Modify import statements for dplyr and tidyr, enhance documentation links, and refine example code in the introduction vignette for clarity and uniqueness.

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.19.2
+Version: 1.19.3
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="[email protected]",
@@ -71,6 +71,6 @@ biocViews:
     AssayDomain, Infrastructure, RNASeq, DifferentialExpression, SingleCell,
     GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues

NAMESPACE

@@ -83,6 +83,7 @@ importFrom(dplyr,group_split)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,right_join)

R/dplyr_methods.R

@@ -198,7 +198,7 @@ filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
 #' @name group_by
 #' @rdname group_by
 #' @inherit dplyr::group_by
-#' @seealso \code{}
+#' @seealso \code{\link[dplyr]{group_by}}
 #'
 #' @examples
 #' data(pbmc_small)

R/methods.R

@@ -157,7 +157,7 @@ tidy.SingleCellExperiment <- function(object) {
 #' @importFrom dplyr mutate
 #' @importFrom dplyr pull
 #' @importFrom dplyr left_join
-#' @importFrom dplyr unnest
+#' @importFrom tidyr unnest
 #' @importFrom S4Vectors DataFrame
 #' @importFrom methods as
 #'
@@ -170,6 +170,9 @@ setMethod("aggregate_cells", "SingleCellExperiment", function(.data,
 
     # Fix NOTEs
     feature <- NULL
+    .feature <- NULL
+    my_id_to_split_by___ <- NULL
+    assay_name <- NULL
     .sample <- enquo(.sample)
 
     # Subset only wanted assays

R/tidyr_methods.R

@@ -93,6 +93,7 @@ unnest_single_cell_experiment  <-  function(data, cols, ...,
 #' @importFrom tidyr nest
 #' @importFrom rlang enquos
 #' @importFrom rlang :=
+#' @importFrom dplyr n
 #' @export
 nest.SingleCellExperiment <- function(.data, ..., .names_sep = NULL) {
 

man/group_by.Rd

@@ -184,7 +184,7 @@ Here we plot abundance of two features for each group.
 
 ```{r}
 pbmc_small_polished %>%
-    join_features(features=c("HLA-DRA", "LYZ")) %>%
+    join_features(features=c("HLA-DRA", "LYZ"), shape="long") %>%
     ggplot(aes(groups, .abundance_counts + 1, fill=groups)) +
     geom_boxplot(outlier.shape=NA) +
     geom_jitter(aes(size=nCount_RNA), alpha=0.5, width=0.2) +
@@ -267,11 +267,12 @@ marker_genes <-
     map(~ .x %>%
         head(10) %>%
         rownames()) %>%
-    unlist()
+    unlist() %>%
+    unique()
 
 # Plot heatmap
 pbmc_small_cluster %>%
-    join_features(features=marker_genes) %>%
+    join_features(features=marker_genes, shape="long") %>%
     group_by(label) %>%
     heatmap(
         .row=.feature, .column=.cell,