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reneshbedre / bioinfokit

Bioinformatics data analysis and visualization toolkit
MIT License
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It is possible to create a volcano plot without significant genes? #50

Closed diitaz93 closed 2 years ago

diitaz93 commented 2 years ago

Hi! I have read through #22, #31 and #39 which are similar, as they show the error AssertionError: either significant or non-significant genes are missing; try to change lfc_thr or pv_thr to include both significant and non-significant genes, but I can't find a way to plot a volcano plot when there are no significant genes. I am using these plots as an exploratory analysis of several datasets and it would be very useful for me to see cases where there are no significant genes.

Thanks!

reneshbedre commented 2 years ago

Yes, it could be possible. Change the threshold of log fold change and p values just to make a few genes at a significant level (based on your criteria). You can also keep the same color using a color parameter.