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only output PNGs for the plotting
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@swvanderlaan
swvanderlaan committed Nov 29, 2023
1 parent 6ad4bb1 commit ec595a1
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10 changes: 5 additions & 5 deletions gwastoolkit.plotter.qc.sh
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Expand Up @@ -83,9 +83,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
echobold " GWASTOOLKIT PLOTTER -- AFTER QC"
echobold " plotting of SNPTEST analysis results after quality control"
echobold ""
echobold " Version : v1.1.5"
echobold " Version : v1.1.6"
echobold ""
echobold " Last update: 2018-01-24"
echobold " Last update: 2023-11-29"
echobold " Written by : Sander W. van der Laan ([email protected])."
echobold ""
echobold " Testers : - Saskia Haitjema ([email protected])"
Expand Down Expand Up @@ -140,15 +140,15 @@ else
#### QQ-plot including 95%CI and compute lambda [P]
echo "Making QQ-plot including 95%CI and compute lambda..."
zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${FILENAME}.QQplot.txt
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.QQplot.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
# Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.QQplot.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.QQplot.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""
### Manhattan plot for publications [CHR, BP, P]
echo "Manhattan plot for publications ..."
zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col CHR,BP,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c FULL -f PDF -t ${FILENAME}
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c FULL -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c FULL -f PNG -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c TWOCOLOR -f PDF -t ${FILENAME}
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c TWOCOLOR -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c TWOCOLOR -f PNG -t ${FILENAME}
echo "Finished plotting, zipping up and re-organising intermediate files!"
rm -v ${OUTPUT_DIR}/${FILENAME}.QQplot.txt
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18 changes: 9 additions & 9 deletions gwastoolkit.plotter.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
echobold " GWASTOOLKIT PLOTTER"
echobold " plotting of SNPTEST analysis results"
echobold ""
echobold " Version : v1.1.6"
echobold " Version : v1.1.7"
echobold ""
echobold " Last update: 2018-01-24"
echobold " Last update: 2023-11-29"
echobold " Written by : Sander W. van der Laan ([email protected])."
echobold ""
echobold " Testers : - Saskia Haitjema ([email protected])"
Expand Down Expand Up @@ -141,49 +141,49 @@ else
### QQ-plot including 95%CI and compute lambda [P]
echo "Making QQ-plot including 95%CI and compute lambda..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
# Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""

### QQ-plot stratified by effect allele frequency [P, EAF]
echo "QQ-plot stratified by effect allele frequency..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P,CAF | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt
Rscript ${SCRIPTS}/plotter.qq_by_caf.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
# Rscript ${SCRIPTS}/plotter.qq_by_caf.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq_by_caf.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""

## QQ-plot stratified by imputation quality (info -- imputation quality) [P, INFO]
echo "QQ-plot stratified by imputation quality..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P,Info | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt
Rscript ${SCRIPTS}/plotter.qq_by_info.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
# Rscript ${SCRIPTS}/plotter.qq_by_info.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq_by_info.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""

### Plot the imputation quality (info) in a histogram [INFO]
echo "Plot the imputation quality (info) in a histogram..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col Info | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt
Rscript ${SCRIPTS}/plotter.infoscore.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt -o ${OUTPUT_DIR} -f PDF
# Rscript ${SCRIPTS}/plotter.infoscore.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt -o ${OUTPUT_DIR} -f PDF
Rscript ${SCRIPTS}/plotter.infoscore.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt -o ${OUTPUT_DIR} -f PNG
echo ""

### Plot the BETAs in a histogram [BETA]
echo "Plot the BETAs in a histogram..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col BETA | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt
Rscript ${SCRIPTS}/plotter.effectsize.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt -o ${OUTPUT_DIR} -f PDF
# Rscript ${SCRIPTS}/plotter.effectsize.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt -o ${OUTPUT_DIR} -f PDF
Rscript ${SCRIPTS}/plotter.effectsize.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt -o ${OUTPUT_DIR} -f PNG
echo ""

### Plot the Z-score based p-value (calculated from beta/se) and P [BETA, SE, P]
echo "Plot the Z-score based p-value (calculated from beta/se) and P..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col BETA,SE,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt
Rscript ${SCRIPTS}/plotter.p_z.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt -o ${OUTPUT_DIR} -s 500000 -f PDF
# Rscript ${SCRIPTS}/plotter.p_z.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt -o ${OUTPUT_DIR} -s 500000 -f PDF
Rscript ${SCRIPTS}/plotter.p_z.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt -o ${OUTPUT_DIR} -s 500000 -f PNG
echo ""

### Manhattan plot for quick inspection (truncated upto -log10(p-value)) [CHR, BP, P]
echo "Manhattan plot for quick inspection (truncated upto -log10(p-value)=2)..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col CHR,BP,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt -o ${OUTPUT_DIR} -c QC -f PDF -t ${FILENAME}
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt -o ${OUTPUT_DIR} -c QC -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt -o ${OUTPUT_DIR} -c QC -f PNG -t ${FILENAME}
echo ""

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