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Manhattanplot option to annotate highlighted SNVs #13

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Manhattanplot option to annotate highlighted SNVs #13

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10 changes: 10 additions & 0 deletions qmplot/modules/_manhattan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ def manhattanplot(data, chrom="#CHROM", pos="POS", pv="P", snp="ID", logp=True,
sign_marker_p=None, sign_marker_color="r",
is_annotate_topsnp=False, highlight_other_SNPs_indcs=None,
highlight_other_SNPs_color="r", highlight_other_SNPs_kwargs=None,
annotate_highlighted_SNPs=False,
text_kws=None, ld_block_size=50000, **kwargs):
"""Creates a manhattan plot from PLINK assoc output (or any data frame with chromosome, position, and p-value).

Expand Down Expand Up @@ -123,6 +124,9 @@ def manhattanplot(data, chrom="#CHROM", pos="POS", pv="P", snp="ID", logp=True,
highlight_other_SNPs_kwargs=None : Dict, or None, optional
Dict of keyword arguments passed to the command highlighting the other SNPs.

annotate_highlighted_SNPs=False : bool, optional
Set to True to annotated SNVs highlted with "highlight_other_SNPs_indcs".

text_kws: key, value pairings, or None, optional
keyword arguments for plotting in`` matplotlib.axes.Axes.text(x, y, s, fontdict=None, **kwargs)``

Expand Down Expand Up @@ -312,6 +316,12 @@ def manhattanplot(data, chrom="#CHROM", pos="POS", pv="P", snp="ID", logp=True,
for i in highlight_other_SNPs_indcs:
ax.scatter(x[i], y[i], c=highlight_other_SNPs_color,
alpha=alpha, edgecolors="none", **highlight_other_SNPs_kwargs)
if annotate_highlighted_SNPs and (snp is not None): # to annotate highlighted SNVs
texts = []
for i in highlight_other_SNPs_indcs:
snp_id = data[snp].iloc[i]
texts.append(ax.text(x[i], y[i], snp_id)) # x_pos, y_value, text (snp ID)
adjust_text(texts, ax=ax, **text_kws)

# Add GWAS significant lines
if "color" in hline_kws:
Expand Down