Metadata-Version: 2.1
Name: volcanoPlot
Version: 0.0.2
Summary: creating a volcano plot in python for the given data, and save it as a png file.
Home-page: https://github.com/avivleemann/volcanoPlot
Author: avivleemann
Author-email: avivleemann@gmail.com
License: Apache Software License 2.0
Keywords: nbdev jupyter notebook python
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: pathlib
Requires-Dist: typing
Requires-Dist: adjustText
Provides-Extra: dev

# 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()
```

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }
&#10;    .dataframe tbody tr th {
        vertical-align: top;
    }
&#10;    .dataframe thead th {
        text-align: right;
    }
</style>

|     | 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')
```

![](index_files/figure-commonmark/cell-3-output-1.png)

``` python
df
```

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }
&#10;    .dataframe tbody tr th {
        vertical-align: top;
    }
&#10;    .dataframe thead th {
        text-align: right;
    }
</style>

|       | 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>
