Commit 151dc9dd authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Switched to Rlib (step 5 - except limma).

parent 50c80d2e
......@@ -6,4 +6,6 @@ clean:
clean_outputs:
@rm -rf ${OUTPUT_FOLDER}/*
run:
@Rscript --vanilla ${CODE_FOLDER}/get_DEGs.R > ${OUTPUT_FOLDER}/run_log.out 2> ${OUTPUT_FOLDER}/run_log.err
@sbatch ${CODE_FOLDER}/run.sh
doc:
@/bin/bash ${CODE_FOLDER}/doc.sh
# I/Os and parameters
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/05/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/05-Get_DEGs/
# All datasets for LIMMA.
DATASETS=(GSE20163 GSE20164 GSE20292 GSE8397 Simunovic GSE20141 GSE7307 GSE7621 E-MEXP-1416 HG-U133A HG-U133_Plus_2)
# Clean start
rm -rf ${OUTPUT_FOLDER}/results_summary.*
# Print header
echo '\documentclass[]{article}' > ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\usepackage{graphicx}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\title{GeneDER - step 04 - Clean datasets}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\author{Leon-Charles Tranchevent}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\begin{document}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\maketitle' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\textsl{}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\begin{abstract}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo 'This document summarizes the results of the step 04-Clean\_datasets. Age distributions' >> ${OUTPUT_FOLDER}/results_summary.tex
echo 'for various sample categories are displayed for all datasets. Categories are defined' >> ${OUTPUT_FOLDER}/results_summary.tex
echo 'based on gender, disease status or both (see color codes in the legend). \\' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo 'Note: this document is automatically generated.' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\end{abstract}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
for i in "${DATASETS[@]}"
do
echo '\begin{figure}[ht]' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' \centering' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' \includegraphics[scale=0.23]{'"$OUTPUT_FOLDER"''"$i"'_agebias_wrt_gender.png}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' \includegraphics[scale=0.23]{'"$OUTPUT_FOLDER"''"$i"'_agebias_wrt_disease_status.png}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' \includegraphics[scale=0.23]{'"$OUTPUT_FOLDER"''"$i"'_agebias_wrt_gender_and_disease_status.png}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' \caption{Distributions of patient age for dataset '"$i"' and different sample categories. Each' | sed -r 's/_/\\_/g' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' sample is represented by a single point, colors have different meanings on the different plots. (Left) age' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' distributions of females (green) and males (orange). (Center) age distributions of controls (green) and' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' PD patients (orange). (Right) Combined representations for female controls (green), female PD patients' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' (orange), male controls (violet), and male PD patients (pink). NOTE: boxplots should be interpreted with' >> ${OUTPUT_FOLDER}/results_summary.tex
echo ' caution due to the low number of samples per category.}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\end{figure}' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
done
# Print footer
echo '' >> ${OUTPUT_FOLDER}/results_summary.tex
echo '\end{document}' >> ${OUTPUT_FOLDER}/results_summary.tex
# Compilation
pdflatex -synctex=1 -interaction=nonstopmode ${OUTPUT_FOLDER}/results_summary.tex
mv results_summary.pdf ${OUTPUT_FOLDER}/
rm results_summary*
This diff is collapsed.
local_input_data_dir: !!str '04/'
local_data_dir: !!str '05/'
local_code_dir: !!str '05-Get_DEGs/'
# Name Plateform Has.F.PD Has.pairs
datasets:
- ['GSE20141', 'HGU133Plus2', TRUE, FALSE]
- ['GSE20163', 'HGU133A', TRUE, FALSE]
- ['GSE20164', 'HGU133A', TRUE, FALSE]
- ['GSE20292', 'HGU133A', TRUE, FALSE]
- ['GSE7307', 'HGU133Plus2', FALSE, FALSE]
- ['GSE7621', 'HGU133Plus2', TRUE, FALSE]
- ['GSE8397', 'HGU133A', TRUE, TRUE]
- ['Simunovic', 'HGU133A', TRUE, FALSE]
- ['E-MEXP-1416', 'U133_X3P', TRUE, FALSE]
- ['HG-U133A', 'HGU133A', TRUE, FALSE]
- ['HG-U133_Plus_2', 'HGU133Plus2', TRUE, FALSE]
#!/bin/bash -l
#SBATCH -J geneder:05:limma
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --time=0-01:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
echo "== Node list: ${SLURM_NODELIST}"
echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/05/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/05-Get_DEGs/
# Loading modules.
module load lang/R/3.4.4-intel-2018a-X11-20180131-bare
# Actual job.
Rscript --vanilla ${CODE_FOLDER}/get_DEGs.R > ${OUTPUT_FOLDER}/run_log.out 2> ${OUTPUT_FOLDER}/run_log.err
# Moving the slurm log file to data
mv ${CODE_FOLDER}/slurm-*out ${OUTPUT_FOLDER}/
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