Manhattan Inputs and Outputs
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To visualize results from the PheWAS, the PyPheWAS-package has a command called "make_manhattan" that allows users to generate a Manhattan plot of the results.


Manhattan Inputs:
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**Input Arguments**

* **--input-file**, **-i**: Input file with the results from the PheWAS. This file should be tab-separated and have the columns 'phecode_category', 'phecode_description', and 'converged'.

* **--output-file**, **-o**: Filepath to output the Manhattan plot to. Default value is "test.png".

* **--pval-col**: Name of the column that has the p-values for the variable of interest. Default value is "pval".

* **--beta-col**: Name of the column that has betas for the variables of interest. Default value is "beta".

* **--dpi**: Quality of the image to output. Default value is 300.


Output Plot:
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Notable features of the output plot are described below:

* Different phecode categories are illustrated by different colors on the x-axis

* Bonferroni significance threshold is indicated by the red dashed line

* Infinity lines are indicated by the dashed blue lines. In some PheWASes, the results can be so significant that they get rounded to zero. To account for this, the PyPheWAS-package finds the most significant non-zero result and multiplies that value by 1.02 to replace all zero values. The infinity lines are drawn at this non-zero value to indicate which values were replaced.

* Positive and negative betas are indicated by the direction of the symbols on the plots