This code generates the 3D lineage trees of (1) all clones; (2) individual clones; (3) all clones , but with only those cells that survived to the end of simulation; and (4) individual clones containing only those cells that survived to the end of simulation – see the quick guide to LinG3D routines. The code is generated in three programming languages: Matlab, R, and Python.

MATLAB software (the R2020b version on a Mac computer was used for all testing)

R language (the R version 4.1.1 on a Mac computer (macOS Big Sur) was used for all testing)

Python (version >3.8 on a Mac computer was used for testing)

Matlab: this code does not need installation

R: the required libraries are readr, rapportools, rgl, and devtools.

    install.packages("readr")   

    install.packages("rapportools")
    
    install.packages("rgl")

    install.packages("devtools")

Python: It requires the following libraries:

Numpy
Scipy
Matplotlib

Matlab: Download all MATLAB files (add all files and folders to your MATLAB path) Run one of the routines listed below.

R:

OPTION 1 (Install the LinG3D package)

    library(devtools)  # load the devtools library

    install_github("rejniaklab/r_LinG3D")  # install the package from GitHub

    library(LinG3D)  # load the LinG3D library

    linG3DClone(arguments)  # run the routine (example)

OPTION 2 (Use the routines)

    1.	Download all R codes and data folders to your computer.
    
    2.	Source each function. For example, to source linG3DClone.R saved in your_folder on the desktop type on the console,
            source("~/Desktop/your_folder/linG3DClone.R").
            
    3.	Run the function. For example, to run linG3DClone.R type on the console,
            linG3DClone(arguments).

Python: You can run the .py scripts from the terminal

$ git clone https://github.com/rejniaklab/LinG3D.git
$ cd LinG3D
$ python3 linG3DAliveAll.py
$ python3 linG3DAliveClone.py
$ python3 linG3DAll.py
$ python3 linG3DClone.py

The codes are also available as Jupyter notebooks

The following set of functions are available, and explained in detail in the quick guide to LinG3D routines. i) linG3DAliveAll ii) linG3DAliveClone iii) linG3DAll iv) linG3DClone

linG3DClone(pathData='exampleB05',cloneNum=5,IsGradient = 1,xmin=-100,xmax=100,ymin=-100,ymax=100,tmin=0,tmax=100000,fileStep = 2000,toPrint=1)

Anjun Hu, Awino Maureiq E. Ojwang’, Kayode Olumoyin, Katarzyna Rejniak

0.1 Initial release

This project is licensed under the GNU General Public License v3.0.