printing volcano plot

Question

[Gil Rodriguez]

hey friends, i need your help in using " volcano plot" ,

I have two questions about volcano plot,

1) i have a df and i want to add a volcano plot to see the gene expression 2) i want to print the volcano plot in a way i would be abble to see the "graph"

thank you a lot!

Edited: Tags

[Ram]

What have you tried?

[Gil Rodriguez]

as I understood after importing:

from bioinfokit import analys, visuz

I tried the following code:

visuz.gene_exp.volcano(df=df, lfc='log2FC', pv='p-value')

but cant understand if it is really the way and if it is so how to print it

[cpad0112]

here is the tutorial on volcanoplot using bioinfokit: https://www.reneshbedre.com/blog/volcano.html

[cpad0112]

provide an example df and what you want to plot on x and y. Please post your code if you went through any tutorials. If you are a newbie, try in R:

1. Load ggplot library
2. On x-axis, plot fold changes (log2)
3. On Y-axis, plot -log10 p-value or FDR.

If you do not want to code, try online volcano plotting service here with example data and your data: https://huygens.science.uva.nl/VolcaNoseR/

[ponganta]

library(tidyverse)

df %>%
  ggplot() +
  aes(x = l2fc, y =  -log(padj)) +
  geom_point()