# volcanoPlot
<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
This file will become your README and also the index of your
documentation.
## Install
``` sh
pip install volcanoPlot
```
## How to use
# Example
``` markdown
Description:
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-count
```
``` python
import 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 |
</div>
``` python
from volcanoPlot.volcano import *
plot(df=df,x='log2FC', y ='log10p')
```
``` python
df
```
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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 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 19202 | PAK1 | 2658.104961 | -0.314881 | 0.129934 | -2.423387 | 0.015377 | 0.143495 | 1.813142 | False | p_value |
| 19203 | PRKD3 | 722.336078 | 0.175513 | 0.290260 | 0.604675 | 0.545395 | 0.827693 | 0.263289 | False | non-sig |
| 19204 | MLC1 | 10.608723 | -0.444787 | 0.810487 | -0.548790 | 0.583150 | 0.846594 | 0.234220 | False | non-sig |
| 19205 | ZBTB41 | 508.407691 | -0.547094 | 0.350267 | -1.561933 | 0.118304 | 0.427640 | 0.927002 | False | non-sig |
| 19206 | TMEM181 | 1506.912048 | -0.395167 | 0.160578 | -2.460906 | 0.013859 | 0.135332 | 1.858278 | False | p_value |
<p>19207 rows × 10 columns</p>
</div>
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"description": "# volcanoPlot\n\n<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->\n\nThis file will become your README and also the index of your\ndocumentation.\n\n## Install\n\n``` sh\npip install volcanoPlot\n```\n\n## How to use\n\n# Example\n\n``` markdown\nDescription:\nRSV or RS virus, short for respiratory syncytial virus, is a single-stranded RNA virus belonging to the pneumovirus genus of the virus family.\nSymptoms are usually mild, similar to a cold, but can cause very serious illness in infants.\n\nDataset:\nWe prepared a total of 8 RNA-Seq data from acute and chronic phases in nasal samples of 4 infants\nThe dataset was taken from Kaggle using the following API command:\nkaggle datasets download -d yoshifumimiya/rsv-rnaseq-count\n```\n\n``` python\nimport pandas as pd\nfrom pathlib import Path\ndf = pd.read_csv(Path.cwd() / 'res_example.csv')\ndf.head()\n```\n\n<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n .dataframe tbody tr th {\n vertical-align: top;\n }\n .dataframe thead th {\n text-align: right;\n }\n</style>\n\n| | gene_id | baseMean | log2FC | lfcSE | stat | p_value | p_adj | log10p | sig | regulated |\n|-----|-----------|-------------|-----------|----------|-----------|----------|----------|----------|-------|------------------|\n| 0 | WASH7P | 4.587857 | 2.458706 | 1.116766 | 2.201630 | 0.027691 | 0.202064 | 1.557654 | True | lfc2 and p_value |\n| 1 | LOC729737 | 122.155762 | 1.342039 | 0.716822 | 1.872207 | 0.061178 | 0.309724 | 1.213405 | False | non-sig |\n| 2 | TGIF1 | 1400.037490 | -0.099168 | 0.142399 | -0.696411 | 0.486171 | 0.796121 | 0.313211 | False | non-sig |\n| 3 | PRDX6 | 4794.111981 | -0.008120 | 0.200802 | -0.040440 | 0.967742 | 0.991057 | 0.014240 | False | non-sig |\n| 4 | CIC | 1581.916300 | 0.053769 | 0.177791 | 0.302430 | 0.762324 | 0.925608 | 0.117860 | False | non-sig |\n\n</div>\n\n``` python\nfrom volcanoPlot.volcano import *\nplot(df=df,x='log2FC', y ='log10p')\n```\n\n\n\n``` python\ndf\n```\n\n<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n .dataframe tbody tr th {\n vertical-align: top;\n }\n .dataframe thead th {\n text-align: right;\n }\n</style>\n\n| | gene_id | baseMean | log2FC | lfcSE | stat | p_value | p_adj | log10p | sig | regulated |\n|-------|-----------|-------------|-----------|----------|-----------|----------|----------|----------|-------|------------------|\n| 0 | WASH7P | 4.587857 | 2.458706 | 1.116766 | 2.201630 | 0.027691 | 0.202064 | 1.557654 | True | lfc2 and p_value |\n| 1 | LOC729737 | 122.155762 | 1.342039 | 0.716822 | 1.872207 | 0.061178 | 0.309724 | 1.213405 | False | non-sig |\n| 2 | TGIF1 | 1400.037490 | -0.099168 | 0.142399 | -0.696411 | 0.486171 | 0.796121 | 0.313211 | False | non-sig |\n| 3 | PRDX6 | 4794.111981 | -0.008120 | 0.200802 | -0.040440 | 0.967742 | 0.991057 | 0.014240 | False | non-sig |\n| 4 | CIC | 1581.916300 | 0.053769 | 0.177791 | 0.302430 | 0.762324 | 0.925608 | 0.117860 | False | non-sig |\n| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |\n| 19202 | PAK1 | 2658.104961 | -0.314881 | 0.129934 | -2.423387 | 0.015377 | 0.143495 | 1.813142 | False | p_value |\n| 19203 | PRKD3 | 722.336078 | 0.175513 | 0.290260 | 0.604675 | 0.545395 | 0.827693 | 0.263289 | False | non-sig |\n| 19204 | MLC1 | 10.608723 | -0.444787 | 0.810487 | -0.548790 | 0.583150 | 0.846594 | 0.234220 | False | non-sig |\n| 19205 | ZBTB41 | 508.407691 | -0.547094 | 0.350267 | -1.561933 | 0.118304 | 0.427640 | 0.927002 | False | non-sig |\n| 19206 | TMEM181 | 1506.912048 | -0.395167 | 0.160578 | -2.460906 | 0.013859 | 0.135332 | 1.858278 | False | p_value |\n\n<p>19207 rows \u00d7 10 columns</p>\n</div>\n",
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