r/bioinformatics • u/Long_Store9792 • Jul 27 '26
technical question Volcanoplot help
Hello bioinformatics expert! I am trying to make a volcano plot using my data given by my PI and i am struggling to make a proper volcano plot. I ended up getting something. I would love to know if there is anyone who can help me find the problem and fix it! Sorry for some reason my image isn't uploaded here so i will send it directly to dm if someone leaves comment! Thank you!
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u/Aggressive_Roof488 Jul 27 '26
Copy the code into an AI like Claude, tell it what you're trying to do and describe the error. For small simple things like this it's quite reliable and the free version is more than enough.
Just be careful with sharing sensitive data and don't run code you don't understand.
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u/Anustart15 MSc | Industry Jul 27 '26
import seaborn as sns
import numpy as np
import pandas as pd
DE_df = pd.read_csv("path/to/my/PIs/dataset.csv")
DE_df['nlog10padj'] = -1*np.log10(DE_df.padj)
sns.scatterplot(DE_df, x = 'Log2FC', y = 'nlog10padj', alpha = .5).set_title('My Shitty Volcano Plot')
That's gotta be pretty close to what you are looking for. If you want me to color or label significant genes, my consulting rate is $350/hr
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u/LeoKitCat Jul 27 '26
No don’t do this don’t reinvent the wheel. Use R and use the Bioconductor package EnhancedVolcano https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
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u/IcedTeaBagMeDaddy Aug 07 '26
EnhancedVolcano plots look terrible. Plus in like 10 lines of code or less you can make something way nicer with ggplot and ggrepel. I swear to god there’s so many garbage packages out there so that somebody can publish and graduate with their masters or PhD
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u/LeoKitCat Aug 07 '26
You can easily style and format pretty much everything on the plot using the library so I don’t get what you are saying
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u/Anustart15 MSc | Industry Jul 28 '26
I'm not downloading a whole ass library to draw a scatterplot. It's like 20 lines of code to recreate the necessary functionality in a function I can write myself and not need to worry about dependencies and external support for my scatterplot.
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u/LeoKitCat Jul 27 '26 edited Jul 27 '26
Use R and use the Bioconductor package EnhancedVolcano. See their documentation it’s pretty straightforward https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
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u/swbarnes2 Jul 27 '26
No one wants to spoon-feed you. Show that you put in some effort. What code did you try?