devtools::check passed

DESCRIPTION

@@ -75,7 +75,6 @@ Imports:
     limma (>= 3.54.0),
     magrittr (>= 2.0.3),
     MAST (>= 1.24.0),
-    lme4,
     methods,
     monocle3 (>= 1.3.1),
     paletteer (>= 1.5.0),

R/cluster_sce.R

@@ -7,10 +7,17 @@
 #' UMAP_Liger, tSNE_Liger.
 #' @param resolution Clustering resolution. If NULL, clustering method will be
 #' set to louvain.
-#' @param K Integer number of nearest neighbors to use when creating the k
+#' @param k Integer number of nearest neighbors to use when creating the k
 #' nearest neighbor graph for Louvain/Leiden clustering.
 #' k is related to the resolution of the clustering result, a bigger k will
 #' result in lower resolution and vice versa. Default is 50.
+#' @param louvain_iter Integer number of iterations used for Louvain clustering.
+#' The clustering result giving the largest modularity score will be used
+#' as the final clustering result. Default is 1. Note that if num_iter
+#' is greater than 1, the random_seed argument will be ignored
+#' for the louvain method.
+#' @param verbose A logic flag to determine whether or not we should print
+#' the run details.
 #' @param ... see monocle3::cluster_cells for more clustering options.
 #'
 #' @return sce a SingleCellExperiment object annotated with reducedDims
@@ -23,9 +30,9 @@
 #' @export
 
 cluster_sce <- function(sce,
-                        cluster_method = "leiden",
+                        cluster_method = "louvain",
                         reduction_method = "UMAP_Liger",
-                        resolution = 1e-5,
+                        resolution = NULL,
                         k = 50,
                         louvain_iter = 1,
                         verbose = T,

R/map_with_ewce.R

@@ -263,9 +263,9 @@ map_celltypes_sce <- function(sce,
 ### Allow variation in annotation level
 
 .map_celltypes <- function(ctdToMap,
-                           ctdToMapAgainst = MAGMA.Celltyping::ctd_Tasic,
+                           ctdToMapAgainst,
                            inputSpecies = "human",
-                           mapAgainstSpecies = "mouse",
+                           mapAgainstSpecies = "human",
                            annotLevel = 1,
                            numTopMarkers = 50,
                            mappingLevel = 2,