package website url: https://avivleemann.github.io/volcanoPlot/
pip install volcanoPlotDescription:
RSV or RS virus, short for respiratory syncytial virus, is a single-stranded RNA virus belonging to the pneumovirus genus of the virus family.
Symptoms are usually mild, similar to a cold, but can cause very serious illness in infants.
Dataset:
We prepared a total of 8 RNA-Seq data from acute and chronic phases in nasal samples of 4 infants
The dataset was taken from Kaggle using the following API command:
kaggle datasets download -d yoshifumimiya/rsv-rnaseq-countimport pandas as pd
from pathlib import Path
df = pd.read_csv(Path.cwd() / 'res_example.csv')
df.head()
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| gene_id | baseMean | log2FC | lfcSE | stat | p_value | p_adj | log10p | sig | regulated | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | WASH7P | 4.587857 | 2.458706 | 1.116766 | 2.201630 | 0.027691 | 0.202064 | 1.557654 | True | lfc2 and p_value |
| 1 | LOC729737 | 122.155762 | 1.342039 | 0.716822 | 1.872207 | 0.061178 | 0.309724 | 1.213405 | False | non-sig |
| 2 | TGIF1 | 1400.037490 | -0.099168 | 0.142399 | -0.696411 | 0.486171 | 0.796121 | 0.313211 | False | non-sig |
| 3 | PRDX6 | 4794.111981 | -0.008120 | 0.200802 | -0.040440 | 0.967742 | 0.991057 | 0.014240 | False | non-sig |
| 4 | CIC | 1581.916300 | 0.053769 | 0.177791 | 0.302430 | 0.762324 | 0.925608 | 0.117860 | False | non-sig |
from volcanoPlot import volcano
volcano.plot(df=df,x='log2FC', y ='log10p')