fixes

Yichen Wang authored on 13/04/2021 07:25:29
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @f19cfab84
... ... 
@@ -14,7 +14,7 @@
14 14 
 #' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
15 15 
 #' @param overwrite Boolean. Default \code{TRUE}.
16 16 
 #' @param compression If output file compression is required, this variable accepts
17 
-#' 'gzip', 'lzf' or "None" as inputs. Default \code{gzip"}.
17 
+#' 'gzip', 'lzf' or "None" as inputs. Default \code{"gzip"}.
18 18 
 #' @param compressionOpts Integer. Sets the compression level
19 19 
 #' @param forceDense Default \code{False} Write sparse data as a dense matrix.
20 20 
 #' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
Browse code

Fix exporting bugs

Yichen Wang authored on 13/04/2021 06:04:25
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @ef39dc245
... ... 
@@ -14,7 +14,7 @@
14 14 
 #' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
15 15 
 #' @param overwrite Boolean. Default \code{TRUE}.
16 16 
 #' @param compression If output file compression is required, this variable accepts
17 
-#' 'gzip' or 'lzf' as inputs. Default \code{None}.
17 
+#' 'gzip', 'lzf' or "None" as inputs. Default \code{gzip"}.
18 18 
 #' @param compressionOpts Integer. Sets the compression level
19 19 
 #' @param forceDense Default \code{False} Write sparse data as a dense matrix.
20 20 
 #' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
... ... 
@@ -30,15 +30,14 @@ exportSCEtoAnnData <- function(sce,
30 30 
                                 outputDir = "./",
31 31 
                                 prefix = "sample",
32 32 
                                 overwrite = TRUE,
33 
-                                compression = c('None','lzf','gzip'),
33 
+                                compression = c('gzip','lzf', "None"),
34 34 
                                 compressionOpts = NULL,
35 
-                                forceDense = c('False','True')){
35 
+                                forceDense = FALSE){
36 36 
   compression <- match.arg(compression)
37 
-  forceDense <- match.arg(forceDense)
37 
+  #forceDense <- match.arg(forceDense)
38 38 
   if (compression == 'None'){
39 39 
     compression <- NULL
40 40 
   }
41 
-
42 41 
   if (!reticulate::py_module_available(module = "scanpy")) {
43 42 
     warning("Cannot find python module 'scanpy', please install Conda and",
44 43 
             " run sctkPythonInstallConda() or run sctkPythonInstallVirtualEnv().",
... ... 
@@ -50,24 +49,26 @@ exportSCEtoAnnData <- function(sce,
50 49 
             " function from the 'reticulate' package can be used to select the",
51 50 
             " correct Python environment.")
52 51 
     return(sce)}
53 
-
54 
-  AssayName <- SummarizedExperiment::assayNames(sce)
55 
-  for (assay in AssayName){
56 
-    if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
57 
-      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
58 
-    }
59 
-  }
60 
-
61 
-
62 52 
   dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
63 
-  annData <- .sce2adata(sce,useAssay)
64 53 
   fileName <- paste0(prefix,".h5ad")
65 54 
   filePath <- file.path(outputDir,fileName)
66 
-
67 55 
   if (file.exists(filePath) && !isTRUE(overwrite)) {
68 56 
     stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
57 
+  }
58 
+  if (isTRUE(forceDense)) {
59 
+    forceDense <- "True"
60 
+  } else if (isFALSE(forceDense)) {
61 
+    forceDense <- "False"
62 
+  } else {
63 
+    stop("Argument `forceDense` should be `TRUE` or `FALSE`")
64 
+  }
65 
+  AssayName <- SummarizedExperiment::assayNames(sce)
66 
+  for (assay in AssayName){
67 
+    if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
68 
+      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
69 69 
     }
70 
-
70 
+  }
71 
+  annData <- .sce2adata(sce, useAssay)
71 72 
   annData$write_h5ad(filePath,
72 73 
                      compression = compression,
73 74 
                      compression_opts = compressionOpts,
Browse code

Merge upstream

Yusuke Koga authored on 16/10/2020 01:47:26
Showing0 changed files
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Put dontrun around examples that were outputting files. Removed Remotes from DESCRIPTION. Further compressed data objects

Joshua D. Campbell authored on 16/10/2020 00:52:57
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @c802b90fc
... ... 
@@ -20,8 +20,9 @@
20 20 
 #' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
21 21 
 #' @examples
22 22 
 #' data(sce_chcl, package = "scds")
23 
+#' \dontrun{
23 24 
 #' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
24 
-#'
25 
+#' }
25 26 
 #' @export
26 27 
 exportSCEtoAnnData <- function(sce,
27 28 
                                 useAssay = 'counts',
Browse code

Merge branch 'master' of github.com:compbiomed/singleCellTK

Yusuke Koga authored on 16/10/2020 00:27:01
Showing0 changed files
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Add Runnable functions

Yusuke Koga authored on 15/10/2020 16:44:51
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @0ccddee17
... ... 
@@ -1,5 +1,5 @@
1 
-#' @title Export a \link[SingleCellExperiment]{SingleCellExperiment} R object as
2 
-#' Python annData object
1 
+#' @title Export a \link[SingleCellExperiment]{SingleCellExperiment} R object as
2 
+#' Python annData object
3 3 
 #' @description Writes all assays, colData, rowData, reducedDims, and altExps objects in a
4 4 
 #' \link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format
5 5 
 #' All parameters of Anndata.write_h5ad function (https://icb-anndata.readthedocs-hosted.com/en/stable/anndata.AnnData.write_h5ad.html)
... ... 
@@ -9,7 +9,7 @@
9 9 
 #'  exported.
10 10 
 #' @param useAssay Character. The name of assay of
11 11 
 #' interests that will be set as the primary matrix of the output AnnData.
12 
-#' Default \code{"counts"}.
12 
+#' Default \code{"counts"}.
13 13 
 #' @param outputDir Path to the directory where .h5ad outputs will be written. Default is the current working directory.
14 14 
 #' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
15 15 
 #' @param overwrite Boolean. Default \code{TRUE}.
... ... 
@@ -17,15 +17,13 @@
17 17 
 #' 'gzip' or 'lzf' as inputs. Default \code{None}.
18 18 
 #' @param compressionOpts Integer. Sets the compression level
19 19 
 #' @param forceDense Default \code{False} Write sparse data as a dense matrix.
20 
-#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
20 
+#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
21 21 
 #' @examples
22 
-#' \dontrun{
23 22 
 #' data(sce_chcl, package = "scds")
24 23 
 #' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
25 
-#' }
26 
-#'
24 
+#'
27 25 
 #' @export
28 
-exportSCEtoAnnData <- function(sce,
26 
+exportSCEtoAnnData <- function(sce,
29 27 
                                 useAssay = 'counts',
30 28 
                                 outputDir = "./",
31 29 
                                 prefix = "sample",
... ... 
@@ -50,7 +48,7 @@ exportSCEtoAnnData <- function(sce,
50 48 
             " function from the 'reticulate' package can be used to select the",
51 49 
             " correct Python environment.")
52 50 
     return(sce)}
53 
-
51 
+
54 52 
   AssayName <- SummarizedExperiment::assayNames(sce)
55 53 
   for (assay in AssayName){
56 54 
     if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
... ... 
@@ -58,18 +56,18 @@ exportSCEtoAnnData <- function(sce,
58 56 
     }
59 57 
   }
60 58
61 
-
59 
+
62 60 
   dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
63 61 
   annData <- .sce2adata(sce,useAssay)
64 62 
   fileName <- paste0(prefix,".h5ad")
65 63 
   filePath <- file.path(outputDir,fileName)
66 
-
64 
+
67 65 
   if (file.exists(filePath) && !isTRUE(overwrite)) {
68 66 
     stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
69 67 
     }
70 68
71 69 
   annData$write_h5ad(filePath,
72 
-                     compression = compression,
70 
+                     compression = compression,
73 71 
                      compression_opts = compressionOpts,
74 72 
                      force_dense = forceDense)
75 73 
 }
Browse code

Merge devel branch (Oct 5) into master branch

Yusuke Koga authored on 09/10/2020 17:57:06
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @3a66a1024
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,75 @@
1 
+#' @title Export a \link[SingleCellExperiment]{SingleCellExperiment} R object as
2 
+#' Python annData object
3 
+#' @description Writes all assays, colData, rowData, reducedDims, and altExps objects in a
4 
+#' \link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format
5 
+#' All parameters of Anndata.write_h5ad function (https://icb-anndata.readthedocs-hosted.com/en/stable/anndata.AnnData.write_h5ad.html)
6 
+#' are available as parameters to this export function and set to defaults. Defaults can be
7 
+#' overridden at function call.
8 
+#' @param sce \link[SingleCellExperiment]{SingleCellExperiment} R object to be
9 
+#'  exported.
10 
+#' @param useAssay Character. The name of assay of
11 
+#' interests that will be set as the primary matrix of the output AnnData.
12 
+#' Default \code{"counts"}.
13 
+#' @param outputDir Path to the directory where .h5ad outputs will be written. Default is the current working directory.
14 
+#' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
15 
+#' @param overwrite Boolean. Default \code{TRUE}.
16 
+#' @param compression If output file compression is required, this variable accepts
17 
+#' 'gzip' or 'lzf' as inputs. Default \code{None}.
18 
+#' @param compressionOpts Integer. Sets the compression level
19 
+#' @param forceDense Default \code{False} Write sparse data as a dense matrix.
20 
+#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
21 
+#' @examples
22 
+#' \dontrun{
23 
+#' data(sce_chcl, package = "scds")
24 
+#' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
25 
+#' }
26 
+#'
27 
+#' @export
28 
+exportSCEtoAnnData <- function(sce,
29 
+                                useAssay = 'counts',
30 
+                                outputDir = "./",
31 
+                                prefix = "sample",
32 
+                                overwrite = TRUE,
33 
+                                compression = c('None','lzf','gzip'),
34 
+                                compressionOpts = NULL,
35 
+                                forceDense = c('False','True')){
36 
+  compression <- match.arg(compression)
37 
+  forceDense <- match.arg(forceDense)
38 
+  if (compression == 'None'){
39 
+    compression <- NULL
40 
+  }
41 
+
42 
+  if (!reticulate::py_module_available(module = "scanpy")) {
43 
+    warning("Cannot find python module 'scanpy', please install Conda and",
44 
+            " run sctkPythonInstallConda() or run sctkPythonInstallVirtualEnv().",
45 
+            "If one of these have been previously run to install the modules,",
46 
+            "make sure to run selectSCTKConda() or selectSCTKVirtualEnvironment(),",
47 
+            " respectively, if R has been restarted since the module installation.",
48 
+            " Alternatively, Scrublet can be installed on the local machine",
49 
+            "with pip (e.g. pip install --user scanpy) and then the 'use_python()'",
50 
+            " function from the 'reticulate' package can be used to select the",
51 
+            " correct Python environment.")
52 
+    return(sce)}
53 
+
54 
+  AssayName <- SummarizedExperiment::assayNames(sce)
55 
+  for (assay in AssayName){
56 
+    if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
57 
+      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
58 
+    }
59 
+  }
60 
+
61 
+
62 
+  dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
63 
+  annData <- .sce2adata(sce,useAssay)
64 
+  fileName <- paste0(prefix,".h5ad")
65 
+  filePath <- file.path(outputDir,fileName)
66 
+
67 
+  if (file.exists(filePath) && !isTRUE(overwrite)) {
68 
+    stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
69 
+    }
70 
+
71 
+  annData$write_h5ad(filePath,
72 
+                     compression = compression,
73 
+                     compression_opts = compressionOpts,
74 
+                     force_dense = forceDense)
75 
+}
Browse code

Revert "Sctk documentation "

Joshua D. Campbell authored on 09/06/2020 23:22:05 • GitHub committed on 09/06/2020 23:22:05
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @043c8eab2
1 1 
deleted file mode 100644
... ... 
@@ -1,75 +0,0 @@
1 
-#' @title Export a \link[SingleCellExperiment]{SingleCellExperiment} R object as
2 
-#' Python annData object
3 
-#' @description Writes all assays, colData, rowData, reducedDims, and altExps objects in a
4 
-#' \link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format
5 
-#' All parameters of Anndata.write_h5ad function (https://icb-anndata.readthedocs-hosted.com/en/stable/anndata.AnnData.write_h5ad.html)
6 
-#' are available as parameters to this export function and set to defaults. Defaults can be
7 
-#' overridden at function call.
8 
-#' @param sce \link[SingleCellExperiment]{SingleCellExperiment} R object to be
9 
-#'  exported.
10 
-#' @param useAssay Character. The name of assay of
11 
-#' interests that will be set as the primary matrix of the output AnnData.
12 
-#' Default \code{"counts"}.
13 
-#' @param outputDir Path to the directory where .h5ad outputs will be written. Default is the current working directory.
14 
-#' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
15 
-#' @param overwrite Boolean. Default \code{TRUE}.
16 
-#' @param compression If output file compression is required, this variable accepts
17 
-#' 'gzip' or 'lzf' as inputs. Default \code{None}.
18 
-#' @param compressionOpts Integer. Sets the compression level
19 
-#' @param forceDense Default \code{False} Write sparse data as a dense matrix.
20 
-#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
21 
-#' @examples
22 
-#' \dontrun{
23 
-#' data(sce_chcl, package = "scds")
24 
-#' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
25 
-#' }
26 
-#'
27 
-#' @export
28 
-exportSCEtoAnnData <- function(sce,
29 
-                                useAssay = 'counts',
30 
-                                outputDir = "./",
31 
-                                prefix = "sample",
32 
-                                overwrite = TRUE,
33 
-                                compression = c('None','lzf','gzip'),
34 
-                                compressionOpts = NULL,
35 
-                                forceDense = c('False','True')){
36 
-  compression <- match.arg(compression)
37 
-  forceDense <- match.arg(forceDense)
38 
-  if (compression == 'None'){
39 
-    compression <- NULL
40 
-  }
41 
-
42 
-  if (!reticulate::py_module_available(module = "scanpy")) {
43 
-    warning("Cannot find python module 'scanpy', please install Conda and",
44 
-            " run sctkPythonInstallConda() or run sctkPythonInstallVirtualEnv().",
45 
-            "If one of these have been previously run to install the modules,",
46 
-            "make sure to run selectSCTKConda() or selectSCTKVirtualEnvironment(),",
47 
-            " respectively, if R has been restarted since the module installation.",
48 
-            " Alternatively, Scrublet can be installed on the local machine",
49 
-            "with pip (e.g. pip install --user scanpy) and then the 'use_python()'",
50 
-            " function from the 'reticulate' package can be used to select the",
51 
-            " correct Python environment.")
52 
-    return(sce)}
53 
-
54 
-  AssayName <- SummarizedExperiment::assayNames(sce)
55 
-  for (assay in AssayName){
56 
-    if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
57 
-      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
58 
-    }
59 
-  }
60 
-
61 
-
62 
-  dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
63 
-  annData <- .sce2adata(sce,useAssay)
64 
-  fileName <- paste0(prefix,".h5ad")
65 
-  filePath <- file.path(outputDir,fileName)
66 
-
67 
-  if (file.exists(filePath) && !isTRUE(overwrite)) {
68 
-    stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
69 
-    }
70 
-
71 
-  annData$write_h5ad(filePath,
72 
-                     compression = compression,
73 
-                     compression_opts = compressionOpts,
74 
-                     force_dense = forceDense)
75 
-}
Browse code

Merge conflict

rz2333 authored on 04/05/2020 02:25:09
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @4a58e6ab9
... ... 
@@ -53,7 +53,7 @@ exportSCEtoAnnData <- function(sce,
53 53
54 54 
   AssayName <- SummarizedExperiment::assayNames(sce)
55 55 
   for (assay in AssayName){
56 
-    if (!is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
56 
+    if (!methods::is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
57 57 
       SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
58 58 
     }
59 59 
   }
Browse code

Fixed and merge conflict from compbiomed-devel

rz2333 authored on 01/05/2020 03:00:48
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @8d7cbd298
... ... 
@@ -7,29 +7,32 @@
7 7 
 #' overridden at function call.
8 8 
 #' @param sce \link[SingleCellExperiment]{SingleCellExperiment} R object to be
9 9 
 #'  exported.
10 
-#'  @param useAssay Character, default `"counts"`. The name of assay of
10 
+#' @param useAssay Character. The name of assay of
11 11 
 #' interests that will be set as the primary matrix of the output AnnData.
12 
-#' @param outputDir Path to the directory where .h5ad outputs will be written
12 
+#' Default \code{"counts"}.
13 
+#' @param outputDir Path to the directory where .h5ad outputs will be written. Default is the current working directory.
14 
+#' @param prefix Prefix to use for the name of the output file. Default \code{"sample"}.
13 15 
 #' @param overwrite Boolean. Default \code{TRUE}.
14 
-#' @param compression Default \code{None}.If output file compression is required, this variable accepts
15 
-#' 'gzip' or 'lzf' as inputs.
16 
-#' @param compression_opts Integer. Default \code{NULL} Sets the compression level
16 
+#' @param compression If output file compression is required, this variable accepts
17 
+#' 'gzip' or 'lzf' as inputs. Default \code{None}.
18 
+#' @param compressionOpts Integer. Sets the compression level
17 19 
 #' @param forceDense Default \code{False} Write sparse data as a dense matrix.
18 
-#' Refer anndata.write_h5ad documentation for details
20 
+#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.
19 21 
 #' @examples
22 
+#' \dontrun{
20 23 
 #' data(sce_chcl, package = "scds")
21 24 
 #' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
22 
-#'
25 
+#' }
26 
+#'
23 27 
 #' @export
24 
-
25 28 
 exportSCEtoAnnData <- function(sce,
26 
-                                useAssay='counts',
27 
-                                outputDir="./",
28 
-                                sample = "sample",
29 
-                                overwrite=TRUE,
30 
-                                compression= c('None','lzf','gzip'),
29 
+                                useAssay = 'counts',
30 
+                                outputDir = "./",
31 
+                                prefix = "sample",
32 
+                                overwrite = TRUE,
33 
+                                compression = c('None','lzf','gzip'),
31 34 
                                 compressionOpts = NULL,
32 
-                                forceDense= c('False','True')){
35 
+                                forceDense = c('False','True')){
33 36 
   compression <- match.arg(compression)
34 37 
   forceDense <- match.arg(forceDense)
35 38 
   if (compression == 'None'){
... ... 
@@ -58,12 +61,12 @@ exportSCEtoAnnData <- function(sce,
58 61
59 62 
   dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
60 63 
   annData <- .sce2adata(sce,useAssay)
61 
-  fileName <- paste0(sample,".h5ad")
64 
+  fileName <- paste0(prefix,".h5ad")
62 65 
   filePath <- file.path(outputDir,fileName)
63 
-
66 
+
64 67 
   if (file.exists(filePath) && !isTRUE(overwrite)) {
65 68 
     stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
66 
-  }
69 
+    }
67 70
68 71 
   annData$write_h5ad(filePath,
69 72 
                      compression = compression,
Browse code

Fix exportSCEtoAnndata.R

rz2333 authored on 22/04/2020 17:34:30
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @7191c3e4e
... ... 
@@ -48,9 +48,13 @@ exportSCEtoAnnData <- function(sce,
48 48 
             " correct Python environment.")
49 49 
     return(sce)}
50 50
51 
-  if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {
52 
-    SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))
51 
+  AssayName <- SummarizedExperiment::assayNames(sce)
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+  for (assay in AssayName){
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+    if (!is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {
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+      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
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+    }
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   }
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+
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   dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
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   annData <- .sce2adata(sce,useAssay)
Browse code

Fix directory not found issue in exportSCEtoAnndata.R

rz2333 authored on 21/04/2020 15:28:15
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @2d50f9bc4
... ... 
@@ -51,14 +51,15 @@ exportSCEtoAnnData <- function(sce,
51 51 
   if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {
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     SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))
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   }
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-
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+
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+  dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)
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   annData <- .sce2adata(sce,useAssay)
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   fileName <- paste0(sample,".h5ad")
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   filePath <- file.path(outputDir,fileName)
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-
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+
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   if (file.exists(filePath) && !isTRUE(overwrite)) {
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     stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
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-    }
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+  }
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   annData$write_h5ad(filePath,
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                      compression = compression,
Browse code

Update exportSCEtoAnndata.R to support exporting dgTMatrix and DelayedArray

rz2333 authored on 20/04/2020 16:14:31
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @194670e9b
... ... 
@@ -48,6 +48,10 @@ exportSCEtoAnnData <- function(sce,
48 48 
             " correct Python environment.")
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     return(sce)}
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+  if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {
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+    SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))
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+  }
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+
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   annData <- .sce2adata(sce,useAssay)
52 56 
   fileName <- paste0(sample,".h5ad")
53 57 
   filePath <- file.path(outputDir,fileName)
Browse code

Resolve conflict from upstream devel

rz2333 authored on 17/04/2020 18:43:57
Showing1 changed files
R/exportSCEtoAnndata.R
History View file @06ab60301
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,63 @@
1 
+#' @title Export a \link[SingleCellExperiment]{SingleCellExperiment} R object as
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+#' Python annData object
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+#' @description Writes all assays, colData, rowData, reducedDims, and altExps objects in a
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+#' \link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format
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+#' All parameters of Anndata.write_h5ad function (https://icb-anndata.readthedocs-hosted.com/en/stable/anndata.AnnData.write_h5ad.html)
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+#' are available as parameters to this export function and set to defaults. Defaults can be
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+#' overridden at function call.
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+#' @param sce \link[SingleCellExperiment]{SingleCellExperiment} R object to be
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+#'  exported.
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+#'  @param useAssay Character, default `"counts"`. The name of assay of
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+#' interests that will be set as the primary matrix of the output AnnData.
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+#' @param outputDir Path to the directory where .h5ad outputs will be written
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+#' @param overwrite Boolean. Default \code{TRUE}.
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+#' @param compression Default \code{None}.If output file compression is required, this variable accepts
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+#' 'gzip' or 'lzf' as inputs.
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+#' @param compression_opts Integer. Default \code{NULL} Sets the compression level
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+#' @param forceDense Default \code{False} Write sparse data as a dense matrix.
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+#' Refer anndata.write_h5ad documentation for details
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+#' @examples
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+#' data(sce_chcl, package = "scds")
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+#' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
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+#'
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+#' @export
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+
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+exportSCEtoAnnData <- function(sce,
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+                                useAssay='counts',
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+                                outputDir="./",
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+                                sample = "sample",
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+                                overwrite=TRUE,
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+                                compression= c('None','lzf','gzip'),
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+                                compressionOpts = NULL,
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+                                forceDense= c('False','True')){
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+  compression <- match.arg(compression)
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+  forceDense <- match.arg(forceDense)
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+  if (compression == 'None'){
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+    compression <- NULL
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+  }
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+
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+  if (!reticulate::py_module_available(module = "scanpy")) {
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+    warning("Cannot find python module 'scanpy', please install Conda and",
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+            " run sctkPythonInstallConda() or run sctkPythonInstallVirtualEnv().",
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+            "If one of these have been previously run to install the modules,",
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+            "make sure to run selectSCTKConda() or selectSCTKVirtualEnvironment(),",
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+            " respectively, if R has been restarted since the module installation.",
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+            " Alternatively, Scrublet can be installed on the local machine",
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+            "with pip (e.g. pip install --user scanpy) and then the 'use_python()'",
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+            " function from the 'reticulate' package can be used to select the",
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+            " correct Python environment.")
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+    return(sce)}
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+
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+  annData <- .sce2adata(sce,useAssay)
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+  fileName <- paste0(sample,".h5ad")
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+  filePath <- file.path(outputDir,fileName)
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+
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+  if (file.exists(filePath) && !isTRUE(overwrite)) {
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+    stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
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+    }
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+
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+  annData$write_h5ad(filePath,
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+                     compression = compression,
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+                     compression_opts = compressionOpts,
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+                     force_dense = forceDense)
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+}