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visualize.sh
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visualize.sh
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#!/bin/bash
python ../../../pype/visualize.py \
--phewas_results ../example_output/genotype_pheWAS_categories_aggregated.tsv \
--directory_name ../example_output/genotype_pheWAS_plots \
--output_prefix 'example' \
--output_format 'png' \
--dpi 300 \
--height 6 \
--width 10 \
--phewas_type 'genotype' \
--mapping ../../../pype/cached/category_mappings.txt \
--clear_old_files \
--single_category \
--variant_files ../example_data/variant_files/example_pheWAS_SNPS.tsv \
--seed 0 \
--plot_manhattan \
--plot_top_data_field_categories \
--plot_volcano \
--annotate_top_N_volcano 10 \
--compare_original_betas \
--plot_category_enrichment \
--annotate
python ../../../pype/visualize.py \
--phewas_results ../example_output/phenotype_pheWAS_categories_aggregated.tsv \
--directory_name ../example_output/phenotype_pheWAS_plots \
--output_prefix 'example' \
--output_format 'png' \
--dpi 300 \
--height 6 \
--width 10 \
--phewas_type 'phenotype' \
--mapping ../../../pype/cached/category_mappings.txt \
--clear_old_files \
--single_category \
--seed 0 \
--plot_manhattan \
--plot_top_data_field_categories \
--plot_volcano \
--annotate_top_N_volcano 10 \
--plot_category_enrichment \
--annotate