From 51c63b3ce30d3b318fa960dfa6e77997bb420c8a Mon Sep 17 00:00:00 2001
From: nilsmechtel <nils.mech@gmail.com>
Date: Thu, 16 Nov 2023 22:32:45 +0100
Subject: [PATCH] update R CMD Check badge

---
 .github/workflows/R-CMD-check.yaml |  27 +++++++------------
 DESCRIPTION                        |   4 ++-
 NAMESPACE                          |  13 ++++++++++
 R/calculate_log2FC.R               |   5 ++--
 R/impute_data.R                    |   4 +--
 R/plot_network.R                   |   2 +-
 R/transform_data.R                 |   4 +--
 README.md                          |   2 +-
 data/example_meta_data.RDS         | Bin 0 -> 176 bytes
 man/aggregate_data.Rd              |   2 +-
 man/apply_linear_model.Rd          |  18 +++++++++++++
 man/calc_CV.Rd                     |  22 ++++++++++++++++
 man/calculate_log2FC.Rd            |  39 ++++++++++++++++++++++++++++
 man/impute_data.Rd                 |  25 ++++++++++++++++++
 man/plot_log2FC.Rd                 |  40 +++++++++++++++++++++++++++++
 man/read_named_region.Rd           |  28 ++++++++++++++++++++
 man/set_threshold.Rd               |  17 ++++++++++++
 man/transform.Rd                   |  18 +++++++++++++
 man/transform_data.Rd              |  20 +++++++++++++++
 man/zero_imputation.Rd             |  20 +++++++++++++++
 20 files changed, 282 insertions(+), 28 deletions(-)
 create mode 100755 data/example_meta_data.RDS
 create mode 100644 man/apply_linear_model.Rd
 create mode 100644 man/calc_CV.Rd
 create mode 100644 man/calculate_log2FC.Rd
 create mode 100644 man/impute_data.Rd
 create mode 100644 man/plot_log2FC.Rd
 create mode 100644 man/read_named_region.Rd
 create mode 100644 man/set_threshold.Rd
 create mode 100644 man/transform.Rd
 create mode 100644 man/transform_data.Rd
 create mode 100644 man/zero_imputation.Rd

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index f74fa68..a3ac618 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.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'}
@@ -29,9 +29,9 @@ 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:
@@ -39,20 +39,11 @@ jobs:
           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
diff --git a/DESCRIPTION b/DESCRIPTION
index fa01052..d9c07f8 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MetAlyzer
 Type: Package
 Title: Read and Analyze 'MetIDQ&trade;' Software Output Files
-Version: 0.2.0
+Version: 1.0.0
 Authors@R: 
     c(person("Nils", "Mechtel",
             email = "nils.mech@gmail.com",
@@ -28,6 +28,8 @@ Imports:
     stringr,
     utils,
     rlang,
+    ggplot2,
+    ggrepel,
     SummarizedExperiment,
     S4Vectors,
     BiocManager,
diff --git a/NAMESPACE b/NAMESPACE
index 73b8953..09e1fc7 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/calculate_log2FC.R b/R/calculate_log2FC.R
index 6d1d6fc..b2e9378 100644
--- a/R/calculate_log2FC.R
+++ b/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) {
diff --git a/R/impute_data.R b/R/impute_data.R
index 9abfe93..1375a56 100644
--- a/R/impute_data.R
+++ b/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)
 }
diff --git a/R/plot_network.R b/R/plot_network.R
index 4edc700..079c26c 100644
--- a/R/plot_network.R
+++ b/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.
 #'
diff --git a/R/transform_data.R b/R/transform_data.R
index be180fc..0b1234a 100644
--- a/R/transform_data.R
+++ b/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)
 }
\ No newline at end of file
diff --git a/README.md b/README.md
index c86d5fc..68eacb2 100755
--- a/README.md
+++ b/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 -->
diff --git a/data/example_meta_data.RDS b/data/example_meta_data.RDS
new file mode 100755
index 0000000000000000000000000000000000000000..7303ceb2efa54185d1c79650a58fcf997e0f70cc
GIT binary patch
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z%uOwZCUz#MAe(P$Nk)DOl*bvAT9A{OoLG{It~WU+u^6ToCdieNSdyrhRs=K_O*v;#
eez_jZI$n@<4M5`m|NlFH)IR_f%zSSj1^@uCMnYi#

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diff --git a/man/aggregate_data.Rd b/man/aggregate_data.Rd
index 8b2dd5f..5bd70ae 100644
--- a/man/aggregate_data.Rd
+++ b/man/aggregate_data.Rd
@@ -18,7 +18,7 @@ aggregated data frame}
 }
 \description{
 This function reshapes conc_values, quant_status,
-metatabolitesand sample IDs and combines them into a tibble data frame
+metatabolites and sample IDs and combines them into a tibble data frame
 for filtering with dplyr and plotting with 'ggplot2'. "aggregated_data"
 is grouped by metabolites.
 }
diff --git a/man/apply_linear_model.Rd b/man/apply_linear_model.Rd
new file mode 100644
index 0000000..499b4dc
--- /dev/null
+++ b/man/apply_linear_model.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calculate_log2FC.R
+\name{apply_linear_model}
+\alias{apply_linear_model}
+\title{Calculate log2 fold change}
+\usage{
+apply_linear_model(df, ...)
+}
+\arguments{
+\item{df}{A subset data frame}
+
+\item{...}{}
+}
+\description{
+This function applies a linear model to calculate the log2 fold change and
+its significance
+}
+\keyword{internal}
diff --git a/man/calc_CV.Rd b/man/calc_CV.Rd
new file mode 100644
index 0000000..b65cbfa
--- /dev/null
+++ b/man/calc_CV.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calc_cv.R
+\name{calc_CV}
+\alias{calc_CV}
+\title{Add mean, SD and CV}
+\usage{
+calc_CV(aggregated_data, cv_thresholds = c(0.1, 0.2, 0.3))
+}
+\arguments{
+\item{aggregated_data}{aggregated_data tibble data frame}
+
+\item{cv_threshs}{A numeric vector of upper thresholds (CV <= t) between 0
+and 1 for CV categorization.}
+}
+\value{
+An updated aggregated_data tibble data frame
+}
+\description{
+This function calculates the mean, standard deviation (SD)
+and the coefficient of variation (CV) for each group and adds them to
+aggregated_data.
+}
diff --git a/man/calculate_log2FC.Rd b/man/calculate_log2FC.Rd
new file mode 100644
index 0000000..0db6986
--- /dev/null
+++ b/man/calculate_log2FC.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calculate_log2FC.R
+\name{calculate_log2FC}
+\alias{calculate_log2FC}
+\title{Calculate log2 fold change}
+\usage{
+calculate_log2FC(
+  metalyzer_se,
+  categorical,
+  perc_of_min = 0.2,
+  impute_NA = FALSE,
+  installation_type = "binary"
+)
+}
+\arguments{
+\item{categorical}{A column specifying the two groups}
+
+\item{perc_of_min}{A numeric value below 1}
+
+\item{impute_NA}{Logical value whether to impute NA values
+download and install. Options: ["binary", "source", "both"]}
+
+\item{installation_type}{A character, indicating the type of package to}
+
+\item{metalyzer}{A Metalyzer object}
+}
+\value{
+A data frame containing the log2 fold change for each metabolite
+}
+\description{
+This function calculates the log2 fold change of two groups from
+plotting_data.
+}
+\examples{
+metalyzer_se <- MetAlyzer_dataset(file_path = extraction_data())
+metalyzer_se <- renameMetaData(metalyzer_se, Method = `Sample Description`)
+
+log2FC <- calculate_log2FC(metalyzer_se, Method, perc_of_min = 0.2, impute_NA = TRUE)
+}
diff --git a/man/impute_data.Rd b/man/impute_data.Rd
new file mode 100644
index 0000000..65f6ace
--- /dev/null
+++ b/man/impute_data.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/impute_data.R
+\name{impute_data}
+\alias{impute_data}
+\title{Impute aggregated data}
+\usage{
+impute_data(metalyzer_se, perc_of_min, impute_NA)
+}
+\arguments{
+\item{perc_of_min}{A numeric value between 0 and 1. Percentage
+of the minimal positive value, that is taken for imputation}
+
+\item{impute_NA}{Logical value whether to impute NA values}
+
+\item{metalyzer}{A MetAlyzer object}
+}
+\value{
+An updated aggregated_data tibble data frame
+}
+\description{
+This function imputes zero concentration values
+with a percentage of the minimal positive value. If all values
+are zero or NA, they are set to NA. The imputed values are added
+to plotting_data in an extra column imputed_Conc.
+}
diff --git a/man/plot_log2FC.Rd b/man/plot_log2FC.Rd
new file mode 100644
index 0000000..d8c2a1c
--- /dev/null
+++ b/man/plot_log2FC.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_log2FC.R
+\name{plot_log2FC}
+\alias{plot_log2FC}
+\title{Plot log2 fold change}
+\usage{
+plot_log2FC(
+  log2FC_df,
+  signif_colors = c(`#5F5F5F` = 1, `#FEBF6E` = 0.1, `#EE5C42` = 0.05, `#8B1A1A` = 0.01),
+  hide_labels_for = c(),
+  class_colors = "MetAlyzer",
+  polarity_file = "MxPQuant500",
+  vulcano = FALSE
+)
+}
+\arguments{
+\item{log2FC_df}{fold change data frame}
+
+\item{signif_colors}{signif_colors}
+
+\item{hide_labels_for}{vector of Metabolites or Classes for which no labels
+are printed}
+
+\item{class_colors}{class_colors}
+
+\item{polarity_file}{polarity_file}
+}
+\value{
+ggplot object
+}
+\description{
+This method plots the log2 fold change for each metabolite.
+}
+\examples{
+metalyzer_se <- MetAlyzer_dataset(file_path = extraction_data())
+metalyzer_se <- renameMetaData(metalyzer_se, Method = 'Sample Description')
+
+log2FC_df <- calculate_log2FC(metalyzer_se, Method, perc_of_min = 0.2, impute_NA = TRUE)
+network <- plot_network(log2FC_df, q_value = 0.05)
+}
diff --git a/man/read_named_region.Rd b/man/read_named_region.Rd
new file mode 100644
index 0000000..6cc7def
--- /dev/null
+++ b/man/read_named_region.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_network.R
+\name{read_named_region}
+\alias{read_named_region}
+\title{Plot Pathway Network}
+\usage{
+read_named_region(file_path, named_region)
+}
+\arguments{
+\item{log2FC_df}{A data frame with the log2 fold change for each metabolite}
+
+\item{q_value}{The q-value threshold for significance}
+}
+\value{
+ggplot object
+}
+\description{
+This function plots the log2 fold change for each metabolite and visualizes it, in a pathway network.
+}
+\examples{
+metalyzer_se <- MetAlyzer_dataset(file_path = extraction_data())
+metalyzer_se <- renameMetaData(metalyzer_se, Method = 'Sample Description')
+
+log2FC_df <- calculate_log2FC(metalyzer_se, Method, perc_of_min = 0.2, impute_NA = TRUE)
+
+p_vulcano <- plot_log2FC(log2FC_df, hide_labels_for = rownames(rowData(MetAlyzer_proj)), vulcano=TRUE)
+p_fc <- plot_log2FC(log2FC_df, hide_labels_for = rownames(rowData(MetAlyzer_proj)), vulcano=FALSE)
+}
diff --git a/man/set_threshold.Rd b/man/set_threshold.Rd
new file mode 100644
index 0000000..2beb9df
--- /dev/null
+++ b/man/set_threshold.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calc_cv.R
+\name{set_threshold}
+\alias{set_threshold}
+\title{Threshold CV}
+\usage{
+set_threshold(x, cv_threshs)
+}
+\arguments{
+\item{x}{A CV value}
+
+\item{cv_threshs}{A numeric vector of thresholds}
+}
+\description{
+This function assigns a CV value according to a vector of thresholds.
+}
+\keyword{internal}
diff --git a/man/transform.Rd b/man/transform.Rd
new file mode 100644
index 0000000..0503c80
--- /dev/null
+++ b/man/transform.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/transform_data.R
+\name{transform}
+\alias{transform}
+\title{Transformation}
+\usage{
+transform(vec, func)
+}
+\arguments{
+\item{vec}{MetAlyzer metalyzer}
+
+\item{func}{A function for transformation}
+}
+\description{
+This function performs transformation of imputed concentration values
+(imputed_Conc).
+}
+\keyword{internal}
diff --git a/man/transform_data.Rd b/man/transform_data.Rd
new file mode 100644
index 0000000..4941fa6
--- /dev/null
+++ b/man/transform_data.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/transform_data.R
+\name{transform_data}
+\alias{transform_data}
+\title{Transform aggregated data}
+\usage{
+transform_data(metalyzer_se)
+}
+\arguments{
+\item{aggregated_data}{aggregated_data tibble data frame}
+}
+\value{
+An updated aggregated_data tibble data frame
+}
+\description{
+This function performs a transformation of imputed concentration
+values (imputed_Conc) with a given function. NA values are skipped. The
+transformed values are added to aggregated_data in an extra column
+transf_Conc.
+}
diff --git a/man/zero_imputation.Rd b/man/zero_imputation.Rd
new file mode 100644
index 0000000..0344eb7
--- /dev/null
+++ b/man/zero_imputation.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/impute_data.R
+\name{zero_imputation}
+\alias{zero_imputation}
+\title{Zero imputation}
+\usage{
+zero_imputation(vec, perc_of_min, impute_NA)
+}
+\arguments{
+\item{vec}{A numeric vector containing the concentration values}
+
+\item{perc_of_min}{A numeric value below 1}
+
+\item{impute_NA}{Logical value whether to impute NA values}
+}
+\description{
+This function performs zero imputation with the minimal positive value times
+perc_of_min.
+}
+\keyword{internal}