Metadata-Version: 2.1
Name: levseq_vis
Version: 1.2.4
Home-page: https://github.com/fhalab/levseq/
Author: Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li
Author-email: ylong@caltech.edu
License: GPL3
Project-URL: Bug Tracker, https://github.com/fhalab/levseq/
Project-URL: Documentation, https://github.com/fhalab/levseq/
Project-URL: Source Code, https://github.com/fhalab/levseq/
Keywords: Nanopore,ONT,evSeq,LevSeq
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: Bio
Requires-Dist: biopython
Requires-Dist: holoviews
Requires-Dist: jupyterlab
Requires-Dist: mappy
Requires-Dist: matplotlib
Requires-Dist: ninetysix
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: sciutil
Requires-Dist: seaborn
Requires-Dist: scikit-learn
Requires-Dist: statsmodels
Requires-Dist: tqdm
Requires-Dist: biopandas

# A Beta project LevSeq vis

Web app for combining and visualising [LevSeq](https://github.com/fhalab/LevSeq) sequence function data.

Test it out with the [data](data/) in the data folder. Use the columns in the screenshot below. 

Once you have your figures you can download the csv results by hovering on any of the tables.

## Upload with data

Using the `visualization_partial.csv` file as the variant file and the `300-1` in the `ep1` folder.

### Tables for download
We join the data based on user selected columns (in this case `cis` and `trans`) from a LC-MS run.

![table](images/table.png)

### Overview of alignment count
The alignment count is how many reads assigned to each type were assigned to each well.
![align](images/alignment_count.png)

### Scatterplot of multiple features
This shows the fitness values of two plotted against eachother, if only one feature is provided we will plot it against 
the alignment count.

![align](images/cis_trans.png)
![align](images/single_feature.png)

## Please provide feedback
Leave a feature request in the issues or on [LevSeq](https://github.com/fhalab/LevSeq) . 

## Cite
Cite our [paper](https://doi.org/10.1101/2024.09.04.611255) please if you use it.

## Developers

```
streamlit run app.py
```

## References
Streamlit app based on: https://share.streamlit.io/streamlit/example-app-csv-wrangler/
Thanks to you who made it <3 
