search

scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
92 stars 19 forks source link

Fixing incorrect y-axis in volcano plot #621

Closed pakiessling closed 3 weeks ago

pakiessling commented 4 weeks ago

Report

Hi, I want to fix the incorrect y-axis scaling which is caused by max_log2fc being used as y-axis maximum.

However I have not been able to execute the code in https://github.com/theislab/pertpy-tutorials/blob/main/differential_gene_expression.ipynb

----> pydeseq2.volcano(res_df, log2fc_thresh=0)

AttributeError: 'PyDESeq2' object has no attribute 'volcano'

Is there a specific branch I should be looking at?

Ty!

Version information

No response

Zethson commented 3 weeks ago

Sorry, it got renamed to plot_volcano. I'll fix it in the example.