Manhattanplot option to annotate highlighted SNVs

[igumnov-daniel]

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()

Resultant picture:

[YuandanZhang]

just check if the additional annotation options has updated in the current release of qmp.lot?

[igumnov-daniel]

@YuandanZhang
Dunno, I've switched to https://github.com/Cloufield/gwaslab last winter