From 02ad30ad4625236a7ad3b0556142118ee4088afc Mon Sep 17 00:00:00 2001
From: oliviaAB <olivia.angelinbonnet@gmail.com>
Date: Wed, 17 Apr 2024 11:53:50 +1200
Subject: [PATCH] Removed here from dependencies, using where() from tidyselect
 and not dplyr

---
 DESCRIPTION              | 3 +--
 NAMESPACE                | 1 -
 NEWS.md                  | 4 ++++
 R/data_import.R          | 5 ++++-
 R/diablo.R               | 2 +-
 R/import_from_packages.R | 2 +-
 R/multidataset_utils.R   | 4 ++--
 R/output_plot.R          | 2 +-
 R/so2pls.R               | 2 +-
 man/diablo_plot_tune.Rd  | 6 +++---
 10 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d50830c..b8a6a7c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: moiraine
 Title: Construction of Reproducible Pipelines for Testing and Comparing Multi-omics Integration Tools
-Version: 1.0.0
+Version: 1.0.0.9000
 Authors@R: 
     c(person("Olivia", "Angelin-Bonnet", 
     email = "O.Angelin-Bonnet@massey.ac.nz",
@@ -30,7 +30,6 @@ Imports:
     ggpubr,
     ggrepel,
     grid,
-    here,
     methods,
     mixOmics,
     MOFA2,
diff --git a/NAMESPACE b/NAMESPACE
index c02e9b0..5d8967b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -177,5 +177,4 @@ importClassesFrom(Biobase,SnpSet)
 importClassesFrom(Biobase,eSet)
 importClassesFrom(MultiDataSet,MultiDataSet)
 importFrom(dplyr,sym)
-importFrom(dplyr,where)
 importFrom(ggplot2,aes)
diff --git a/NEWS.md b/NEWS.md
index aff67b4..2f0aa6f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
 # moiraine (development version)
 
 - In `comparison_heatmap_corr()`, the user can now choose the legend position through the `legend_position` parameter.
+
+- Package here has been removed from dependencies (not needed).
+
+- `where()` function now imported from tidyselect instead of dplyr (as it required a newer version of dplyr).
diff --git a/R/data_import.R b/R/data_import.R
index 22c037a..03e3b72 100644
--- a/R/data_import.R
+++ b/R/data_import.R
@@ -180,7 +180,10 @@ import_fmetadata_gff <- function(file, feature_type, add_fields = NULL) {
       ## become vector
       tibble::as_tibble() |>
       dplyr::mutate(
-        dplyr::across(where(is.list), ~ sapply(.x, paste, collapse = " "))
+        dplyr::across(
+          tidyselect::where(is.list),
+          ~ sapply(.x, paste, collapse = " ")
+        )
       )
 
     .check_names(
diff --git a/R/diablo.R b/R/diablo.R
index 529fafb..af92cf9 100644
--- a/R/diablo.R
+++ b/R/diablo.R
@@ -595,7 +595,7 @@ diablo_table_optim_keepX <- function(tune_res) {
       )
   }) |>
     purrr::reduce(dplyr::bind_rows) |>
-    dplyr::mutate(Total = rowSums(dplyr::across(where(is.numeric))))
+    dplyr::mutate(Total = rowSums(dplyr::across(tidyselect::where(is.numeric))))
 
   return(res)
 }
diff --git a/R/import_from_packages.R b/R/import_from_packages.R
index 499cdb8..3649c1a 100644
--- a/R/import_from_packages.R
+++ b/R/import_from_packages.R
@@ -7,7 +7,7 @@ NULL
 #' @import methods
 NULL
 
-#' @importFrom dplyr sym where
+#' @importFrom dplyr sym
 NULL
 
 #' @importFrom ggplot2 aes
diff --git a/R/multidataset_utils.R b/R/multidataset_utils.R
index 3d0c0d8..7daf686 100644
--- a/R/multidataset_utils.R
+++ b/R/multidataset_utils.R
@@ -238,7 +238,7 @@ join_features_metadata <- function(df, mo_data) {
     dplyr::filter(feature_id %in% df$feature_id) |>
     dplyr::select(
       feature_id,
-      where(~ any(!is.na(.x)))
+      tidyselect::where(~ any(!is.na(.x)))
     )
 
   if (nrow(fmeta) == 0) {
@@ -285,7 +285,7 @@ join_samples_metadata <- function(df, mo_data, datasets = NULL) {
     dplyr::filter(id %in% df$id) |>
     dplyr::select(
       id,
-      where(~ any(!is.na(.x)))
+      tidyselect::where(~ any(!is.na(.x)))
     )
 
   if (nrow(smeta) == 0) {
diff --git a/R/output_plot.R b/R/output_plot.R
index 1293a71..be334f8 100644
--- a/R/output_plot.R
+++ b/R/output_plot.R
@@ -1122,7 +1122,7 @@ plot_features_weight_covariate <- function(method_output,
         ) |>
         dplyr::mutate(
           dplyr::across(
-            .cols = dplyr::where(\(x){!is.numeric(x)}),
+            .cols = tidyselect::where(\(x){!is.numeric(x)}),
             .fns = as.character
           )
         ),
diff --git a/R/so2pls.R b/R/so2pls.R
index a5d8c32..dd8e445 100644
--- a/R/so2pls.R
+++ b/R/so2pls.R
@@ -666,7 +666,7 @@ so2pls_print_cv_sparsity <- function(cv_res_optim) {
       names_from = joint_component,
       values_from = n_features
     ) |>
-    dplyr::mutate(Total = rowSums(dplyr::across(where(is.numeric))))
+    dplyr::mutate(Total = rowSums(dplyr::across(tidyselect::where(is.numeric))))
 }
 
 #' Plot sparsity cross-validation results for sO2PLS
diff --git a/man/diablo_plot_tune.Rd b/man/diablo_plot_tune.Rd
index 85fcade..237f2aa 100644
--- a/man/diablo_plot_tune.Rd
+++ b/man/diablo_plot_tune.Rd
@@ -7,12 +7,12 @@
 diablo_plot_tune(tune_res)
 }
 \arguments{
-\item{tune_res}{The cross-validation results, computed with \code{\link{diablo_tune}}.}
+\item{tune_res}{The cross-validation results, computed with \code{\link[=diablo_tune]{diablo_tune()}}.}
 }
 \value{
 A \code{ggplot2} object.
 }
 \description{
-Displays the error rate of a DIABLO run cross-validation to estimate the optimal number of features to retain from
-each dataset (\code{keepX}).
+Displays the error rate of a DIABLO run cross-validation to estimate the
+optimal number of features to retain from each dataset (\code{keepX}).
 }