Description + R CMD Check

.Rbuildignore

@@ -14,10 +14,8 @@
 ^R/do_anova_2w\.R$
 ^R/filter_groupwise\.R$
 ^R/perform_ANOVA\.R$
-
-^R/draw_FC_network\.R$
+^R/two_way_anova\.R$
 ^R/plot_2w_anvova\.R$
-^R/plot_network\.R$
 
 ^tests$
 

DESCRIPTION

@@ -14,7 +14,11 @@ Authors@R:
      person("Daniel", "Huebschmann",
             email = "[email protected]",
             role = c("aut"),
-            comment = c(ORCID = "0000-0002-6041-7049")))
+            comment = c(ORCID = "0000-0002-6041-7049")),
+     person("Luis", "Herfurth",
+            email = "[email protected]",
+            role = c("aut"),
+            comment = c(ORCID = "0009-0000-9933-3056")))
 Depends:
     R (>= 4.0.0)
 Imports:
@@ -30,7 +34,9 @@ Imports:
     rlang,
     grDevices,
     SummarizedExperiment,
-    S4Vectors
+    S4Vectors,
+    BiocManager,
+    qvalue
 Description: The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).
 License: GPL-3
 Encoding: UTF-8

R/plot_log2FC.R

@@ -18,9 +18,11 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' print(1)
-#' }
+#' 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)
 
 # classes <- c('Acylcarnitines', 'Alkaloids', 'Amine Oxides', 'Aminoacids',
 #              'Aminoacids Related', 'Bile Acids', 'Biogenic Amines', 'Carboxylic Acids',

R/plot_network.R

@@ -1,8 +1,20 @@
-# Load the required packages
-library(dplyr)
-library(ggplot2)
-library(ggrepel)
-
+#' @title Plot Pathway Network
+#'
+#' @description This function plots the log2 fold change for each metabolite and visualizes it, in a pathway network.
+#'
+#' @param log2FC_df A data frame with the log2 fold change for each metabolite
+#' @param q_value The q-value threshold for significance
+#' @return ggplot object
+#' @export
+#' 
+#' @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)
 
 read_named_region <- function(file_path, named_region) {
   full_sheet <- openxlsx::read.xlsx(
@@ -237,7 +249,7 @@ plot_network <- function(log2FC_df, q_value=0.05) {
     theme(plot.title = element_text(hjust = 0.5))
   network
 
-  ggsave("network.pdf", network, width = 15, height = 10, bg = "white")
+  #ggsave("network.pdf", network, width = 15, height = 10, bg = "white")
 }