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qtl_heatmap.sh
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#!/bin/bash -l
#PBS -q short -l nodes=1:ppn=1,walltime=3:59:00
cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
module load R/3.4.1
# Arguments:
# INFILE: full path to the LOD matrix for all phenotypes, stored as a *.rds file.
# OUTFILE: full path to the figure file, saved as PNG.
# LODTHR: LOD threshold above which LOD scores will be truncated.
LODTHR=8
#### Rankz Phenotypes ####
##########
# Cecum lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum_rankZ/lipids/cecum_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Cecum_rankZ/lipids/cecum_lipids_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_cecum_lipids_jax_norm.Rout
##########
# Cecum metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum_rankZ/metabolites/cecum_metabolites_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Cecum_rankZ/metabolites/cecum_metabolites_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_cecum_metabolites_jax_norm.Rout
##########
# Liver lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver_rankZ/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Liver_rankZ/lipids/liver_lipids_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_lipids_jax_norm.Rout
##########
# Liver metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Liver_rankZ/metabolites/liver_metabolites_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_jax_norm.Rout
##########
# Plasma lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma_rankZ/lipids/plasma_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Plasma_rankZ/lipids/plasma_lipids_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_lipids_jax_norm.Rout
##########
# Plasma metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma_rankZ/metabolites/plasma_metabolites_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Plasma_rankZ/metabolites/plasma_metabolites_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_metabolites_jax_norm.Rout
#### Non-RankZ Transformed phenotypes ####
##########
# Liver lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/liver_lipids_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_lipids_jax_norm.Rout
##########
# Known liver lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl_known_only.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/known_liver_lipids_jax_qtl_heatmap.png
LODTHR=8
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_liver_lipids_jax_norm.Rout
##########
# Liver lipids, U. Wisc. normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/liver_lipids_uwisc_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_lipids_uwisc_norm.Rout
##########
# Known liver lipids, U. Wisc. normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl_known_only.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/known_liver_lipids_uwisc_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_liver_lipids_uwisc_norm.Rout
##########
# Liver metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax/liver_metabolites_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_jax_norm.Rout
##########
# Liver metabolites, JAX normalized, sex & gen.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/liver_metabolites_jax_sex_gen_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_sex_gen_jax_norm.Rout
##########
# Liver metabolites, U. Wisc. normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/liver_metabolites_uwisc_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_uwisc_norm.Rout
##########
# Liver metabolites, U. Wisc. normalized, sex & gen.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_sex_gen_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_uwisc_sex_gen_norm.Rout
##########
# Plasma lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/plasma_lipids_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_lipids_jax_norm.Rout
##########
# Known plasma lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl_known_only.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/known_plasma_lipids_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_plasma_lipids_jax_norm.Rout
##########
# Plasma metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/metabolites/plasma_metabolites_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_metabolites/plasma_metabolites_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_metabolites_jax_norm.Rout
##########
# Plasma lipids, U. Wisc. normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/plasma_lipids_uwisc_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_lipids_uwisc_norm.Rout
##########
# Known plasma lipids, U. Wisc. normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl_known_only.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/known_plasma_lipids_uwisc_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_plasma_lipids_uwisc_norm.Rout
##########
# Cecum lipids, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum/lipids_norm_jax/cecum_lipids_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/cecum_lipids_norm_jax/cecum_lipids_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_cecum_lipids_jax_norm.Rout
##########
# Cecum metabolites, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum/metabolites/cecum_metabolites_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/cecum_metabolites/cecum_metabolites_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_cecum_metabolites.Rout
##########
# Islet proteins, JAX normalized, sex, gen & batch.
INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Islet/proteins/islet_proteins_jax_norm_all_qtl.rds
OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/islet_proteins/islet_proteins_jax_qtl_heatmap.png
R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_islet_proteins_jax_norm.Rout