Hi!
Here I've added an option to also annotate SNVs provided with "highlight_other_SNPs_indcs" argument.
So if one wants to compare to GWAS results via Manhattanplot or just they just have genes of interest they want to highlight then there is an example below:
# let's consider that processing and creation of a list with SNVs indices is above
# so we have 2 different GWAS experiments and a set of target SNVs
fig, axs = plt.subplots(2, 1, figsize=(10, 8))
manhattanplot(
data = GWAS_1,
chrom = 'CHROM',
pos = 'GENPOS',
pv = 'pval',
snp = 'Gene',
suggestiveline=1e-6,
genomewideline=1e-8,
highlight_other_SNPs_indcs=SNVs_to_annotate,
highlight_other_SNPs_color='magenta',
ax=axs[0],
annotate_highlighted_SNPs=True # NEW ARGUMENT
)
manhattanplot(
data = GWAS_2,
chrom = 'CHROM',
pos = 'GENPOS',
pv = 'pval',
snp = 'Gene',
suggestiveline=1e-6,
genomewideline=1e-8,
highlight_other_SNPs_indcs=SNVs_to_annotate,
highlight_other_SNPs_color='magenta',
annotate_highlighted_SNPs=True, # NEW ARGUMENT
ax=axs[1]
)
plt.show()
Hi! Here I've added an option to also annotate SNVs provided with "highlight_other_SNPs_indcs" argument.
So if one wants to compare to GWAS results via Manhattanplot or just they just have genes of interest they want to highlight then there is an example below:
Resultant picture: