update scKirkby

neurogenomics · Apr 21, 2024 · 008d72d · 008d72d
1 parent 3ba75d8
commit 008d72d
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Showing 25 changed files with 19 additions and 71 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -87,48 +87,19 @@ export(to_se)
 export(to_seurat)
 export(to_sparse)
 export(update_seurat)
+import(Seurat)
 import(data.table)
 import(orthogene)
-importClassesFrom(SeuratObject,Graph)
 importFrom(DelayedArray,DelayedArray)
 importFrom(EWCE,generate_celltype_data)
 importFrom(EWCE,merge_sce)
 importFrom(EWCE,standardise_ctd)
-importFrom(Matrix,t)
-importFrom(Seurat,CreateAssayObject)
-importFrom(Seurat,CreateSeuratObject)
-importFrom(Seurat,DefaultAssay)
-importFrom(Seurat,FindClusters)
-importFrom(Seurat,FindNeighbors)
-importFrom(Seurat,FindVariableFeatures)
-importFrom(Seurat,GetAssayData)
-importFrom(Seurat,LogNormalize)
-importFrom(Seurat,NormalizeData)
-importFrom(Seurat,RunPCA)
-importFrom(Seurat,RunUMAP)
-importFrom(Seurat,ScaleData)
-importFrom(Seurat,as.CellDataSet)
-importFrom(SeuratObject,CreateDimReducObject)
-importFrom(SeuratObject,Graphs)
-importFrom(SeuratObject,as.Graph)
 importFrom(SingleCellExperiment,colData)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,assayNames)
-importFrom(data.table,as.data.table)
-importFrom(data.table,data.table)
-importFrom(data.table,setkeyv)
-importFrom(data.table,tstrsplit)
 importFrom(echoconda,activate_env)
 importFrom(future,plan)
-importFrom(methods,.hasSlot)
-importFrom(methods,as)
-importFrom(methods,is)
-importFrom(methods,slot)
 importFrom(orthogene,map_orthologs)
-importFrom(sceasy,convertFormat)
-importFrom(stats,setNames)
 importFrom(tidyr,all_of)
 importFrom(tidyr,unite)
-importFrom(utils,data)
 importFrom(utils,getFromNamespace)
-importFrom(utils,installed.packages)
diff --git a/R/_docs.R b/R/_docs.R
@@ -11,7 +11,7 @@
 #' @inheritParams converters
 #' @inheritParams map_data
 #' @inheritParams to_se
-#' @inheritParams orthogene::aggregate_rows
+#' @inheritParams orthogene::aggregate_mapped_genes
 #' @inheritParams EWCE::generate_celltype_data
 #' @inheritParams EWCE::standardise_ctd
 #' @returns Converted object.

diff --git a/R/anndata_to_seurat.R b/R/anndata_to_seurat.R
@@ -2,7 +2,6 @@
 #'
 #' @param ... Parameters passed to \code{sceasy::convertFormat}.
 #' @export
-#' @importFrom sceasy convertFormat
 #' @examples
 #' obj <- example_obj("anndata")
 #' seurat <- anndata_to_seurat(obj)

diff --git a/R/calc_cor.R b/R/calc_cor.R
@@ -9,8 +9,6 @@
 #' @returns A single-cell object with a graph.
 #'
 #' @keywords internal
-#' @importFrom Matrix t
-#' @importFrom methods as slot
 calc_cor <- function(obj,
                      keys = NULL,
                      graph_key = NULL,

diff --git a/R/converters.R b/R/converters.R
@@ -1,18 +1,16 @@
 #' Converters
 #'
-#' @describeIn converters
 #' Functions to convert one single-cell format to another.
 #' @param obj A single-cell object supported by \pkg{scKirby}.
-#'  See \link[scKirby]{converters} for a table of all supported conversions.
+#'  See \link{converters} for a table of all supported conversions.
 #' @param verbose Print messages.
-#' @param ... Additional arguments passed to the respective
-#' \link[scKirby]{converters} function.
+#' @param ... Additional arguments passed to the respective converter function.
+#' \link{converters} function.
 #'
 #' @export
-#' @importFrom data.table data.table tstrsplit setkeyv
 #' @examples
 #' map_dt <- converters()
-converters <- function(){
+converters <- function(obj, verbose, ...){
   func <- NULL;
 
   ns <- getNamespaceExports("scKirby")

diff --git a/R/example_obj.R b/R/example_obj.R
@@ -17,9 +17,6 @@
 #' @returns A single-cell object.
 #'
 #' @export
-#' @importFrom utils data
-#' @importClassesFrom SeuratObject Graph
-#' @importFrom SeuratObject Graphs
 #' @examples
 #' se <- example_obj("se")
 #' sce <- example_obj("sce")

diff --git a/R/get_obsm.R b/R/get_obsm.R
@@ -17,7 +17,6 @@
 #' @returns A matrix of cell embeddings coordinates.
 #'
 #' @export
-#' @importFrom methods is
 #' @examples
 #' obj <- example_obj("cds")
 #' obsm <- get_obsm(obj)

diff --git a/R/get_obsp.R b/R/get_obsp.R
@@ -7,7 +7,6 @@
 #' @returns Named list of graph objects.
 #'
 #' @export
-#' @importFrom methods is
 #' @examples
 #' obj <- example_obj("seurat")
 #' g <- get_obsp(obj)

diff --git a/R/get_varm.R b/R/get_varm.R
@@ -16,7 +16,6 @@
 #' @returns A named list of matrices containing the feature loadings.
 #'
 #' @export
-#' @importFrom methods is
 #' @examples
 #' obj <- example_obj("seurat")
 #' varm <- get_varm(obj)

diff --git a/R/get_x.R b/R/get_x.R
@@ -10,7 +10,6 @@
 #' @returns A named list of matrices.
 #'
 #' @export
-#' @importFrom Matrix t
 #' @examples
 #' obj <- example_obj("seurat")
 #' X <- get_x(obj)

diff --git a/R/is_class.R b/R/is_class.R
@@ -5,7 +5,7 @@
 #' When \code{group} is supplied,
 #' determine whether a single-cell object belongs to a particular group of
 #' object classes.
-#' See \linkp[scKirby]{dict_class} for details.
+#' See \link{dict_class} for details.
 #' @inheritParams converters
 #' @inheritParams dict_class
 #'

diff --git a/R/is_installed.R b/R/is_installed.R
@@ -7,7 +7,6 @@
 #' @returns Boolean
 #'
 #' @keywords internal
-#' @importFrom utils installed.packages
 is_installed <- function(pkg,
                          error=FALSE) {
   bool <- requireNamespace(pkg, quietly = TRUE)

diff --git a/R/list_to_dimreduc.R b/R/list_to_dimreduc.R
@@ -14,7 +14,6 @@
 #' @inheritDotParams SeuratObject::CreateDimReducObject
 #'
 #' @export
-#' @importFrom SeuratObject CreateDimReducObject
 list_to_dimreduc <- function(obj,
                              assay,
                              key,

diff --git a/R/matrices_to_assayobjects.R b/R/matrices_to_assayobjects.R
@@ -5,7 +5,7 @@
 #' @param X_list A named list of matrices (one per unique assay in
 #' \code{X_list}) to be put in the \code{counts} slot of each
 #' \code{AssayObject}.
-#' @param var_features [Optional] A named list of feature metadata data.frames
+#' @param var_features (Optional) A named list of feature metadata data.frames
 #'  (one per unique assay in \code{X_list}) to be put in the
 #'   \code{meta.features} slot of each \code{AssayObject}.
 #' @inheritParams converters

diff --git a/R/process_seurat.R b/R/process_seurat.R
@@ -32,19 +32,18 @@
 #' @inheritParams Seurat::FindVariableFeatures
 #' @inheritParams Seurat::ScaleData
 #' @inheritParams Seurat::RunUMAP
+#' @inheritParams Seurat::FindClusters
 #' @returns A preprocessed \link[SeuratObject]{Seurat} object.
 #'
 #' @export
-#' @importFrom Seurat CreateSeuratObject GetAssayData CreateAssayObject
-#' DefaultAssay FindVariableFeatures NormalizeData LogNormalize ScaleData
-#' RunPCA FindNeighbors RunUMAP FindClusters
+#' @import Seurat
 #' @importFrom future plan
 #' @examples
 #' obj <- example_obj("seurat")
 #' obj2 <- process_seurat(obj = obj)
 process_seurat <- function(obj = NULL,
                            meta.data = NULL,
-                           nfeatures = 2000,
+                           nfeatures = NULL,
                            reduction="pca",
                            dims = seq(100),
                            add_specificity = FALSE,
@@ -56,6 +55,8 @@ process_seurat <- function(obj = NULL,
                            scale_data=TRUE,
                            vars.to.regress = NULL,
                            cluster_reduction = "umap",
+                           algorithm = 1,
+                           resolution = 0.8,
                            workers = 1,
                            max_mem = 8000*1024^2,
                            seed = 2020,
@@ -116,7 +117,10 @@ process_seurat <- function(obj = NULL,
                                   reduction = cluster_reduction,
                                   dims = seq_len(n.components))
   }
-  obj2 <- Seurat::FindClusters(obj2)
+  obj2 <- Seurat::FindClusters(obj2,
+                               algorithm=algorithm,
+                               resolution=resolution,
+                               random.seed=seed)
   #### Return ####
   return(obj2)
 }
diff --git a/R/se_to_anndata.R b/R/se_to_anndata.R
@@ -7,7 +7,6 @@
 #' @returns \link[anndata]{AnnData} object.
 #'
 #' @export
-#' @importFrom sceasy convertFormat
 #' @examples
 #' obj <- example_obj("se")
 #' obj2 <- se_to_anndata(obj)

diff --git a/R/se_to_loom.R b/R/se_to_loom.R
@@ -1,6 +1,5 @@
 #' Convert: \code{SummarizedExperiment} ==> \code{loom}
 #'
-#' @describeIn converters Convert
 #' \link[SummarizedExperiment]{SummarizedExperiment} to
 #' \link[SeuratDisk]{loom}
 #' @inheritParams converters

diff --git a/R/set_obsp.R b/R/set_obsp.R
@@ -7,7 +7,6 @@
 #' @returns Named list of graph objects.
 #'
 #' @export
-#' @importFrom methods is
 #' @examples
 #' obj <- example_obj("seurat")
 #' g <- get_cor(obj)

diff --git a/R/seurat_to_cds.R b/R/seurat_to_cds.R
@@ -8,7 +8,6 @@
 #' \link[monocle]{CellDataSet} object.
 #'
 #' @export
-#' @importFrom Seurat as.CellDataSet
 #' @examples
 #' obj <- example_obj("seurat")
 #' obj2 <- seurat_to_cds(obj)

diff --git a/R/seurat_to_hdf5se.R b/R/seurat_to_hdf5se.R
@@ -1,21 +1,18 @@
 #' Convert: \code{Seurat} ==> \code{hdf5se}
 #'
-#' @inheritDotParams save_hdf5se
 #' @inheritParams converters
 #' @export
 #' @examples
 #' obj <- example_obj("seurat")
 #' obj2 <- seurat_to_hdf5se(obj)
 seurat_to_hdf5se <- function(obj,
                              save_path = tempfile(),
-                             verbose = TRUE,
-                             ...){
+                             verbose = TRUE){
 
   messager("+ Seurat ==> hdf5se",v=verbose)
   obj <- seurat_to_se(obj = obj,
                       verbose = verbose)
   save_hdf5se(obj = obj,
               save_dir = save_path,
-              verbose = verbose,
-              ...)
+              verbose = verbose)
 }
diff --git a/R/seurat_to_list.R b/R/seurat_to_list.R
@@ -4,8 +4,6 @@
 #' @returns A named list.
 #'
 #' @export
-#' @importFrom methods .hasSlot slot
-#' @importFrom stats setNames
 #' @examples
 #' obj <- example_obj("seurat")
 #' obj2 <- seurat_to_list(obj)

diff --git a/R/to_anndata.R b/R/to_anndata.R
@@ -1,6 +1,5 @@
 #' To \code{AnnData}
 #'
-#' @describeIn converters
 #' Convert any single-cell object to \link[anndata]{AnnData} format.
 #' @param reimport Save and re-import the \link[anndata]{AnnData} object
 #' into R to ensure all data has been converted from Python-native to

diff --git a/R/to_cds.R b/R/to_cds.R
@@ -1,6 +1,5 @@
 #' Convert: to \code{CellDataSet}
 #'
-#' @describeIn converters
 #' Convert any object to \code{CellDataSet} format.
 #' @inheritParams converters
 #' @returns A \code{CellDataSet} object.

diff --git a/R/to_datatable.R b/R/to_datatable.R
@@ -8,7 +8,6 @@
 #' @returns A \code{data.table} object.
 #'
 #' @export
-#' @importFrom data.table as.data.table
 #' @examples
 #' obj <- example_obj("cds")
 #' obj2 <- to_dataframe(obj)

diff --git a/R/to_graph.R b/R/to_graph.R
@@ -8,7 +8,6 @@
 #' @returns A sparse \link[SeuratObject]{as.Graph} object.
 #'
 #' @export
-#' @importFrom SeuratObject as.Graph
 #' @examples
 #' obj <- example_obj("matrix")
 #' obj2 <- to_graph(obj)