ascend version 0.9.9

Author: asenabouth

DESCRIPTION

@@ -28,18 +28,19 @@ Imports: utils,
     MASS,
     GenomeInfoDb,
     GenomeInfoDbData,
-    BiocGenerics
-Suggests: umap,
+    BiocGenerics,
+    umap,
+    Rtsne,
+    irlba,
+    fastcluster
+Suggests: 
     scater,
     scran,
     Seurat,
     scone,
     devtools,
-    Rtsne,
-    irlba,
     knitr,
     locfit,    
-    fastcluster,
     rmarkdown,
     testthat,
     KernSmooth,

NAMESPACE

@@ -107,6 +107,7 @@ importFrom(dplyr,intersect)
 importFrom(dplyr,left_join)
 importFrom(dplyr,semi_join)
 importFrom(dynamicTreeCut,cutreeDynamic)
+importFrom(fastcluster,hclust)
 importFrom(fields,interp.surface)
 importFrom(ggbeeswarm,geom_quasirandom)
 importFrom(ggplot2,aes)
@@ -133,6 +134,7 @@ importFrom(ggplot2,ylab)
 importFrom(graphics,legend)
 importFrom(graphics,smoothScatter)
 importFrom(gridExtra,grid.arrange)
+importFrom(irlba,prcomp_irlba)
 importFrom(methods,is)
 importFrom(reshape2,melt)
 importFrom(stats,as.dendrogram)
@@ -147,3 +149,4 @@ importFrom(stats,p.adjust)
 importFrom(stats,reorder)
 importFrom(stats,setNames)
 importFrom(tidyr,gather)
+importFrom(umap,umap)

R/ascend_clustering.R

@@ -347,6 +347,7 @@ retrieveCluster <- function(x, hclust_obj = NULL, distance_matrix = NULL){
 #' @include ascend_objects.R
 #' @include ascend_dimreduction.R
 #' @importFrom stats dist setNames
+#' @importFrom fastcluster hclust
 #' @importFrom dynamicTreeCut cutreeDynamic
 #' @importFrom BiocParallel bplapply
 #' @export
@@ -383,7 +384,7 @@ setMethod("runCORE", signature("EMSet"), function(object,
     remove.outliers = FALSE
   }
 
-  if (!("PCA" %in% reducedDimNames(object))){
+  if (!("PCA" %in% SingleCellExperiment::reducedDimNames(object))){
     stop("Please calculate PCA values using runPCA before using this function.")
   }
 

R/ascend_dimreduction.R

@@ -16,6 +16,7 @@
 #' @param ... Additional arguments to pass to the UMAP function
 #' @return UMAP matrix stored in "UMAP" slot in reducedDims
 #' 
+#' @importFrom umap umap
 #' @importFrom SummarizedExperiment assayNames
 #' @export
 setGeneric("runUMAP", def = function(object, ..., method, config){
@@ -164,6 +165,8 @@ calcVariance <- function(x, axis = c("row", "column")){
 #' @return An \linkS4class{EMSet} with a PCA-reduced matrix stored in the PCA
 #' slot.
 #' @include ascend_objects.R
+#' 
+#' @importFrom irlba prcomp_irlba
 #' @importFrom SingleCellExperiment normcounts reducedDim
 #' @export
 setGeneric("runPCA", def = function(object, ..., ngenes, scaling) {

R/ascend_plots.R

@@ -738,8 +738,7 @@ plotMDS <- function(object, Dim1 = 1, Dim2 = 2, group = NULL, density = FALSE, P
 #' EMSet <- runUMAP(EMSet, method = "naive", config = umap.config)
 #' 
 #' # Plot with t-SNE 
-#' tsne_plot <- plotUMAP(EMSet, Dim1 = 1, Dim2 = 2, group = "cluster", density = FALSE)
-#' 
+#' umap_plot <- plotUMAP(EMSet, Dim1 = 1, Dim2 = 2, group = "cluster", density = FALSE)
 #' }
 #' @importFrom ggplot2 ggplot aes geom_point labs ggtitle scale_alpha theme_bw
 #' @export