Manhattan plot not showing up

Hail Query & hailctl
1

Hi all,

I don’t know why the manhattan plot is not showing up for my analysis. For reference, my matrix table dimensions are (8401, 75). I want to do the manhattan plot based on age just in one chromosomal region.

Here is my code:

lin_reg = hl.linear_regression_rows(y=mt2.pheno.current_age, x=mt.GT.n_alt_alleles(), covariates=[1.0])
h = lin_reg.filter(~hl.is_nan(lin_reg.p_value))
p = hl.plot.manhattan(h.p_value)

To my understanding, 199 points should be plotted (h.count() = 199). However, is there an issue with just confining my points to one region? I just want to see the distribution within a given gene, not the entire genome.

Thanks!

2

Hi @njain,
Can you explain what you mean by “the manhattan plot is not showing up”? Do you not see a figure window at all? Or are you not seeing any points?
Best,

3

i’ve been having this problem with any bokeh plot i try to produce from either a hail table or matrix table through a jupyter notebook. the commands will run but no figure window opens or any points.

4

Oh I understand. Are you using a web browser to interact with your nodebook or an editor like vscode?

5

Have you tried running the following at the top of your notebook?

hl.plot.output_notebook()
6

it turns out that my notebook needed to run on bokeh 3.3.4 instead of the current version!