Manhattan Plot for association results

Feature Requests
1

A Hail Manhattan Plot function would be very useful for summarizing association results. It would be much simpler to implement than the regional plot feature that was requested previously.

Here is an R code example:

2

Hi Tim,

I know your plotting functionality is in early stages. Do you think that it would be possible to customize the Manhattan plot (adding colors, the Bonferroni line, and the FDR line) please?

Thanks,

Laura

3

The manhattan plot function returns a bokeh Figure object, which can be used with other bokeh functionality:

https://bokeh.pydata.org/en/latest/docs/reference/plotting.html

Depending on how you want to add colors, that will need to happen inside the manhattan function, so you may need to copy/edit that code.

4

Hi Tim,

Thanks for the Bonferroni line. With Ines, we added the FDR line too. I attached the code if it can help someone.

import numpy as np
mt.count_rows()
Bonferroni_line = -np.log10(0.05/ mt.count_rows())
FDR_line = -np.log10(1*10**-5)
manhattan = hl.plot.manhattan(gwas.p_value, title=“Manhattan Plot”, size=4)
from bokeh.models import Span
hline1 = Span(location=Bonferroni_line, dimension=‘width’, line_color=‘red’, line_width=1)
hline2 = Span(location=FDR_line, dimension=‘width’, line_color=‘orange’, line_width=1)
manhattan.renderers.extend([hline1,hline2])
show(manhattan)

Best,

Laura

5

Is there a way to save the manhattan and qq plots programmatically to a png or pdf file?

6

Hail plots use Bokeh, so you can use the Bokeh facilities for exporting: https://bokeh.pydata.org/en/latest/docs/user_guide/export.html