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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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Making scatter plot directly from gl object instead of going from file #32

Open michaelofrancis opened 1 year ago

michaelofrancis commented 1 year ago

Hi Cloufield,

This is more of a suggestion than a requirement or bug. But it would be nice for the scatter plot to use the same gl object as the other functions like Manhattan. For example if using a .vcf I had to create a new file as a .tsv to then read it back in for the scatter plot. Is there a better way to do this without having to create a new, non-vcf file?

Cloufield commented 1 year ago

Hi, Thanks for the suggestion. Indeed it will be much more convenient if the stand-alone functions can directly use gwaslab object. I am currently working on this. gl.compare_effect() will be updated so that it can accept Sumstats Object or pandas dataframe.

Cloufield commented 1 year ago

Hi, gl.compare_effect() has been greatly updated in v3.4.17. It now supports gwaslab object and pandas dataframe. Some parameters are also changed. For details, please check https://cloufield.github.io/gwaslab/EffectSize/ or https://github.com/Cloufield/gwaslab/blob/main/examples/visualization_compare_effec.ipynb. Thank you again for your feedback!