Initiate log file at the beginning of exported functions

saezlab · Oct 31, 2024 · 94d345c · 94d345c
1 parent 5d1941c
commit 94d345c
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Showing 10 changed files with 82 additions and 33 deletions.
diff --git a/R/DifferentialMetaboliteAnalysis.R b/R/DifferentialMetaboliteAnalysis.R
@@ -62,6 +62,11 @@ DMA <-function(InputData,
                FolderPath = NULL
 ){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+  logger::log_info("DMA: Differential metabolite analysis.")
+
   ## ------------ Check Input files ----------- ##
   # HelperFunction `CheckInput`
   CheckInput(InputData=InputData,
@@ -363,6 +368,9 @@ Log2FC_fun <-function(InputData,
                       CoRe,
                       Transform
 ){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   if("Denominator" %in% names(SettingsInfo)==FALSE  & "Numerator" %in% names(SettingsInfo) ==FALSE){
     # all-vs-all: Generate all pairwise combinations
     conditions = SettingsFile_Sample[[SettingsInfo[["Conditions"]]]]
@@ -641,6 +649,8 @@ DMA_Stat_single <- function(InputData,
                             Log2FC_table,
                             StatPval,
                             StatPadj){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ## ------------ Check Missingness ------------- ##
   Num <- InputData %>%#Are sample numbers enough?
@@ -758,6 +768,9 @@ AOV <-function(InputData,
                SettingsInfo,
                Log2FC_table){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Denominator/numerator ----------- ##
   # Denominator and numerator: Define if we compare one_vs_one, one_vs_all or all_vs_all.
   if("Denominator" %in% names(SettingsInfo)==FALSE  & "Numerator" %in% names(SettingsInfo) ==FALSE){
@@ -888,6 +901,9 @@ Kruskal <-function(InputData,
                    StatPadj
 ){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Denominator/numerator ----------- ##
   # Denominator and numerator: Define if we compare one_vs_one, one_vs_all or all_vs_all.
   if("Denominator" %in% names(SettingsInfo)==FALSE  & "Numerator" %in% names(SettingsInfo) ==FALSE){
@@ -1007,6 +1023,9 @@ Welch <-function(InputData,
                  SettingsInfo,
                  Log2FC_table
 ){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Denominator/numerator ----------- ##
   # Denominator and numerator: Define if we compare one_vs_one, one_vs_all or all_vs_all.
   if("Denominator" %in% names(SettingsInfo)==FALSE  & "Numerator" %in% names(SettingsInfo) ==FALSE){
@@ -1126,6 +1145,9 @@ DMA_Stat_limma <- function(InputData,
                            CoRe,
                            Transform){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Denominator/numerator ----------- ##
   # Denominator and numerator: Define if we compare one_vs_one, one_vs_all or all_vs_all.
   if("Denominator" %in% names(SettingsInfo)==FALSE  & "Numerator" %in% names(SettingsInfo) ==FALSE){
@@ -1381,6 +1403,9 @@ Shapiro <-function(InputData,
                    QQplots=TRUE
 ){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Setup and installs ----------- ##
   RequiredPackages <- c("tidyverse", "gtools")
   new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
@@ -1614,6 +1639,9 @@ Bartlett <-function(InputData,
                     SettingsFile_Sample,
                     SettingsInfo){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   ## ------------ Setup and installs ----------- ##
   RequiredPackages <- c("tidyverse")
   new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
@@ -1669,6 +1697,9 @@ Bartlett <-function(InputData,
 
 vst <- function(InputData){
 
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   # model the mean and variance relationship on the data
   suppressMessages(melted <- reshape2::melt(InputData))
   het.data <- melted %>% group_by(variable) %>% # make a dataframe to save the values

diff --git a/R/GetPriorKnoweldge.R b/R/GetPriorKnoweldge.R
@@ -347,10 +347,10 @@ InspectID <- function(Input_DataFrame,
 #'
 #'
 LoadKEGG <- function(){
-  #Get the package:
-  RequiredPackages <- c("rappdirs")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)) install.packages(new.packages)
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+  logger::log_info("Load KEGG.")
 
   #------------------------------------------------------------------
   #Get the directory and filepath of cache results of R
@@ -444,6 +444,9 @@ LoadKEGG <- function(){
 #' @export
 #'
 LoadHallmarks <- function() {
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   # Read the .csv files
   Hallmark <- system.file("data", "Hallmarks.csv", package = "MetaProViz")
   Hallmark <- read.csv(Hallmark, check.names=FALSE)
@@ -474,11 +477,10 @@ Make_GeneMetabSet <- function(Input_GeneSet,
                               SaveAs_Table = "csv",
                               FolderPath = NULL){
 
-  ## ------------ Setup and installs ----------- ##
-  RequiredPackages <- c("tidyverse","cosmosR")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)) install.packages(new.packages)
-  suppressMessages(library(tidyverse))
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+  logger::log_info("Make_GeneMetabSet.")
 
   ## ------------ Check Input files ----------- ##
   # 1. The input data:
@@ -586,11 +588,11 @@ LoadMetalinks <- function(types = NULL,
                           uniprot_ids = NULL,
                           SaveAs_Table="csv",
                           FolderPath=NULL){
-  #------------------------------------------------------------------
-  #Get the package:
-  RequiredPackages <- c("rappdirs")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)) install.packages(new.packages)
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+  logger::log_info("MetaLinksDB.")
+
 
   #------------------------------------------------------------------
   if((any(c(types, cell_location, tissue_location, biospecimen_location, disease, pathway, hmdb_ids, uniprot_ids)=="?"))==FALSE){

diff --git a/R/HelperLog.R b/R/HelperLog.R
@@ -96,8 +96,7 @@ MPV_trace <- function() {#MPV=MetaProViz
 #'
 MetaProViz_Init <- function(){
   # Only run the first time a MetaProViz function is used in an environment --> Creates log file
-  if(!is.null(metaproviz.env$init)){
-    print("We want to see you!")
+  if(is.null(metaproviz.env$init)){
     #Initial log
     OmnipathR:::init_config(pkg = "MetaProViz")
     OmnipathR:::init_log(pkg = "MetaProViz")

diff --git a/R/MetaDataAnalysis.R b/R/MetaDataAnalysis.R
@@ -51,11 +51,8 @@ MetaAnalysis <- function(InputData,
 
 ){
 
-  ## ------------ Setup and installs ----------- ##
-  RequiredPackages <- c("tidyverse")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)) install.packages(new.packages)
-  suppressMessages(library(tidyverse))
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ################################################################################################################################################################################################
   ## ------------ Check Input files ----------- ##
@@ -304,11 +301,9 @@ MetaPK <- function(InputData,
                    SaveAs_Table = "csv",
                    FolderPath = NULL){
 
-  ## ------------ Setup and installs ----------- ##
-  RequiredPackages <- c("tidyverse")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)) install.packages(new.packages)
-  suppressMessages(library(tidyverse))
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
 
   ################################################################################################################################################################################################
   ## ------------ Check Input files ----------- ##

diff --git a/R/MetaboliteClusteringAnalysis.R b/R/MetaboliteClusteringAnalysis.R
@@ -438,13 +438,8 @@ MCA_CoRe <- function(InputData_Intra,
                      FolderPath=NULL
                      ){
 
-  ## ------------ Setup and installs ----------- ##
-  RequiredPackages <- c("tidyverse")
-  new.packages <- RequiredPackages[!(RequiredPackages %in% installed.packages()[,"Package"])]
-  if(length(new.packages)>0){
-    install.packages(new.packages)
-  }
-  suppressMessages(library(tidyverse))
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ################################################################################################################################################################################################
   ## ------------ Check Input files ----------- ##
@@ -1032,6 +1027,9 @@ MCA_CoRe <- function(InputData_Intra,
 #' @export
 #'
 MCA_rules<- function(Method){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   # Read the .csv files
   Cond <- system.file("data", "MCA_2Cond.csv", package = "MetaProViz")
   Cond<- read.csv( Cond, check.names=FALSE)
@@ -1089,6 +1087,9 @@ CheckInput_MCA <- function(InputData_C1,
                            FeatureID,
                            SaveAs_Table
                            ){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   #------------- InputData
   if(is.null(InputData_C1)==FALSE){
     if(class(InputData_C1) != "data.frame"| class(InputData_C2) != "data.frame"){

diff --git a/R/OverRepresentationAnalysis.R b/R/OverRepresentationAnalysis.R
@@ -50,6 +50,10 @@ ClusterORA <- function(InputData,
                        maxGSSize=1000 ,
                        SaveAs_Table= "csv",
                        FolderPath = NULL){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+
    ## ------------ Check Input files ----------- ##
   Pathways <- CheckInput_ORA(InputData=InputData,
                                           SettingsInfo=SettingsInfo,
@@ -185,6 +189,10 @@ StandardORA <- function(InputData,
                         FolderPath = NULL
 
 ){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+
  ## ------------ Check Input files ----------- ##
   Pathways <- CheckInput_ORA(InputData=InputData,
                                           SettingsInfo=SettingsInfo,

diff --git a/R/Processing.R b/R/Processing.R
@@ -280,6 +280,8 @@ ReplicateSum <- function(InputData,
                          SettingsInfo = c(Conditions="Conditions", Biological_Replicates="Biological_Replicates", Analytical_Replicates="Analytical_Replicates"),
                          SaveAs_Table = "csv",
                          FolderPath = NULL){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ## ------------------ Check Input ------------------- ##
   # HelperFunction `CheckInput`
@@ -623,6 +625,10 @@ FeatureFiltering <-function(InputData,
                             CoRe=FALSE,
                             FeatureFilt="Modified",
                             FeatureFilt_Value=0.8){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
+
   ## ------------------ Prepare the data ------------------- ##
   feat_filt_data <- as.data.frame(replace(InputData, InputData==0, NA))
 

diff --git a/R/ToyData.R b/R/ToyData.R
@@ -51,6 +51,9 @@
 #' @export
 #'
 ToyData <- function(Dataset) {
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
+
   #Available Datasets:
   datasets <- list(
     IntraCells_Raw = "MS55_RawPeakData.csv",

diff --git a/R/VizHeatmap.R b/R/VizHeatmap.R
@@ -67,6 +67,8 @@ VizHeatmap <- function(InputData,
                        PrintPlot=TRUE,
                        FolderPath = NULL
 ){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ## ------------ Check Input files ----------- ##
   # HelperFunction `CheckInput`

diff --git a/R/VizVolcano.R b/R/VizVolcano.R
@@ -89,6 +89,8 @@ VizVolcano <- function(PlotSettings="Standard",
                        FolderPath = NULL,
                        Features="Metabolites",
                        PrintPlot=TRUE){
+  ## ------------ Create log file ----------- ##
+  MetaProViz_Init()
 
   ## ------------ Check Input files ----------- ##
   # HelperFunction `CheckInput`