# Introduction
Python software for simulating celluar/microbial clonal evolution with Gillespie algorithm usage
# Installation and Usage
The simpliest installation:
```
python -m pip install clonalEvolution
```
Usage in python:
```
from microbialClonalEvolution import mainView
mainView.run()
```
Usage from console:
```
python -m clonalEvolution
# for simply run graphic verion of software
python -m clonalEvolution -h
# to see instructions for command line parametrization
```
# Usage Instructions
## General Tab:
 \
file name - used in multiple functions: saving files, plots, parameters; specify name of file (according to windows acceptable characters), data files will have cycle number (name_number.csv/.txt) \
file path - used in multiple functions: saving files, plots, parameters; specify absolute path to folder where simulation data should be saved \
file description - 'TODO' add description in params/data file about simulation specyfied by user \
\
clone diagram - button, fire the muller plot creation. It is needed to specify path with muller plot data generated from simulaiton \
file structure (file-name_muller_plot_'binned'_data.txt):
```
clone, cells, previous clone
(0, 5000, 0)
```
mutations histograms - button, fire the VAF plot creation for all clones in specified file. File is needed to be one of generated simulation data \
file structure (file-name_cycle.csv/.txt):
```
,Clone number,Cells number,Mean fitness,Mean mutation number,Driver mutation list,Passener mutation list,Previous clone number
0,0,5000,1,0,[],[],0
```
## Generated tab:
 \
select which files should be saved automaticaly after one cycle specified in parameters (skip). Not all types works for both algorithm versions 'TODO'
## Parameters tab:
## Plot tab:
## Threads tab:
## Main controls:
# License
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
## Disclaimer
Cellular/Microbial Clonal Evolution simulations basing on Gillespie algorithm.
Copyright (C) 2022 by Jarosław Gil
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
# Author
Jarosław Gil, Silesian Univeristy of Technology, Department of Computer Graphics, Vision and Digital Systems.
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