Merge pull request #9 from stemangiola/comply-Bioconductor

Comply bioconductor

Author: stemangiola

DESCRIPTION

@@ -1,14 +1,11 @@
 Type: Package
 Package: tidySCE
-Title: 'Brings SingleCellExperiment to the Tidyverse 
+Title: Brings SingleCellExperiment to the Tidyverse 
 Version: 0.99.0
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")) )
-Description: tidySCE creates an invisible layer that enables using the 
-    Bioconductor 'SingleCellExperiment' object as a tibble and interacting 
-    seamlessly with the tidyverse. Tidyverse packages such as dplyr, tidyr, 
-    ggplot and plotly can all be used with the tidy SingleCellExperiment object.
-    This allows users to get the best of both Bioconductor and tidyverse worlds.
+Description: tidySCE is an adapter that abstracts the 'SingleCellExperiment' container 
+    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse' 
 License: GPL-3
 Depends:
     R (>= 4.0.0),
@@ -24,10 +21,10 @@ Imports:
     lifecycle,
     methods,
     plotly,
-    ellipsis,
-    tidyselect,
     utils,
-    S4Vectors
+    S4Vectors,
+    tidyselect,
+    ellipsis
 Suggests:
     BiocStyle,
     testthat,

NAMESPACE

@@ -18,7 +18,7 @@ S3method(filter,default)
 S3method(filter,tidySCE)
 S3method(full_join,default)
 S3method(full_join,tidySCE)
-S3method(ggplot,default)
+S3method(ggplot,tbl_df)
 S3method(ggplot,tidySCE)
 S3method(group_by,default)
 S3method(group_by,tidySCE)
@@ -95,12 +95,15 @@ export(unite)
 export(unnest)
 import(SingleCellExperiment)
 importFrom(S4Vectors,DataFrame)
+importFrom(SingleCellExperiment,colData)
 importFrom(dplyr,count)
 importFrom(dplyr,group_by_drop_default)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
 importFrom(dplyr,select)
 importFrom(dplyr,select_if)
+importFrom(ellipsis,check_dots_unnamed)
+importFrom(ellipsis,check_dots_used)
 importFrom(ggplot2,aes)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
@@ -128,4 +131,5 @@ importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,spread)
 importFrom(tidyr,unnest)
+importFrom(tidyselect,eval_select)
 importFrom(utils,tail)

R/data.R

@@ -1,14 +1,46 @@
-#' Example data set
+#' pbmc_small
 #'
+#' PBMC single cell RNA-seq data in SingleCellExperiment format
 #'
+#' @format  A SingleCellExperiment object containing 80 Peripheral Blood 
+#'          Mononuclear Cells (PBMC) from 10x Genomics. Generated by subsampling the PBMC dataset of 2,700 single cells.
+#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
+#' @usage data(pbmc_small)
 "pbmc_small"
 
-#' Example data set 2
-#'
+#' Cell types of 80 PBMC single cells
+#' 
+#' A dataset containing the barcodes and cell types of 80 PBMC single cells.
 #'
+#' @format  A tibble containing 80 rows and 2 columns. Cells are a subsample of 
+#'          the Peripheral Blood Mononuclear Cells (PBMC) dataset of 2,700 single 
+#'          cell. Cell types were identified with SingleR.
+#' \describe{
+#'   \item{cell}{cell identifier, barcode}
+#'   \item{first.labels}{cell type}
+#' }
+#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
+#' @usage data(cell_type_df)
 "cell_type_df"
 
-#' Example data set 2
+#' Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.
 #'
+#' A dataset containing ligand-receptor interactions withibn a sample. There are 38 ligands from a single cell cluster versus 
+#' 35 receptors in 6 other clusters.
 #'
+#' @format  A tibble containing 100 rows and 9 columns. Cells are a subsample of 
+#'         the PBMC dataset of 2,700 single cells. Cell interactions were identified with SingleCellSignalR.
+#' \describe{
+#'   \item{sample}{sample identifier}
+#'   \item{ligand}{cluster and ligand identifier}
+#'   \item{receptor}{cluster and receptor identifier}
+#'   \item{ligand.name}{ligand name}
+#'   \item{receptor.name}{receptor name}
+#'   \item{origin}{cluster containing ligand}
+#'   \item{destination}{cluster containing receptor}
+#'   \item{interaction.type}{type of interation, paracrine or autocrine}
+#'   \item{LRscore}{interaction score}
+#' }
+#' @source \url{https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html}
+#' @usage data(pbmc_small_nested_interactions)
 "pbmc_small_nested_interactions"