Merge pull request #71 from noriakis/update-documentation

Documentation revision
stemangiola · Aug 25, 2023 · 4c7cde6 · 4c7cde6
2 parents 32381c7 + 7effd27
commit 4c7cde6
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Showing 57 changed files with 4,961 additions and 3,919 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -38,64 +38,30 @@ S3method(slice_min,Seurat)
 S3method(slice_sample,Seurat)
 S3method(slice_tail,Seurat)
 S3method(summarise,Seurat)
+S3method(summarize,Seurat)
 S3method(tbl_format_header,tidySeurat)
 S3method(tidy,Seurat)
 S3method(unite,Seurat)
 S3method(unnest,tidyseurat_nested)
 export("%>%")
-export()
-export(add_count)
-export(arrange)
-export(as_tibble)
-export(bind_rows)
-export(count)
-export(distinct)
-export(extract)
-export(filter)
-export(full_join)
 export(get_abundance_sc_long)
 export(get_abundance_sc_wide)
-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(slice_head)
-export(slice_max)
-export(slice_min)
-export(slice_sample)
-export(slice_tail)
-export(summarise)
-export(tbl_format_header)
 export(tidy)
-export(unite)
-export(unnest)
 export(unnest_seurat)
 exportMethods(aggregate_cells)
+exportMethods(join_features)
 importFrom(Matrix,rowSums)
 importFrom(Seurat,Assays)
 importFrom(Seurat,GetAssayData)
 importFrom(Seurat,SplitObject)
 importFrom(Seurat,VariableFeatures)
 importFrom(SeuratObject,"DefaultAssay<-")
-importFrom(cli,cat_line)
+importFrom(SeuratObject,DefaultAssay)
 importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
+importFrom(dplyr,contains)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
@@ -122,6 +88,7 @@ importFrom(dplyr,slice_min)
 importFrom(dplyr,slice_sample)
 importFrom(dplyr,slice_tail)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_used)
 importFrom(fansi,strwrap_ctl)
@@ -152,15 +119,13 @@ 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_name)
 importFrom(rlang,quo_squash)
 importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
-importFrom(stringr,str_replace)
 importFrom(tibble,as_tibble)
 importFrom(tibble,column_to_rownames)
 importFrom(tibble,enframe)
@@ -173,6 +138,7 @@ importFrom(tidyr,separate)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
+importFrom(tidyselect,eval_select)
 importFrom(ttservice,aggregate_cells)
 importFrom(ttservice,bind_cols)
 importFrom(ttservice,bind_rows)

diff --git a/R/attach.R b/R/attach.R
@@ -0,0 +1,23 @@
+core <- c("dplyr", "tidyr", "ttservice", "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)
+}
diff --git a/R/data.R b/R/data.R
@@ -1,9 +1,41 @@
-#' 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)
+#' @return `tibble`
 "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 within 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)
+#' @return `tibble`
 "pbmc_small_nested_interactions"