Merge branch 'master' of https://github.com/stemangiola/nanny

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nanny
 Type: Package
 Title: High-Level Data Analysis and Manipulation in 'tidyverse' Style
-Version: 0.1.5
+Version: 0.1.6
 Authors@R: 
     person(given = "Stefano",
            family = "Mangiola",
@@ -20,10 +20,10 @@ LazyData: true
 RoxygenNote: 7.1.0
 Imports: 
     lifecycle,
-    ggplot2,
     magrittr,
     tibble,
     dplyr,
+    tidyselect,
     purrr,
     rlang,
     tidyr,
@@ -33,15 +33,15 @@ Imports:
     utils,
     knitr,
     widyr,
-    Rtsne
+    Rtsne,
+    gtools
 RdMacros: lifecycle
 Suggests: 
     testthat,
     Seurat,
-    gtools,
     limma,
     GGally,
-    tidyverse
+    ggplot2
 VignetteBuilder: 
     knitr
 Biarch: true

NAMESPACE

@@ -7,6 +7,7 @@ export(fill_missing)
 export(impute_missing)
 export(keep_variable)
 export(lower_triangular)
+export(nest_subset)
 export(permute_nest)
 export(reduce_dimensions)
 export(remove_redundancy)
@@ -16,12 +17,15 @@ import(dplyr)
 import(tibble)
 import(tidyr)
 importFrom(Rtsne,Rtsne)
+importFrom(gtools,combinations)
+importFrom(gtools,permutations)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,`%$%`)
 importFrom(magrittr,equals)
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,as_mapper)
+importFrom(purrr,imap)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dfr)
@@ -35,13 +39,16 @@ importFrom(rlang,quo_is_symbol)
 importFrom(rlang,quo_is_symbolic)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(rlang,set_names)
 importFrom(stats,as.formula)
 importFrom(stats,dist)
 importFrom(stats,kmeans)
 importFrom(stats,model.matrix)
 importFrom(stats,prcomp)
 importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(tidyr,nest)
+importFrom(tidyselect,eval_select)
 importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(widyr,pairwise_cor)

R/data.R

@@ -1,14 +1,20 @@
 #' Example data set
+#' 
+#' @keywords internal
 #'
 #'
 "test_data"
 
 #' Example data set reduced
+#' 
+#' @keywords internal
 #'
 #'
 "test_data2"
 
 #' Cibersort reference
+#' 
+#' @keywords internal
 #'
 #'
 "mtcars_tidy"

R/functions.R

@@ -1,4 +1,6 @@
 #' Get K-mean clusters to a tibble
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -86,6 +88,8 @@ get_clusters_kmeans_bulk <-
 	}
 
 #' Get SNN shared nearest neighbour clusters to a tibble
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -177,6 +181,8 @@ get_clusters_SNN_bulk <-
 	}
 
 #' Get dimensionality information to a tibble using MDS
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -275,6 +281,8 @@ get_reduced_dimensions_MDS_bulk <-
 	}
 
 #' Get principal component information to a tibble using PCA
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -434,6 +442,8 @@ get_reduced_dimensions_PCA_bulk <-
 	}
 
 #' Get principal component information to a tibble using tSNE
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -553,6 +563,8 @@ get_reduced_dimensions_TSNE_bulk <-
 	}
 
 #' Get rotated dimensions of two principal components or MDS dimension of choice, of an angle
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -640,6 +652,8 @@ get_rotated_dimensions =
 	}
 
 #' Drop redundant elements (e.g., elements) for which feature (e.g., genes) aboundances are correlated
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -769,6 +783,8 @@ remove_redundancy_elements_through_correlation <- function(.data,
 }
 
 #' Identifies the closest pairs in a MDS contaxt and return one of them
+#' 
+#' @keywords internal
 #'
 #' @importFrom stats setNames
 #' @importFrom stats dist
@@ -847,6 +863,8 @@ remove_redundancy_elements_though_reduced_dimensions <-
 
 
 #' This function is needed for DE in case the matrix is not rectangular, but includes NA
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -968,6 +986,8 @@ fill_NA_using_formula = function(.data,
 }
 
 #' This function is needed for DE in case the matrix is not rectangular, but includes NA
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr