method documentation & vignette revision

DESCRIPTION

@@ -1,11 +1,19 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.11.3
-Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
-                  role = c("aut", "cre")) )
-Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of a tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
+Version: 1.11.4
+Authors@R: c(person("Stefano", "Mangiola", 
+    email="[email protected]",
+    role=c("aut", "cre")))
+Description: 'tidySingleCellExperiment' is an adapter that abstracts
+    the 'SingleCellExperiment' container in the form of a 'tibble'.
+    This allows *tidy* data manipulation, nesting, and plotting.
+    For example, a 'tidySingleCellExperiment' is directly compatible
+    with functions from 'tidyverse' packages `dplyr` and `tidyr`,
+    as well as plotting with `ggplot2` and `plotly`.
+    In addition, the package provides various utility
+    functions specific to single-cell omics data analysis
+    (e.g., aggregation of cell-level data to pseudobulks).
 License: GPL-3
 Depends:
     R (>= 4.1.0),
@@ -38,7 +46,7 @@ Suggests:
     BiocStyle,
     testthat,
     knitr,
-    markdown,
+    rmarkdown,
     SingleCellSignalR,
     SingleR,
     scater,
@@ -58,6 +66,5 @@ biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
-Roxygen: list(markdown = TRUE)
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues

NAMESPACE

@@ -33,59 +33,29 @@ S3method(select,SingleCellExperiment)
 S3method(separate,SingleCellExperiment)
 S3method(slice,SingleCellExperiment)
 S3method(summarise,SingleCellExperiment)
+S3method(summarize,SingleCellExperiment)
 S3method(tbl_format_header,tidySingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
 S3method(unite,SingleCellExperiment)
 S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
-export(add_count)
-export(aggregate_cells)
-export(arrange)
 export(as_tibble)
-export(bind_cols)
-export(bind_rows)
-export(count)
-export(distinct)
-export(extract)
-export(filter)
-export(full_join)
 export(ggplot)
 export(glimpse)
-export(group_by)
-export(inner_join)
-export(join_features)
 export(join_transcripts)
-export(left_join)
-export(mutate)
-export(nest)
-export(pivot_longer)
 export(plot_ly)
-export(pull)
-export(rename)
-export(right_join)
-export(rowwise)
-export(sample_frac)
-export(sample_n)
-export(select)
-export(separate)
-export(slice)
-export(summarise)
-export(summarize)
-export(tbl_format_header)
 export(tidy)
-export(unite)
-export(unnest)
 export(unnest_single_cell_experiment)
+exportMethods(aggregate_cells)
+exportMethods(join_features)
 importFrom(Matrix,rowSums)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,cbind)
-importFrom(SingleCellExperiment,counts)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
-importFrom(cli,cat_line)
 importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
 importFrom(dplyr,contains)
@@ -110,6 +80,7 @@ importFrom(dplyr,select)
 importFrom(dplyr,select_if)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_unnamed)
 importFrom(ellipsis,check_dots_used)
@@ -121,7 +92,6 @@ importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
-importFrom(methods,as)
 importFrom(methods,getMethod)
 importFrom(pillar,align)
 importFrom(pillar,get_extent)
@@ -141,7 +111,6 @@ importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,expr)
 importFrom(rlang,flatten_if)
-importFrom(rlang,is_empty)
 importFrom(rlang,is_spliced)
 importFrom(rlang,names2)
 importFrom(rlang,quo_is_null)
@@ -152,7 +121,6 @@ importFrom(rlang,quo_squash)
 importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
-importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
@@ -170,5 +138,6 @@ importFrom(ttservice,bind_cols)
 importFrom(ttservice,bind_rows)
 importFrom(ttservice,join_features)
 importFrom(utils,data)
+importFrom(utils,packageDescription)
 importFrom(utils,tail)
 importFrom(vctrs,new_data_frame)

R/attach.R

@@ -0,0 +1,24 @@
+# [HLC:] 'ttservice' required for 'bind_cols/rows', and
+# needs to come before 'dplyr' to assure correct import
+core <- c("dplyr", "tidyr", "ggplot2")
+
+core_unloaded <- function() {
+  search <- paste0("package:", core)
+  core[!search %in% search()]
+}
+
+# Attach the package from the same library it was loaded from before.
+# [source: https://github.com/tidy-biology/tidyverse/issues/171]
+same_library <- function(pkg) {
+  loc <- if (pkg %in% loadedNamespaces()) dirname(getNamespaceInfo(pkg, "path"))
+  library(pkg, lib.loc=loc, character.only=TRUE, warn.conflicts=FALSE)
+}
+
+tidyverse_attach <- function() {
+  to_load <- core_unloaded()
+
+  suppressPackageStartupMessages(
+    lapply(to_load, same_library))
+
+  invisible(to_load)
+}