qmplot

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ax parameter does not work

3

when ax pass to the function, return is empty.

chunkaowang

Consider moving plotting to screen or figure logic in utility rather than library function

2

https://github.com/ShujiaHuang/qmplot/blob/ed1d5a82055ba8c787c2dbae69d533893438390e/qmplot/modules/_qq.py#L232-L235 It would be nice if the above logic can be moved to https://github.com/ShujiaHuang/qmplot/blob/ed1d5a82055ba8c787c2dbae69d533893438390e/qmplot/main.py#L113. That way the underlying qqplot function can be used as a plotting library function, where it...

hguturu

Annotation feature is very limited

1

Is there a way to annotate and highlight more SNPs than just the SNP with the top p-value? For example, by providing a list of SNPs to annotate or regions...

jorgeamaya


ShujiaHuang

Use custom annotations

1

It would be nice if we could pass a dict with custom annotations to the `qm.manhattanplot` function. For example, if I already know the IDs of my top hits and...

julibeg

How to decrease marker size in **kwargs?

1

Hello, I'm reading through the documentation for qmplot and making a Manhattan plot. Very useful! I was wondering if it's possible to decrease the marker size. In ax.scatter(), I can...

andhamel

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...

igumnov-daniel

Thanks for the great tool. There are lots of situations that values other than p-value such number of reads per region, rna-count, etc need to be plotted in manhattan format....

Morteza-M-Saber

Hi, I used your example code to save the image: ` ax = manhattanplot(data=df, xticklabel_kws={"rotation": "vertical"}, sign_marker_p=None, genomewideline=None, suggestiveline=5e-8)` `plt.savefig(os.path.join(output_dir, 'manhattan_qmplot.png'))` but the saved image is empty

anbai106