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vappiah / manhattan-plots

This repo provides a tutorial on how to plot manhattan plots using Fixative index(fst) values in python
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TypeError: get_figure() missing 1 required positional argument: 'theme' #1

Open dalmei33 opened 2 years ago

dalmei33 commented 2 years ago

Hi

Thank you so much for your tutorial for making manhattan-plots using FST values. I was able to successfully use your scripts with my "sorted_filtered_variants.vcf.gz" file, meaning that I got my "snps.filtered.vcf.gz" file.

However, when trying to plot the FST values I get this error:

((fst-env) [dmalmei@node1921 manhattan-plots]$ python3 plot_fst.py 22_chromosomes_neg_vs_pos_ventral.newheader.fst.weir.fst Traceback (most recent call last): File "plot_fst.py", line 13, in mhat(selected,chr='CHROM',fst='WEIR_AND_COCKERHAM_FST',show=False,color=('black','red')) File "/scratch1/dmalmei/9xx_Remove_filtered_variants/b_FST_genome_scan/manhattan-plots/manhattan.py", line 85, in mhat general.get_figure(show, r, figtype, figname) TypeError: get_figure() missing 1 required positional argument: 'theme' (fst-env) [dmalmei@node1921 manhattan-plots]$

Can you please help me to solve it?

Thanks!

vappiah commented 2 years ago

Hi @dalmei33 the scripts were written to analyze variants for _P._falciparum. If you are using it for human genomes then you have to do some modification.

I am planning to write a more generic script. But in the meantime, you may have to modify to suit your needs.