Fix namespace issue with objects created onLoad. (#39)

* Export `cell_type_map` from namespace.

* Use assignInNamespace

* Restore Makefile

* Fix roxygen object names

* Add missing title in roxygen output

DESCRIPTION

@@ -28,7 +28,8 @@ Imports:
     sva,
     GSEABase,
     xCell,
-    MCPcounter
+    MCPcounter,
+    utils
 Suggests:
     testthat,
     knitr,
@@ -47,4 +48,4 @@ Roxygen: list(markdown = TRUE)
 LazyData: true
 URL: https://icbi-lab.github.io/immunedeconv, https://github.com/icbi-lab/immunedeconv
 BugReports: https://github.com/icbi-lab/immunedeconv/issues
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(available_datasets)
+export(cell_type_map)
+export(cell_type_tree)
 export(deconvolute)
 export(deconvolute_cibersort)
 export(deconvolute_epic)
@@ -35,3 +38,4 @@ importFrom(stats,na.omit)
 importFrom(testit,assert)
 importFrom(tibble,as_tibble)
 importFrom(tibble,rowid_to_column)
+importFrom(utils,assignInMyNamespace)

R/cell_type_mapping.R

@@ -6,19 +6,18 @@
 #' @importFrom dplyr select
 #' @importFrom stats na.omit
 #' @import magrittr
-#'
+#' 
 #' @name cell_type_mapping
 NULL
 
-
 #' Table mapping the cell types from methods/datasets to a single, controlled vocabulary.
 #'
 #' Columns: `method_dataset`, `method_cell_type`, `cell_type`.
 #'
 #' See `inst/extdata/cell_type_mapping.xlsx` for more details.
 #'
-#' @name cell_type_map
-NULL
+#' @export
+cell_type_map = NULL
 # gets attached on .onLoad, see zzz.R
 .get_cell_type_map = function() {
   readxl::read_xlsx(system.file("extdata", "cell_type_mapping.xlsx",
@@ -34,14 +33,16 @@ NULL
 #' A list of all methods (e.g. `cibersort`) and datasets (e.g. `schelker_ovarian`) for
 #' that the cell types are mapped to the controlled vocabulary.
 #'
-#' @name available_datasets
-NULL
+#' @export
+available_datasets = NULL
 # gets attached on .onLoad, see zzz.R
 .get_available_datasets = function() {
   cell_type_map %>% pull(method_dataset) %>% unique()
 }
 
 
+#' List with controlled cell-type vocabulary
+cell_type_list = NULL
 .get_cell_type_list = function() {
   tmp_list = readxl::read_excel(system.file("extdata", "cell_type_mapping.xlsx",
                                             package="immunedeconv", mustWork=TRUE),
@@ -57,14 +58,19 @@ NULL
 #'
 #' @details a `data.tree` object
 #' @name cell_type_tree
-NULL
+#' @export
+cell_type_tree = NULL
 # gets attached on .onLoad, see zzz.R
 .get_cell_type_tree = function() {
   cell_type_list %>% as.data.frame() %>% data.tree::FromDataFrameNetwork()
 }
 
 
-# Access nodes by name in O(1). Node names are unique in our tree.
+#' Lookup dictionary for cell-type nodes
+#' 
+#' Access nodes by name in O(1). Node names are unique in our tree.
+#' gets attached on .onLoad, see zzz.R
+node_by_name=NULL
 # gets attached on .onLoad, see zzz.R
 .get_node_by_name = function() {
   cell_type_tree$Get(function(node){node})

R/immune_deconvolution_methods.R

@@ -1,5 +1,7 @@
 #' Collection of immune cell deconvolution methods.
-#'
+#' 
+#' @description Immunedeconv is an an R package for unified access to computational methods for
+#'  estimating immune cell fractions from bulk RNA sequencing data. 
 #' @docType package
 #' @name immunedeconv
 #' @import methods

R/zzz.R

@@ -1,14 +1,17 @@
-# assign the following global variables
-# .onLoad because of 'staged-install'
-#
-# See https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
-# for more details.
-#
+#' assign the following global variables
+#' .onLoad because of 'staged-install'
+#'
+#' See https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
+#' for more details.
+#' 
+#' @name fix_namespace
+#' @importFrom utils assignInMyNamespace
+NULL
 
 .onLoad = function(libname, pkgname) {
-  assign('cell_type_map', .get_cell_type_map(), envir=.GlobalEnv)
-  assign('available_datasets', .get_available_datasets(), envir=.GlobalEnv)
-  assign('cell_type_list', .get_cell_type_list(), envir=.GlobalEnv)
-  assign('cell_type_tree', .get_cell_type_tree(), envir=.GlobalEnv)
-  assign('node_by_name', .get_node_by_name(), envir=.GlobalEnv)
+  assignInMyNamespace('cell_type_map', .get_cell_type_map())
+  assignInMyNamespace('available_datasets', .get_available_datasets())
+  assignInMyNamespace('cell_type_list', .get_cell_type_list())
+  assignInMyNamespace('cell_type_tree', .get_cell_type_tree())
+  assignInMyNamespace('node_by_name', .get_node_by_name())
 }