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Create plots

permGWAS is able to create Manhattan and QQ-plots during a GWAS run and form existing p-value files via the create_plot.py script.

Manhattan plot

  • While running permGWAS, you can use the flag -mplot to generate and save a Manhattan plot with Bonferroni significance threshold for significance level $\alpha=0.05$. If you use permGWAS2 with permutations, additionally the permutation-based threshold will be plotted.
  • If you already have result files generated by permGWAS, you can also create a Manhattan plot afterward. You only need to specify the p-value file (relative or absolute path) and use the flag -mplot:
python3 create_plot.py -p_val PATH_TO_RESULT_P_VALUE_FILE -mplot
  • By default, it uses a significance level of 5%. You can change it via the flag -sig_level, which expects an integer value, e.g.
python3 create_plot.py -p_val PATH_TO_RESULT_P_VALUE_FILE -mplot -sig_level 1
  • If you have a corresponding minimal p-value file available, you can additionally plot the permutation-based significance threshold by giving the path to the file via the flag -min_p_val:
python3 create_plot.py -p_val PATH_TO_RESULT_P_VALUE_FILE -min_p_val PATH_TO_MIN_P_VALUE_FILE -mplot
  • The resulting Manhattan plot will be saved in the same folder where the p-value file is stored, unless you specify a different directory via -out_dir. If no other name is specified via -out_file, the plot will be named manhattan_PHENOTYPE_NAME.png.

QQ-plot

  • While running permGWAS, you can use the flag -qqplot to generate and save a simple QQ-plot including the inflation factor lambda.
  • To generate a QQ-plot afterward based on existing p-value result files, you only need to specify the p-value file (relative or absolute path) and use the flag -qqplot:
python3 create_plot.py -p_val PATH_TO_RESULT_P_VALUE_FILE -qqplot
  • The resulting QQ-plot will be saved in the same folder where the p-value file is stored, unless you specify a different directory via -out_dir. If no other name is specified via -out_file, the plot will be named qq_plot_PHENOTYPE_NAME.png.