Usage of pvals for volcano plots instead of FDR-corrected p-values

[ramadatta]

Question

In the Single cell best practices DGE analysis, it is mentioned:

"Volcano plots are often used to visualize the results of statistical testing, and they show the change in expression on the x-axis (log-fold change) and statistical significance on the y-axis (FDR-corrected p-values)."

But in the volcano plot code, pvalue was used to plot on the y axis.

result["-logQ"] = -np.log(result["pvals"].astype("float"))

It should instead be pvals_adj (since sc_toolbox.tools.de_res_to_anndata renames FDR to pvals_adj)

I found transition from FDR -> pvals_adj -> pvals a bit confusing. Is there some specific reason, please let me know if I missing something.