Analysis Software Accompanying the Publication "Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network"
Using the anaconda package manager to create a virtual environment and install the following packages from the command line:
conda create --name fnoise-env
conda activate fnoise-env
conda install scipy seaborn
pip install statannotations
Change the paths info_files/dir_data.csv. dir_extendend_data is the path to
the directory containing the extended data on your computer. output_dir is
the path to the directory in which you would like analysis output files (plots
and .csv results) stored on your computer.
These scripts can be run from the command line from their parent directory:
python <script_name>.py
Run this script to generate violin plots for series of data in Figure 2 and Figures S6-S11.
This script performs hierarchical clustering of traces within each experiment. The output is a dendrogram plot for EXP013, Figure 3b.
This script performs the time-interval correlation analysis (see Materials and Methods). It outputs the results of the correlation analysis as a .csv file, which is used to create Figure 3c.
This script generates plots indicating how groups of compounds respond collectively to applied perturbations, used to create Figure 5a.