update R CMD Check badge

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MetAlyzer
 Type: Package
 Title: Read and Analyze 'MetIDQ™' Software Output Files
-Version: 0.2.0
+Version: 1.0.0
 Authors@R: 
     c(person("Nils", "Mechtel",
             email = "[email protected]",
@@ -28,6 +28,8 @@ Imports:
     stringr,
     utils,
     rlang,
+    ggplot2,
+    ggrepel,
     SummarizedExperiment,
     S4Vectors,
     BiocManager,

NAMESPACE

@@ -1,15 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
 export(MetAlyzer_dataset)
+export(calc_CV)
+export(calculate_log2FC)
 export(exportConcValues)
 export(extraction_data)
 export(filterMetaData)
 export(filterMetabolites)
+export(impute_data)
 export(pathway)
+export(plot_log2FC)
 export(polarity)
+export(read_named_region)
 export(renameMetaData)
 export(summarizeConcValues)
 export(summarizeQuantData)
+export(transform_data)
 export(treatment_data)
 export(updateMetaData)
+import(SummarizedExperiment)
 import(dplyr)
+import(ggplot2)
+import(ggrepel)
+importFrom(rlang,.data)
+importFrom(stats,lm)
+importFrom(utils,install.packages)
+importFrom(utils,installed.packages)

R/calculate_log2FC.R

@@ -12,6 +12,7 @@
 #' @return A data frame containing the log2 fold change for each metabolite
 #'
 #' @import dplyr
+#' @import SummarizedExperiment
 #' @importFrom utils install.packages
 #' @importFrom utils installed.packages
 #' @importFrom rlang .data
@@ -27,7 +28,7 @@ calculate_log2FC <- function(metalyzer_se, categorical, perc_of_min = 0.2, imput
                              installation_type = "binary") {
   metalyzer_se <- impute_data(metalyzer_se, perc_of_min, impute_NA)
   metalyzer_se <- transform_data(metalyzer_se)
-  aggregated_data <- metadata(metalyzer_se)$aggregated_data
+  aggregated_data <- metalyzer_se@metadata$aggregated_data
   meta_data <- colData(metalyzer_se)
   cat_str <- deparse(substitute(categorical))
 
@@ -39,7 +40,7 @@ calculate_log2FC <- function(metalyzer_se, categorical, perc_of_min = 0.2, imput
                                }),
   levels = unique(mapping_vec)), .after = ID)
 
-  metadata(metalyzer_se)$aggregated_data <- aggregated_data
+  metalyzer_se@metadata$aggregated_data <- aggregated_data
   ## Check for qvalue and BiocManager installation
   installed_packages <- utils::installed.packages()[, "Package"]
   if (! "qvalue" %in% installed_packages) {

R/impute_data.R

@@ -36,7 +36,7 @@ impute_data <- function(
     perc_of_min,
     impute_NA
   ) {
-  aggregated_data <- metadata(metalyzer_se)$aggregated_data
+  aggregated_data <- metalyzer_se@metadata$aggregated_data
   cat("Impute concentrations (groupwise: Metabolite) with",
       paste0(round(perc_of_min * 100), "%"),
       "of the minimal positive value...  ")
@@ -48,7 +48,7 @@ impute_data <- function(
       Concentration, perc_of_min, impute_NA),
            .after = Concentration) %>%
     group_by_at(grouping_vars)
-  metadata(metalyzer_se)$aggregated_data <- aggregated_data
+  metalyzer_se@metadata$aggregated_data <- aggregated_data
   cat("finished!\n")
   return(metalyzer_se)
 }

R/plot_network.R

@@ -1,4 +1,4 @@
-#' @title Plot Pathway Network
+#' Plot Pathway Network
 #'
 #' @description This function plots the log2 fold change for each metabolite and visualizes it, in a pathway network.
 #'

R/transform_data.R

@@ -24,10 +24,10 @@ transform <- function(vec, func) {
 #' @return An updated aggregated_data tibble data frame
 #' @export
 transform_data <- function(metalyzer_se) {
-  aggregated_data <- metadata(metalyzer_se)$aggregated_data
+  aggregated_data <- metalyzer_se@metadata$aggregated_data
   aggregated_data <- mutate(aggregated_data,
                             log2_Conc = transform(imputed_Conc, base::log2),
                             .after = imputed_Conc)
-  metadata(metalyzer_se)$aggregated_data <- aggregated_data
+  metalyzer_se@metadata$aggregated_data <- aggregated_data
   return(metalyzer_se)
 }

README.md

@@ -2,7 +2,7 @@ MetAlyzer
 ========
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/nilsmechtel/MetAlyzer/workflows/R-CMD-check/badge.svg)](https://github.com/nilsmechtel/MetAlyzer/actions)
+[![R-CMD-check](https://github.com/nilsmechtel/MetAlyzer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nilsmechtel/MetAlyzer/actions/workflows/R-CMD-check.yaml)
 [![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
 [![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/MetAlyzer)](https://cran.r-project.org/package=MetAlyzer)
 <!-- badges: end -->