@@ -44,7 +44,7 @@

     tryCatch({

       SingleCellExperiment::reducedDims(sce)[[obsm_name]] <- reticulate::py_to_r(anndata$obsm[obsm_name])

     }, error = function(x){

-      error_message <- paste0("Warning: unable to add '",obsm_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

+      error_message <- paste0("Warning: unable to add '",obsm_name,"' from .obsm AnnData slot to SCE reducedDims. Skipping. ")

       message(error_message)

     })

   }

@@ -96,6 +96,8 @@

 #'  object. Can be one of "Matrix" (as returned by

 #'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default \code{"Matrix"}.

+#' @param rowNamesDedup Boolean. Whether to deduplicate rownames. Default 

+#'  \code{TRUE}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

@@ -120,7 +120,8 @@

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

                           delayedArray = FALSE,

-                          class = c("Matrix", "matrix")) {

+                          class = c("Matrix", "matrix"),

+                          rowNamesDedup = TRUE) {

   if (length(sampleDirs)!=length(sampleNames)){

     stop("Number of sampleDirs must be equal to number of SampleNames. Please provide sample names for all input directories")

@@ -138,6 +139,15 @@ importAnnData <- function(sampleDirs = NULL,

     res[[i]] <- scei

   }

   sce <- do.call(SingleCellExperiment::cbind, res)

+  

+  if (isTRUE(rowNamesDedup)) {

+    if (any(duplicated(rownames(sce)))) {

+      message("Duplicated gene names found, adding '-1', '-2', ",

+              "... suffix to them.")

+    }

+    sce <- dedupRowNames(sce)

+  }

+  

   return(sce)

 }

@@ -1,6 +1,7 @@

 .importAnnDataSample <- function(sampleDir = './',

                                  sampleName = 'sample',

-                                 delayedArray = FALSE){

+                                 delayedArray = FALSE,

+                                 class){

   anndata_file <- file.path(sampleDir, paste0(sampleName,'.h5ad',sep=''))

   if (!file.exists(anndata_file)){

@@ -9,6 +10,13 @@

   anndata <- ad$read_h5ad(anndata_file)

   counts_matrix <- t((reticulate::py_to_r(anndata$X)))

+

+  if (class == "Matrix") {

+    counts_matrix <- .convertToMatrix(counts_matrix)

+  } else if (class == "matrix") {

+    counts_matrix <- base::as.matrix(counts_matrix)

+  }

+

   if (isTRUE(delayedArray)) {

     counts_matrix <- DelayedArray::DelayedArray(counts_matrix)

   }

@@ -84,6 +92,10 @@

 #' }

 #' @param delayedArray Boolean. Whether to read the expression matrix as

 #'  \link{DelayedArray} object. Default \code{FALSE}.

+#' @param class Character. The class of the expression matrix stored in the SCE

+#'  object. Can be one of "Matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

+#'  \link[base]{matrix} function). Default \code{"Matrix"}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

@@ -107,18 +119,22 @@

 #' @export

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

-                          delayedArray = FALSE) {

+                          delayedArray = FALSE,

+                          class = c("Matrix", "matrix")) {

   if (length(sampleDirs)!=length(sampleNames)){

     stop("Number of sampleDirs must be equal to number of SampleNames. Please provide sample names for all input directories")

   }

+  class <- match.arg(class)

+

   res <- vector("list", length = length(sampleDirs))

   for (i in seq_along(sampleDirs)){

     scei <- .importAnnDataSample(sampleDir = sampleDirs[[i]],

                                  sampleName = sampleNames[[i]],

-                                 delayedArray = delayedArray)

+                                 delayedArray = delayedArray,

+                                 class = class)

     res[[i]] <- scei

   }

   sce <- do.call(SingleCellExperiment::cbind, res)

@@ -1,6 +1,6 @@

 .importAnnDataSample <- function(sampleDir = './',

                                  sampleName = 'sample',

-                                 delayedArray = TRUE){

+                                 delayedArray = FALSE){

   anndata_file <- file.path(sampleDir, paste0(sampleName,'.h5ad',sep=''))

   if (!file.exists(anndata_file)){

@@ -83,7 +83,7 @@

 #'   with the sample name appended to each colname in colData

 #' }

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link{DelayedArray} object. Default \code{TRUE}.

+#'  \link{DelayedArray} object. Default \code{FALSE}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

@@ -107,7 +107,7 @@

 #' @export

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

-                          delayedArray = TRUE) {

+                          delayedArray = FALSE) {

   if (length(sampleDirs)!=length(sampleNames)){

     stop("Number of sampleDirs must be equal to number of SampleNames. Please provide sample names for all input directories")

@@ -83,7 +83,7 @@

 #'   with the sample name appended to each colname in colData

 #' }

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.

+#'  \link{DelayedArray} object. Default \code{TRUE}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

@@ -1,25 +1,25 @@

 .importAnnDataSample <- function(sampleDir = './',

                                  sampleName = 'sample',

                                  delayedArray = TRUE){

-  

+

   anndata_file <- file.path(sampleDir, paste0(sampleName,'.h5ad',sep=''))

   if (!file.exists(anndata_file)){

     stop("AnnData file not found at specified location. Please check path provided and/or filename.")

   }

   anndata <- ad$read_h5ad(anndata_file)

-  

+

   counts_matrix <- t((reticulate::py_to_r(anndata$X)))

   if (isTRUE(delayedArray)) {

     counts_matrix <- DelayedArray::DelayedArray(counts_matrix)

   }

-  

+

   sce_rowdata <- S4Vectors::DataFrame(reticulate::py_to_r(anndata$var))

   sce_coldata <- S4Vectors::DataFrame(reticulate::py_to_r(anndata$obs))

   sce <- SingleCellExperiment(list(counts = counts_matrix),

                               rowData = sce_rowdata,

                               colData = sce_coldata)

   colnames(sce) <- paste0(sampleName,"_",colnames(sce))

-  

+

   multidim_observations <- reticulate::py_to_r(anndata$obsm_keys())

   for(obsm_name in multidim_observations){

     tryCatch({

@@ -28,9 +28,9 @@

       error_message <- paste0("Warning: unable to add '",uns_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

       message(error_message)

     })

-    

+

   }

-  

+

   unstructured_data <- reticulate::py_to_r(anndata$uns_keys())

   for(uns_name in unstructured_data){

     tryCatch({

@@ -39,71 +39,72 @@

       error_message <- paste0("Warning: unable to add unstructured data (.uns slot): '",uns_name,"' to SCE metadata. Skipping. ")

       message(error_message)

     })

-    

+

   }

-  

+

   return(sce)

-  

+

 }

 #' @name importAnnData

 #' @rdname importAnnData

 #' @title Create a SingleCellExperiment Object from Python AnnData .h5ad files

-#' @description This function reads in one or more Python AnnData files in the .h5ad format 

-#' and returns a single \link[SingleCellExperiment]{SingleCellExperiment} object containing all the 

+#' @description This function reads in one or more Python AnnData files in the .h5ad format

+#' and returns a single \link[SingleCellExperiment]{SingleCellExperiment} object containing all the

 #' AnnData samples by concatenating their counts matrices and related information slots.

-#' @param sampleDirs Folder containing the .h5ad file. Can be one of - 

+#' @param sampleDirs Folder containing the .h5ad file. Can be one of -

 #' \itemize{

 #'   \item Default \code{current working directory}.

-#'   \item Full path to the directory containing the .h5ad file. 

+#'   \item Full path to the directory containing the .h5ad file.

 #'   E.g \code{sampleDirs = '/path/to/sample'}

-#'   \item A vector of folder paths for the samples to import. 

+#'   \item A vector of folder paths for the samples to import.

 #'   E.g. \code{sampleDirs = c('/path/to/sample1', '/path/to/sample2','/path/to/sample3')}

-#'   importAnnData will return a single SCE object containing all the samples 

+#'   importAnnData will return a single SCE object containing all the samples

 #'   with the sample name appended to each colname in colData

 #' }

-#' @param sampleNames The prefix/name of the .h5ad file without the .h5ad extension 

+#' @param sampleNames The prefix/name of the .h5ad file without the .h5ad extension

 #' e.g. if 'sample.h5ad' is the filename, pass \code{sampleNames = 'sample'}.

-#' Can be one of - 

+#' Can be one of -

 #' \itemize{

 #'   \item Default \code{sample}.

 #'   \item A vector of samples to import. Length of vector must be equal to length of sampleDirs vector

 #'   E.g. \code{sampleDirs = c('sample1', 'sample2','sample3')}

-#'   importAnnData will return a single SCE object containing all the samples 

+#'   importAnnData will return a single SCE object containing all the samples

 #'   with the sample name appended to each colname in colData

 #' }

 #' @param delayedArray Boolean. Whether to read the expression matrix as

 #'  \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

-#' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells 

+#' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

 #' format and becomes the 'counts' matrix in the assay slot. The .vars AnnData slot becomes the SCE rowData

 #' and the .obs AnnData slot becomes the SCE colData. Multidimensional data in the .obsm AnnData slot is

-#' ported over to the SCE reducedDims slot. Additionally, unstructured data in the .uns AnnData slot is 

-#' available through the SCE metadata slot. 

-#' There are 2 currently known minor issues - 

+#' ported over to the SCE reducedDims slot. Additionally, unstructured data in the .uns AnnData slot is

+#' available through the SCE metadata slot.

+#' There are 2 currently known minor issues -

 #' Anndata python module depends on another python module h5pyto read hd5 format files.

 #' If there are errors reading the .h5ad files, such as "ValueError: invalid shape in fixed-type tuple."

-#' the user will need to do downgrade h5py by running \code{pip3 install --user h5py==2.9.0} 

+#' the user will need to do downgrade h5py by running \code{pip3 install --user h5py==2.9.0}

 #' Additionally there might be errors in converting some python objects in the unstructured data slots.

 #' There are no known R solutions at present. Refer \url{https://github.com/rstudio/reticulate/issues/209}

 #' @return A \code{SingleCellExperiment} object.

 #' @examples

+#' file.path <- system.file("extdata/annData_pbmc_3k", package = "singleCellTK")

 #' \dontrun{

-#' sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

+#' sce <- importAnnData(sampleDirs = file.path,

 #'                      sampleNames = 'pbmc3k_20by20')

 #' }

 #' @export

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

                           delayedArray = TRUE) {

-  

+

   if (length(sampleDirs)!=length(sampleNames)){

     stop("Number of sampleDirs must be equal to number of SampleNames. Please provide sample names for all input directories")

   }

-  

+

   res <- vector("list", length = length(sampleDirs))

-  

+

   for (i in seq_along(sampleDirs)){

     scei <- .importAnnDataSample(sampleDir = sampleDirs[[i]],

                                  sampleName = sampleNames[[i]],

@@ -19,18 +19,28 @@

                               rowData = sce_rowdata,

                               colData = sce_coldata)

   colnames(sce) <- paste0(sampleName,"_",colnames(sce))

+

+  multi_Assay <- reticulate::py_to_r(anndata$layers$as_dict())

+  for(assay_name in names(multi_Assay)){

+    tryCatch({

+      SummarizedExperiment::assay(sce, assay_name, withDimnames = FALSE) <- t(reticulate::py_to_r(multi_Assay[[assay_name]]))

+      base::dimnames(SummarizedExperiment::assay(sce, assay_name)) <- base::dimnames(SummarizedExperiment::assay(sce, "counts"))

+    }, error = function(x){

+      error_message <- paste0("Warning: unable to add '",assay_name,"' from .layers AnnData slot to SCE assay. Skipping. ")

+      message(error_message)

+    })

+  }

   multidim_observations <- reticulate::py_to_r(anndata$obsm_keys())

   for(obsm_name in multidim_observations){

     tryCatch({

-      reducedDims(sce)[[obsm_name]] <- reticulate::py_to_r(anndata$obsm[obsm_name])

+      SingleCellExperiment::reducedDims(sce)[[obsm_name]] <- reticulate::py_to_r(anndata$obsm[obsm_name])

     }, error = function(x){

-      error_message <- paste0("Warning: unable to add '",uns_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

+      error_message <- paste0("Warning: unable to add '",obsm_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

       message(error_message)

     })

-    

   }

-  

+

   unstructured_data <- reticulate::py_to_r(anndata$uns_keys())

   for(uns_name in unstructured_data){

     tryCatch({

@@ -89,9 +89,10 @@

 #' There are no known R solutions at present. Refer \url{https://github.com/rstudio/reticulate/issues/209}

 #' @return A \code{SingleCellExperiment} object.

 #' @examples

+#' \dontrun{

 #' sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

 #'                      sampleNames = 'pbmc3k_20by20')

-

+#' }

 #' @export

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

@@ -34,7 +34,6 @@

   unstructured_data <- reticulate::py_to_r(anndata$uns_keys())

   for(uns_name in unstructured_data){

     tryCatch({

-      #metadata(sce)[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

       sce@metadata[[sampleName]]$annData[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

     }, error = function(x){

       error_message <- paste0("Warning: unable to add unstructured data (.uns slot): '",uns_name,"' to SCE metadata. Skipping. ")

@@ -34,7 +34,8 @@

   unstructured_data <- reticulate::py_to_r(anndata$uns_keys())

   for(uns_name in unstructured_data){

     tryCatch({

-      metadata(sce)[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

+      #metadata(sce)[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

+      sce@metadata[[sampleName]]$annData[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

     }, error = function(x){

       error_message <- paste0("Warning: unable to add unstructured data (.uns slot): '",uns_name,"' to SCE metadata. Skipping. ")

       message(error_message)

@@ -90,7 +90,7 @@

 #' @return A \code{SingleCellExperiment} object.

 #' @examples

 #' sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

-#'                      sampleNames = 'pbmc3k')

+#'                      sampleNames = 'pbmc3k_20by20')

 #' @export

 importAnnData <- function(sampleDirs = NULL,

@@ -8,22 +8,22 @@

   }

   anndata <- ad$read_h5ad(anndata_file)

-  counts_matrix <- t((py_to_r(anndata$X)))

+  counts_matrix <- t((reticulate::py_to_r(anndata$X)))

   if (isTRUE(delayedArray)) {

     counts_matrix <- DelayedArray::DelayedArray(counts_matrix)

   }

-  sce_rowdata <- S4Vectors::DataFrame(py_to_r(anndata$var))

-  sce_coldata <- S4Vectors::DataFrame(py_to_r(anndata$obs))

+  sce_rowdata <- S4Vectors::DataFrame(reticulate::py_to_r(anndata$var))

+  sce_coldata <- S4Vectors::DataFrame(reticulate::py_to_r(anndata$obs))

   sce <- SingleCellExperiment(list(counts = counts_matrix),

                               rowData = sce_rowdata,

                               colData = sce_coldata)

   colnames(sce) <- paste0(sampleName,"_",colnames(sce))

-  multidim_observations <- py_to_r(anndata$obsm_keys())

+  multidim_observations <- reticulate::py_to_r(anndata$obsm_keys())

   for(obsm_name in multidim_observations){

     tryCatch({

-      reducedDims(sce)[[obsm_name]] <- py_to_r(anndata$obsm[obsm_name])

+      reducedDims(sce)[[obsm_name]] <- reticulate::py_to_r(anndata$obsm[obsm_name])

     }, error = function(x){

       error_message <- paste0("Warning: unable to add '",uns_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

       message(error_message)

@@ -31,10 +31,10 @@

   }

-  unstructured_data <- py_to_r(anndata$uns_keys())

+  unstructured_data <- reticulate::py_to_r(anndata$uns_keys())

   for(uns_name in unstructured_data){

     tryCatch({

-      metadata(sce)[[uns_name]] <- py_to_r(anndata$uns[uns_name])

+      metadata(sce)[[uns_name]] <- reticulate::py_to_r(anndata$uns[uns_name])

     }, error = function(x){

       error_message <- paste0("Warning: unable to add unstructured data (.uns slot): '",uns_name,"' to SCE metadata. Skipping. ")

       message(error_message)

new file mode 100644

@@ -0,0 +1,127 @@

+.importAnnDataSample <- function(sampleDir = './',

+                                 sampleName = 'sample',

+                                 delayedArray = TRUE){

+  

+  anndata_file <- file.path(sampleDir, paste0(sampleName,'.h5ad',sep=''))

+  if (!file.exists(anndata_file)){

+    stop("AnnData file not found at specified location. Please check path provided and/or filename.")

+  }

+  anndata <- ad$read_h5ad(anndata_file)

+  

+  counts_matrix <- t((py_to_r(anndata$X)))

+  if (isTRUE(delayedArray)) {

+    counts_matrix <- DelayedArray::DelayedArray(counts_matrix)

+  }

+  

+  sce_rowdata <- S4Vectors::DataFrame(py_to_r(anndata$var))

+  sce_coldata <- S4Vectors::DataFrame(py_to_r(anndata$obs))

+  sce <- SingleCellExperiment(list(counts = counts_matrix),

+                              rowData = sce_rowdata,

+                              colData = sce_coldata)

+  colnames(sce) <- paste0(sampleName,"_",colnames(sce))

+  

+  multidim_observations <- py_to_r(anndata$obsm_keys())

+  for(obsm_name in multidim_observations){

+    tryCatch({

+      reducedDims(sce)[[obsm_name]] <- py_to_r(anndata$obsm[obsm_name])

+    }, error = function(x){

+      error_message <- paste0("Warning: unable to add '",uns_name,"' from .obsm AnnData slot to SCE metadata. Skipping. ")

+      message(error_message)

+    })

+    

+  }

+  

+  unstructured_data <- py_to_r(anndata$uns_keys())

+  for(uns_name in unstructured_data){

+    tryCatch({

+      metadata(sce)[[uns_name]] <- py_to_r(anndata$uns[uns_name])

+    }, error = function(x){

+      error_message <- paste0("Warning: unable to add unstructured data (.uns slot): '",uns_name,"' to SCE metadata. Skipping. ")

+      message(error_message)

+    })

+    

+  }

+  

+  return(sce)

+  

+}

+

+#' @name importAnnData

+#' @rdname importAnnData

+#' @title Create a SingleCellExperiment Object from Python AnnData .h5ad files

+#' @description This function reads in one or more Python AnnData files in the .h5ad format 

+#' and returns a single \link[SingleCellExperiment]{SingleCellExperiment} object containing all the 

+#' AnnData samples by concatenating their counts matrices and related information slots.

+#' @param sampleDirs Folder containing the .h5ad file. Can be one of - 

+#' \itemize{

+#'   \item Default \code{current working directory}.

+#'   \item Full path to the directory containing the .h5ad file. 

+#'   E.g \code{sampleDirs = '/path/to/sample'}

+#'   \item A vector of folder paths for the samples to import. 

+#'   E.g. \code{sampleDirs = c('/path/to/sample1', '/path/to/sample2','/path/to/sample3')}

+#'   importAnnData will return a single SCE object containing all the samples 

+#'   with the sample name appended to each colname in colData

+#' }

+#' @param sampleNames The prefix/name of the .h5ad file without the .h5ad extension 

+#' e.g. if 'sample.h5ad' is the filename, pass \code{sampleNames = 'sample'}.

+#' Can be one of - 

+#' \itemize{

+#'   \item Default \code{sample}.

+#'   \item A vector of samples to import. Length of vector must be equal to length of sampleDirs vector

+#'   E.g. \code{sampleDirs = c('sample1', 'sample2','sample3')}

+#'   importAnnData will return a single SCE object containing all the samples 

+#'   with the sample name appended to each colname in colData

+#' }

+#' @param delayedArray Boolean. Whether to read the expression matrix as

+#'  \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.

+#' @details

+#' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

+#' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells 

+#' format and becomes the 'counts' matrix in the assay slot. The .vars AnnData slot becomes the SCE rowData

+#' and the .obs AnnData slot becomes the SCE colData. Multidimensional data in the .obsm AnnData slot is

+#' ported over to the SCE reducedDims slot. Additionally, unstructured data in the .uns AnnData slot is 

+#' available through the SCE metadata slot. 

+#' There are 2 currently known minor issues - 

+#' Anndata python module depends on another python module h5pyto read hd5 format files.

+#' If there are errors reading the .h5ad files, such as "ValueError: invalid shape in fixed-type tuple."

+#' the user will need to do downgrade h5py by running \code{pip3 install --user h5py==2.9.0} 

+#' Additionally there might be errors in converting some python objects in the unstructured data slots.

+#' There are no known R solutions at present. Refer \url{https://github.com/rstudio/reticulate/issues/209}

+#' @return A \code{SingleCellExperiment} object.

+#' @examples

+#' sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

+#'                      sampleNames = 'pbmc3k')

+

+#' @export

+importAnnData <- function(sampleDirs = NULL,

+                          sampleNames = NULL,

+                          delayedArray = TRUE) {

+  

+  if (length(sampleDirs)!=length(sampleNames)){

+    stop("Number of sampleDirs must be equal to number of SampleNames. Please provide sample names for all input directories")

+  }

+  

+  res <- vector("list", length = length(sampleDirs))

+  

+  for (i in seq_along(sampleDirs)){

+    scei <- .importAnnDataSample(sampleDir = sampleDirs[[i]],

+                                 sampleName = sampleNames[[i]],

+                                 delayedArray = delayedArray)

+    res[[i]] <- scei

+  }

+  sce <- do.call(SingleCellExperiment::cbind, res)

+  return(sce)

+}

+

+

+

+

+

+

+

+

+

+

+

+

+