search

reneshbedre / bioinfokit

Bioinformatics data analysis and visualization toolkit
MIT License
333 stars 77 forks source link

Manhattan plot with fst #24

Closed vappiah closed 3 years ago

vappiah commented 3 years ago

Hello developers,

I would like to know if its advisable to use bioinfokit to make manhattan plot on my data which has chromosome(in the format Pf3D7_{1-13}_v3), position and fst values.

Thanks

vappiah commented 3 years ago

Hi @reneshbedre I was able to modify the manhattan plot codes to work with Fixative Index(FST) values . I tried on a Plasmodium falciparum snp data and it worked perfectly. I am willing to send to you just in case you want to have a look and probably include in your package. I am setting up a github repo for it and will share as well. Thanks.

FST-BIOINFOKIT

reneshbedre commented 3 years ago

@vappiah

Thank you for your update on the Manhatten plot with Fst values. Currently, mhat function in bioinfokit takes p values and transforms to the log scale for plotting the Manhatten plot.

I am glad that you found the way around. Yes, sure, you can send me the code and if possible. the subset of the data. You can send me on email reneshbe@gmail.com. Thank you for your input.

reneshbedre commented 3 years ago

@vappiah

I have added the support for Fst values in the Manhattan plot. See this page for updated documentation. Let me know if you have further questions.