modified and added methods

ipb-halle · Jul 23, 2020 · eddf7b3 · eddf7b3
1 parent 8e9bc69
commit eddf7b3
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Showing 4 changed files with 34 additions and 16 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -18,13 +18,12 @@ RUN dpkg-reconfigure locales
 RUN apt-get -y update && apt-get -y dist-upgrade && apt-get -y --allow-unauthenticated install apt-transport-https make gcc gfortran g++ libblas-dev liblapack-dev libxml++2.6-dev libexpat1-dev libxml2-dev libnetcdf-dev libssl-dev pkg-config wget curl git unzip zip python3 python3-pip r-base r-base-dev pandoc pandoc-data openjdk-11-jdk
 
 # Install R packages
-RUN R -e 'install.packages(c("irlba","igraph","ggplot2","digest","lattice","XML","Rcpp","reshape2","plyr","stringi","stringr","intervals","devtools","RColorBrewer","plyr","RANN","knitr","ncdf4","microbenchmark","RUnit","foreach","doMC","curl","jsonlite","treemap","colourpicker","htmltools","shiny","shinyBS","shinyjs","DT","FactoMineR","slam","cba","squash","plotrix","plotly","circlize","matrixStats","Matrix","tools","ape","data.tree","plyr","data.table","kableExtra","htmlwidgets","sunburstR","SparseM","ROCR","PRROC","klaR","e1071","kohonen","nnet","rda","caret","caretEnsemble","RCurl","ontologyIndex"), repos="https://cloud.r-project.org/")'
+RUN R -e 'install.packages(c("irlba","igraph","ggplot2","digest","lattice","XML","Rcpp","reshape2","plyr","stringi","stringr","intervals","devtools","RColorBrewer","plyr","RANN","knitr","ncdf4","microbenchmark","RUnit","foreach","doMC","curl","jsonlite","treemap","colourpicker","htmltools","shiny","shinyBS","shinyjs","DT","FactoMineR","slam","cba","squash","plotrix","plotly","circlize","matrixStats","Matrix","tools","ape","data.tree","plyr","data.table","kableExtra","htmlwidgets","sunburstR","SparseM","ROCR","PRROC","klaR","e1071","kohonen","nnet","rda","caret","caretEnsemble","RCurl","ontologyIndex","party","entropy","binda","MLmetrics"), repos="https://cloud.r-project.org/")'
 
 # Install Bioconductor
 RUN R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install(c("multtest","MSnbase","mzR","MassSpecWavelet","S4Vectors","BiocStyle","faahKO","msdata","xcms","CAMERA","mixOmics","pcaMethods"), ask=FALSE)'
 
 # Install development versions of R packages
-RUN R CMD javareconf
 RUN R -e 'devtools::install_github("https://github.com/MassBank/RMassBank")' && \
     R -e 'devtools::install_github(repo="CDK-R/rinchi@master")'
 
@@ -38,10 +37,6 @@ RUN wget "https://cran.r-project.org/src/contrib/Archive/rda/rda_1.0.2-2.1.tar.g
 RUN apt-get -y --purge --auto-remove remove make gcc gfortran g++
 RUN apt-get -y clean && apt-get -y autoremove && rm -rf /var/lib/{cache,log}/ /tmp/* /var/tmp/*
 
-# Add scripts to docker
-ADD galaxy/*.r /usr/local/bin/
-
 # Add data
 ADD . /data
 WORKDIR /data
-
diff --git a/galaxy/mFam_train_classifier.r b/galaxy/mFam_train_classifier.r
@@ -14,6 +14,15 @@ options(stringAsfactors=FALSE, useFancyQuotes=FALSE)
 
 
 # ---------- Preparations ----------
+# Parallelization
+nSlaves <- parallel::detectCores(all.tests=FALSE, logical=FALSE)
+library(doParallel)
+#registerDoParallel(nSlaves)
+#cluster <- makePSOCKcluster(nSlaves)
+cluster <- makeCluster(nSlaves, setup_strategy="sequential", setup_timeout=10)
+registerDoParallel(cluster)
+setDefaultCluster(cluster)
+
 # Load libraries
 library(SparseM)
 library(slam)
@@ -38,10 +47,20 @@ library(squash)
 library(RCurl)
 library(ontologyIndex)
 library(tools)
+library(entropy)
+library(binda)
+library(party)
+library(MLmetrics)
 
 
 
 # ---------- Arguments and user variables ----------
+args <- list()
+args[1] <- "/Users/kristian/Desktop/Projekte/Habilitation/de.NBI/mFam-Classifier/"
+args[2] <- "/Users/kristian/Desktop/Projekte/Habilitation/de.NBI/mFam-Classifier/data/2018-02-13_pos_21908_MoNA_Spectra.msp"
+args[3] <- "/Users/kristian/Desktop/Projekte/Habilitation/de.NBI/mFam-Classifier/data/2019-05-23_Scaffolds.tsv"
+args[4] <- "/Users/kristian/Desktop/Projekte/Habilitation/de.NBI/mFam-Classifier/data/Classifier_ROC_Analysis"
+
 # Take in trailing command line arguments
 args <- commandArgs(trailingOnly=TRUE)
 if (length(args) < 3) {
@@ -51,8 +70,7 @@ if (length(args) < 3) {
 }
 
 # Working directory
-workdir <- as.character(args[1])
-setwd(workdir)
+setwd(as.character(args[1]))
 
 # Classifier Library, "./data/2018-02-13_neg_11328_MoNA_Spectra.msp", "./data/2018-02-13_pos_21908_MoNA_Spectra.msp"
 thisLibrary <- as.character(args[2])
@@ -73,13 +91,13 @@ resultFolderForClassifiers <- as.character(args[4])
 
 # ---------- Load MetFamily ----------
 # Load MetFamily
-source(paste0(workdir,"/MetFamily/FragmentMatrixFunctions.R"))
-source(paste0(workdir,"/MetFamily/Annotation.R"))
-source(paste0(workdir,"/MetFamily/DataProcessing.R"))
+source("MetFamily/FragmentMatrixFunctions.R")
+source("MetFamily/Annotation.R")
+source("MetFamily/DataProcessing.R")
 
 # Load MFam Classifier
-source(paste0(workdir,"/mFam/SubstanceClassClassifier.R"))
-source(paste0(workdir,"/mFam/SubstanceClassClassifier_classifier.R"))
+source("MFam/SubstanceClassClassifier.R")
+source("MFam/SubstanceClassClassifier_classifier.R")
 
 
 
@@ -99,8 +117,10 @@ proportionTraining <- 0.7
 fragmentColumnSelectionMethod <- "ProportionOfHighestFragmentPresence"
 minimumProportionOfPositiveFragments <- 0.05
 
-thisMethod <- "method=ColSumsPos; smoothIntensities=FALSE"
+#thisMethod <- "method=ColSumsPos; smoothIntensities=FALSE"
 #thisMethod <- "method=caret; smoothIntensities=FALSE, modelName=binda"
+thisMethod <- "method=caret; smoothIntensities=FALSE, classWeights=FALSE, modelName=binda"
+thisMethod <- "method=caret; smoothIntensities=FALSE, classWeights=FALSE, modelName=ctree"
 
 # I/O
 #resultFolderForClassifiers       <- "./data/Classifier_ROC_Analysis"
@@ -227,3 +247,5 @@ parameterSetAll <- list(
 # ---------- MFam Classifier ----------
 runTest(parameterSetAll = parameterSetAll)
 
+stopCluster(cluster)
+
diff --git a/galaxy/mFam_train_classifier.xml b/galaxy/mFam_train_classifier.xml
@@ -19,6 +19,7 @@ echo "    outputdir: /data/data/Classifier_ROC_Analysis/";
 echo "    mfamrdata: $mfamrdata";
 echo "    mfamres: $mfamres";
 echo "    mfaminfo: $mfaminfo";
+;
 mkdir -p /data/data/Classifier_ROC_Analysis;
 mkdir -p /data/data/MetFamily_class_projects;
 mFam_train_classifier.r /data/ $classlib $annofile /data/data/Classifier_ROC_Analysis/;

diff --git a/mFam/SubstanceClassClassifier_classifier.R b/mFam/SubstanceClassClassifier_classifier.R
@@ -103,7 +103,7 @@ caret_classifier <- list(
       #summaryFunction = caret::prSummary, 
       #summaryFunction = caret::twoClassSummary, 
       verboseIter = FALSE,
-      allowParallel = FALSE
+      allowParallel = TRUE
     )
 
     #modelProps <- caret::getModelInfo()[[modelName]]
@@ -216,7 +216,7 @@ caret_classifier_stacked <- list(
       #summaryFunction = caret::prSummary, 
       #summaryFunction = caret::twoClassSummary, 
       verboseIter = FALSE,
-      allowParallel = FALSE,
+      allowParallel = TRUE,
       savePredictions="final",
       #index=createResample(matrix_train_caret$class, 5)
       index=createResample(class, 5)