Unable to create effect size comparison plot without heterogeneity

[Sandyyy123]

I am unable to create effect size comparison plot without the need for conducting heteogeneity test and selective annotating/filtering.

Prepare kwargs for the comparison

kwargs = {
    "label": [label1, label2, "Both", "None"],
    "xylabel_prefix": "Per-allele effect size for ",
    "sig_level": 5e-8,
"anno": True,
    "is_q": False,
    "include_all": True,
    "drop": False,
    "is_q_mc": "fdr",  
    "save": os.path.join(base_path, plot_filename),
    "save_args": {"dpi": 300, "facecolor": "white"}
}

If I remove is_q_mc, I end up with error asking me to include it with bon or fdr option.

Also, I could not figure out how to include gene names instead of SNP ids. It seems the option is missing. It would rather require changing the SNPids directly to gene names.

[Cloufield]

Hi,
Thanks for the feedback.

If I remove is_q_mc, I end up with error asking me to include it with bon or fdr option.

I am wondering which gwaslab version you are using? In recent versions, this has been fixed.

Also, I could not figure out how to include gene names instead of SNP ids. It seems the option is missing. It would rather require changing the SNPids directly to gene names.

For this, I haven't added this to the effect size comparison plot yet. I will implement this in the new version and let you know (probably by the start of next week).

[Sandyyy123]

Hi Cloufield,
Thanks for getting back.
I updated to the latest package 3.4.49.
I am still getting the error:
raise ValueError("Please select either fdr or bon for is_q_mc.")
ValueError: Please select either fdr or bon for is_q_mc. Below is my command:

kwargs = {
"label": [label1, label2, "Both", "None"],
"xylabel_prefix": "Per-allele effect size for ",
"sig_level": 5e-8,
"anno": True,
"save": os.path.join(base_path, plot_filename),
"save_args": {"dpi": 300, "facecolor": "white"}
}

[Cloufield]

Hi,
sorry for my late reply.
I update gwaslab to v3.5.0. It now support annotation with GENENAME.
I tested with your setting and should work now.

kwargs = {
"label": ["label1", "label2", "Both", "None"],
"xylabel_prefix": "Per-allele effect size for ",
"sig_level": 5e-8,
"anno": "GENENAME",
"build":"19",
"save": True,
"save_args": {"dpi": 300, "facecolor": "white"}
}

Additionally, you can pass a SNPID:text dictionary for customized annotation like "anno": {"rs11642015":"Some customized annotation"},

[Sandyyy123]

Thanks, I will check it out in the next few days. I will let you know if the issue persists.

…

On Tue, 29 Oct 2024 at 10:08, Yunye He ***@***.***> wrote: Hi, sorry for my late reply. I update gwaslab to v3.5.0. It now support annotation with GENENAME. I tested with your setting and should work now. kwargs = { "label": ["label1", "label2", "Both", "None"], "xylabel_prefix": "Per-allele effect size for ", "sig_level": 5e-8, "anno": "GENENAME", "build":"19", "save": True, "save_args": {"dpi": 300, "facecolor": "white"} } image.png (view on web) <https://github.com/user-attachments/assets/f84cff06-9c4a-46a4-a95b-6ae58e529114> Additionally, you can pass a SNPID:text dictionary for customized annotation like "anno": {"rs11642015":"Some customized annotation"}, image.png (view on web) <https://github.com/user-attachments/assets/1018dce0-1d58-474d-8725-95301e4a1059> — Reply to this email directly, view it on GitHub <#112 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD5PROMSYGP2MXKP4EGXXW3Z55GBNAVCNFSM6AAAAABQRWSSBGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBTGY2DCNZUHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Sandyyy123]

Hi,
I updated the gwaslab to the latest version available with pip install (3.5.0). I could not find 3.5.1 as per your logs for the updates. I was able to generate plots without heterogeneity. Thanks a lot.

However, it wasn't successful with anno="GENENAMES". I am getting no annotations using the command. I then tried to include build="19", i get an error: TypeError: compare_effect() got an unexpected keyword argument 'build'.

Prepare kwargs for the comparison

kwargs = {
    "label": [label1, label2, "Both", "None"],
    "xylabel_prefix": "Per-allele effect size for ",
    "r_se": True,
    "is_q": True,
    "is_q_mc": "fdr",
    "sig_level": 5e-8,
    "anno": "GENENAME",
    "build": "19",
    "anno_het": True,  # Always include this
    "legend_title": r'$ P < 5 x 10^{-8}$ in:',
    "verbose": True,
    "save": os.path.join(base_path, plot_filename),
    "save_args": {"dpi": 300, "facecolor": "white"}
}

I am also struggling with another issue of overlapping annotations, as two SNP names are completely overlapping. Is there a function like jitter in ggplot in your package?

Thanks

[Cloufield]

Hi,
Sorry for my late reply. I think the annotation function should work well using gwaslab v3.5.2.
For overlapping SNP names, I implemented a similar thing using a package called adjustText (https://adjusttext.readthedocs.io/en/latest/).
Unfortunately, it is not working well sometimes especially when the plot becomes complicated as you can see in the example plot (or maybe I haven't fully understood how this package works).
But You can try adjusting the args using adjust_text_kwargs_l for left side texts and adjust_text_kwargs_l for right side texts.
Or you can manually annotate those variants for now.
I will keep working on this and let you know when I solve this problem.

kwargs = {
"verbose":True,
"is_q":True,
"is_q_mc":"bon",
"label": ["label1", "label2", "Both", "None"],
"xylabel_prefix": "Per-allele effect size for ",
"sig_level": 6e-7,
"anno":"GENENAME",
"save": True,
 "wc_correction":"sig",
"anno_args":{"fontsize":15},
"font_args":{"fontsize":10},
"save_args": {"dpi": 300, "facecolor": "white"},
"adjust_text_kwargs_l":{"lim":2000,"expand_text":(3,3)},
"r_se":True
}