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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
158 stars 65 forks source link

Do Top Hits disappear in pheno page? #46

Closed phuwanat closed 7 years ago

phuwanat commented 7 years ago

Hello,

It seems like there is no top hits shown in my pheno page. Is there any known issues about this?

Regards, Phuwanat

pjvandehaar commented 7 years ago

If your pheweb is public, could you send me a link? If you prefer not to put it online, you could email it to pjvh@umich.edu.

phuwanat commented 7 years ago

Thanks for very fast replying. I am still testing it on my machine. I don't have access to public server.

pjvandehaar commented 7 years ago

Two options: (1) you're on a very old version, or (2) there's a javascript error.

How did you install pheweb? What version do you see in pheweb -h? When you open a pheno page, can you check for errors in the browser console? (open developer tools, probably by right-clicking and choosing "inspect", and then select the tab "console" and look for problems.)

phuwanat commented 7 years ago

I use the latest one (0.9.13) by installing it from git with some modifications on significant threshold (https://github.com/phuwanat/pheweb/). There is no javascript in the console.

phuwanat commented 7 years ago

I tried to comment _.filter(variants, _.property('show_gene')); in function populate_streamtable of pheno.js and it showed all of variants. I am not sure whether it related or not but I haven't found point that insert show_gene in JSON data. Please forgive me if I did wrong.

Thanks, Phuwanat

pjvandehaar commented 7 years ago

Thanks for that catch! You're absolutely right, I removed show_gene about a week ago, but it didn't make any tests fail and I didn't reload the data on our main phewebs, so I didn't notice that I'd broken that table.

I was using show_gene so that I'd only show one variant per hit/loci in that table. I removed while changing things in commit 029baa834c42e895351af17c1ab140c7f9ba6c4a. I shouldn't have done that, because I liked that feature.

I'll add that feature back in later, but for now I've copied the fix that you have.

pjvandehaar commented 7 years ago

If you have any other questions, feel free to open another issue here or email me.