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

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

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[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?

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 https://github.com/statgen/pheweb/issues/230#issuecomment-2181904470, 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