simplify man 2

stemangiola · Jun 7, 2020 · 50c7b6c · 50c7b6c
1 parent 4fd84ee
commit 50c7b6c
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Showing 24 changed files with 65 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,7 +20,6 @@ LazyData: true
 RoxygenNote: 7.1.0
 Imports: 
     lifecycle,
-    ggplot2,
     magrittr,
     tibble,
     dplyr,
@@ -42,7 +41,7 @@ Suggests:
     Seurat,
     limma,
     GGally,
-    tidyverse
+    ggplot2
 VignetteBuilder: 
     knitr
 Biarch: true

diff --git a/R/data.R b/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"

diff --git a/R/utilities.R b/R/utilities.R
@@ -7,6 +7,8 @@ my_stop = function() {
 }
 
 #' This is a generalisation of ifelse that acceots an object and return an objects
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -28,7 +30,9 @@ ifelse_pipe = function(.x, .p, .f1, .f2 = NULL) {
 
 }
 
-#' This is a generalisation of ifelse that acceots an object and return an objects
+#' This is a generalisation of ifelse that accepts an object and return an objects
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -64,6 +68,8 @@ ifelse2_pipe = function(.x, .p1, .p2, .f1, .f2, .f3 = NULL) {
 }
 
 #' Sub function of remove_redundancy_elements_though_reduced_dimensions
+#' 
+#' @keywords internal
 #'
 #' @importFrom stats dist
 #' @importFrom utils head
@@ -98,6 +104,8 @@ select_closest_pairs = function(df) {
 }
 
 #' get_x_y_annotation_columns
+#' 
+#' @keywords internal
 #'
 #' @importFrom magrittr equals
 #'
@@ -277,6 +285,8 @@ drop_internals = function(.data){
 }
 
 #' Add attribute to abject
+#' 
+#' @keywords internal
 #'
 #'
 #' @param var A tibble
@@ -290,6 +300,8 @@ add_attr = function(var, attribute, name) {
 }
 
 #' Drop attribute to abject
+#' 
+#' @keywords internal
 #'
 #'
 #' @param var A tibble
@@ -302,6 +314,8 @@ drop_attr = function(var, name) {
 }
 
 #' Convert array of quosure (e.g. c(col_a, col_b)) into character vector
+#' 
+#' @keywords internal
 #'
 #' @importFrom rlang quo_name
 #' @importFrom rlang quo_squash
@@ -327,6 +341,8 @@ rotation = function(m, d) {
 }
 
 #' .formula parser
+#' 
+#' @keywords internal
 #'
 #' @importFrom stats terms
 #'
@@ -342,6 +358,8 @@ parse_formula <- function(fm) {
 }
 
 #' Remove class to abject
+#' 
+#' @keywords internal
 #'
 #'
 #' @param var A tibble

diff --git a/R/validation.R b/R/validation.R
@@ -1,4 +1,6 @@
 #' Check whether there are NA counts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -23,6 +25,8 @@ error_if_counts_is_na = function(.data, .abundance) {
 
 
 #' Check whether a numeric vector has been log transformed
+#' 
+#' @keywords internal
 #'
 #' @param x A numeric vector
 #' @param .abundance A character name of the transcript/gene abundance column
@@ -43,6 +47,8 @@ error_if_log_transformed <- function(x, .abundance) {
 }
 
 #' Check whether there are duplicated genes/transcripts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -95,6 +101,8 @@ error_if_duplicated_genes <- function(.data,
 
 
 #' Check whether there are NA counts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -128,6 +136,8 @@ error_if_wrong_input = function(.data, list_input, expected_type) {
 }
 
 #' Check whether there are NA counts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -155,6 +165,8 @@ check_if_wrong_input = function(.data, list_input, expected_type) {
 }
 
 #' Check whether there are duplicated genes/transcripts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr
@@ -209,6 +221,8 @@ check_if_duplicated_genes <- function(.data,
 }
 
 #' Check whether there are NA counts
+#' 
+#' @keywords internal
 #'
 #' @import dplyr
 #' @import tidyr

diff --git a/man/add_attr.Rd b/man/add_attr.Rd
diff --git a/man/check_if_counts_is_na.Rd b/man/check_if_counts_is_na.Rd
diff --git a/man/check_if_duplicated_genes.Rd b/man/check_if_duplicated_genes.Rd
diff --git a/man/check_if_wrong_input.Rd b/man/check_if_wrong_input.Rd
diff --git a/man/drop_attr.Rd b/man/drop_attr.Rd
diff --git a/man/drop_class.Rd b/man/drop_class.Rd
diff --git a/man/error_if_counts_is_na.Rd b/man/error_if_counts_is_na.Rd
diff --git a/man/error_if_duplicated_genes.Rd b/man/error_if_duplicated_genes.Rd
diff --git a/man/error_if_log_transformed.Rd b/man/error_if_log_transformed.Rd
diff --git a/man/error_if_wrong_input.Rd b/man/error_if_wrong_input.Rd
diff --git a/man/get_x_y_annotation_columns.Rd b/man/get_x_y_annotation_columns.Rd
diff --git a/man/ifelse2_pipe.Rd b/man/ifelse2_pipe.Rd
diff --git a/man/ifelse_pipe.Rd b/man/ifelse_pipe.Rd
diff --git a/man/mtcars_tidy.Rd b/man/mtcars_tidy.Rd
diff --git a/man/parse_formula.Rd b/man/parse_formula.Rd
diff --git a/man/quo_names.Rd b/man/quo_names.Rd
diff --git a/man/select_closest_pairs.Rd b/man/select_closest_pairs.Rd
diff --git a/man/test_data.Rd b/man/test_data.Rd
diff --git a/man/test_data2.Rd b/man/test_data2.Rd
diff --git a/vignettes/introdution.Rmd b/vignettes/introdution.Rmd
@@ -62,7 +62,10 @@ library(knitr)
 knitr::opts_chunk$set(cache = TRUE, warning = FALSE,
                       message = FALSE, cache.lazy = FALSE)
 
-library(tidyverse)
+library(dplyr)
+library(tidyr)
+library(ggplot2)
+library(purrr)
 library(magrittr)
 library(nanny)