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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
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manhattan plot not show when NaN in variant_bins(json file) #188

Closed hailingfang closed 2 years ago

hailingfang commented 2 years ago

I run pheweb with my data, which some p value is 0, and manhattan plot will not show if it json file contain NaN(jquery .getJSON failed). And this value is generted by self._arounded(math.inf).

pjvandehaar commented 2 years ago

This Manhattan Plot works fine with a pval=0: https://pheweb.org/UKB-TOPMed/pheno/275.1 . I wonder what the difference is. What python --version are you using?

hailingfang commented 2 years ago

Hi, I using python 3.6.12. and the $.getJSON() failed(in pheno.html template). My data contain thousands of 0. and generated following line in variant_bins: {'chrom': '1', 'qvals': [3.325, 3.725], 'qval_extents': [[0.025, 2.675], [nan, nan], [2.975, 3.025]], 'pos': 1500000}

and then the manhattan plot of those probe will not show in webpage.

hailingfang commented 2 years ago

closed

daheise commented 1 year ago

I am also having this issue. What was the solution?