Fix scVIIntegration

DESCRIPTION

@@ -1,15 +1,16 @@
 Package: SeuratWrappers
 Title: Community-Provided Methods and Extensions for the Seurat Object
-Version: 0.3.2
-Date: 2023-11-4
+Version: 0.3.3
+Date: 2024-01-19
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
   person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
   person(given = 'Tim', family = 'Stuart', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')), 
   person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
   person(given = "Austin", family = "Hartman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
-  person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056'))
+  person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')),
+  person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633"))
   )
 Description: SeuratWrappers is a collection of community-provided methods and
     extensions for Seurat, curated by the Satija Lab at NYGC. These methods
@@ -64,7 +65,7 @@ Collate:
     'velocity.R'
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Suggests:
     cipr,
     conos,

R/miqc.R

@@ -165,7 +165,6 @@ RunMiQC <- function(
 #'
 #' @param object Seurat object
 #' @details _Function to plot the miQC mixture model stored in a Seurat object. `RunMiQC` must be run prior to plotting._
-#' @return
 #' @references Hippen et al. (2021) miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. bioRxiv doi: 10.1101/2021.03.03.433798
 #'
 #' @importFrom rlang %||%

R/scVI.R

@@ -4,7 +4,7 @@ NULL
 
 #' Run scVI in seurat5
 #' @param object A merged Seurat object
-#' @param groups A one-column data frame with grouping information
+#' @param groups Name of the metadata column to be used as the 'batch_key'
 #' @param features features to use
 #' @param layers Layers to use
 #' @param conda_env conda environment to run scVI
@@ -61,11 +61,11 @@ scVIIntegration <- function(
   scipy <-  reticulate::import('scipy', convert = FALSE)
   object <- JoinLayers(object = object, layers = 'counts')
   adata <- sc$AnnData(
-    X   = scipy$sparse$csr_matrix(Matrix::t(LayerData(object, layers = 'counts')[features ,]) ), #scVI requires raw counts
-    obs = groups,
-    var = object[][features,]
+    X   = scipy$sparse$csr_matrix(Matrix::t(LayerData(object, layer = 'counts')[features ,]) ), #scVI requires raw counts
+    obs = object[[]],
+    var = object[[DefaultAssay(object)]][[]][features,]
   )
-  scvi$model$SCVI$setup_anndata(adata,  batch_key = 'group')
+  scvi$model$SCVI$setup_anndata(adata,  batch_key = groups)
   model = scvi$model$SCVI(adata = adata,
                           n_latent = as.integer(x = ndims),
                           n_layers = as.integer(x = nlayers),