Some Manhattan Plots don't show up

[jielab]

Dear Peter:

Sorry to bug you on this. I am very puzzled that some of my GWAS do NOT have Manhattan plot displayed. Please see the screenshot below. Even after I clicked the "Manhatten" link, nothing changed.

I don't see any error message on the console either. Please see the screenshot below.

Can you please give me a little hint, so that I know where to look for problems?

Thanks!

JH

[pjvandehaar]

Browser devtools console

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On Wed, Jun 19, 2024 at 12:00 PM Jie Huang ***@***.***> wrote: Dear Peter: Sorry to bug you on this. I am very puzzled that some of my GWAS do NOT have Manhattan plot displayed. Please see the screenshot below. Even after I clicked the "Manhatten" link, nothing changed. image.png (view on web) <https://github.com/statgen/pheweb/assets/26947455/9c513e18-76ef-4ebb-b1de-caf32f30b4df> I don't see any error message on the console either. Please see the screenshot below. image.png (view on web) <https://github.com/statgen/pheweb/assets/26947455/9fe21c56-4118-4924-ab6a-dea0227bb1fd> Can you please give me a little hint, so that I know where to look for problems? Thanks! JH — Reply to this email directly, view it on GitHub <#230>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGSPCIBKVPQATPFWEY3G63ZIGTKLAVCNFSM6AAAAABJSK2AKGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM3DENZRGM4TQMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jielab]

Thanks, Peter!

Please see the screenshot below. The console shows "Manhattan XHR failed".
How could I find the cause and a solution for this?

Thanks!
JH

[pjvandehaar]

Look at browser devtools network tab. Maybe something went wrong loading. Maybe just rerun pheweb processing?

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On Thu, Jun 20, 2024 at 10:58 PM Jie Huang ***@***.***> wrote: Thanks, Peter! Please see the screenshot below. The console shows "*Manhattan XHR failed* ". How could I find the cause and a solution for this? Thanks! JH image.png (view on web) <https://github.com/statgen/pheweb/assets/26947455/890af095-3c42-4b0a-9c96-4c38b83ef68a> — Reply to this email directly, view it on GitHub <#230 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGSPCLFJCL7HG5JMYKBZPTZIOJFTAVCNFSM6AAAAABJSK2AKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBRHEYDINBXGA> . You are receiving this because you commented.Message ID: ***@***.***>

[jielab]

Dear Peter:

I did rerun pheweb processing a couple of times, but still the Manhattan plot does not show up.

To facilitate this communication to identify the cause, and not wasting too much of your precious time, I now post my GWAS data at this link https://drive.google.com/file/d/1wmZiGEzb5Guw6qBH6QKIjB4R_JpKqUJI/view?usp=sharing.

And below is my config.py file

hg_build_number = 19
assoc_max_maf = 1
show_correlations = False
show_manhattan_filter_button = True
cache = "/mnt/d/data/dbsnp/"
field_aliases = {'CHR':'chrom', 'POS':'pos', 'NEA':'ref',  'EA':'alt', 'BETA':'beta', 'SE':'sebeta', 'P':'pval'}

At your convenient time, can you please download this GWAS file and test at your side? I hope this exercise could identify an issue that is useful for many other pheweb users as well.

Many thanks!

JH

[jielab]

I have been so puzzled by this behavior. I would greatly appreciate if someone could clarify this mystery. I hope that it is not just me who got this manhattan plot display problem.

Thanks!
JH

[kmetsalu]

We have a same problem. Most phenotypes work but some don't.

[kmetsalu]

We discovered that some manhattan .json files contained NaN values. Testing if this may be a reason.

[jielab]

Hi,

Thank you very much!

Yes, indeed, I found NaN value in the .jason file for the trait that can't display a Manhattan plot!

This .json file only has one line. My original GWAS file does NOT have any NaN values. Do you know the cause and fix for this NaN issue?

Best regards,
Jie

[kmetsalu]

Sry. No answer yet - people will start investigation in upcoming days. It happens somewhere in data processing pipeline and now the question is, whether it's something related to input data or something unexpected in pheweb processing step.

[jielab]

That's great!

Looking forward to a further investigation and an answer :-)

Best regards,
Jie