# Manhattan plot not showing up

**URL:** <https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083>\
**Category:** Hail Query & hailctl\
**Created:** [March 26, 2025, 10:01pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083 "2025-03-26T22:01:35Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![njain](https://avatars.discourse-cdn.com/v4/letter/n/b77776/32.png) [@njain](https://discuss.hail.is/u/njain)\
**Post date:** [March 26, 2025, 10:01pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/1 "2025-03-26T22:01:35Z")

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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!

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**Author:** ![ehigham](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/ehigham/32/943_2.png) [@ehigham](https://discuss.hail.is/u/ehigham)\
**Post date:** [April 8, 2025, 3:17pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/2 "2025-04-08T15:17:58Z")

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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,

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**Author:** ![njain](https://avatars.discourse-cdn.com/v4/letter/n/b77776/32.png) [@njain](https://discuss.hail.is/u/njain)\
**Post date:** [April 9, 2025, 6:27pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/3 "2025-04-09T18:27:46Z")

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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.

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**Author:** ![ehigham](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/ehigham/32/943_2.png) [@ehigham](https://discuss.hail.is/u/ehigham)\
**Post date:** [April 9, 2025, 6:44pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/4 "2025-04-09T18:44:47Z")

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

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**Author:** ![ehigham](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/ehigham/32/943_2.png) [@ehigham](https://discuss.hail.is/u/ehigham)\
**Post date:** [April 9, 2025, 6:49pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/5 "2025-04-09T18:49:48Z")

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

```python
hl.plot.output_notebook()

```

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**Author:** ![njain](https://avatars.discourse-cdn.com/v4/letter/n/b77776/32.png) [@njain](https://discuss.hail.is/u/njain)\
**Post date:** [April 15, 2025, 11:49pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083/6 "2025-04-15T23:49:43Z")

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