vgrampy

Author: Noel Lefevre (Adapted from Steven Ramsey's LDNH README.md)

Date: January 29, 2024

Python tools for analyzing electrochemistry voltammograms. The script vg2signal.py processes a potentiostat voltammogram data file using a method analogous to LDNH, into a signal value and optionally plots the "detilted" voltammogram. It can also optionally re-center the analysis window on the empirical peak voltage from the first phase of analysis of the data (which is only a good idea to run on a voltammogram that has a clear and unambiguous analyte peak).

Prerequisites for using this software

• Python 3.9 (scikit-learn package does not work on any later version)
• git
• Coding Application/IDE
• A github account

So far, this software has only been tested on Windows11/x86_64. It has not been tested on MacOS 12.6.5 on Apple M1, Linux/x86_64, etc.

How to install and run groupvg2.py for user-friendly branch:

1. Download Python 3.9 (can be 3.9.0-3.9.12)

   1. make sure to select Add Python 3.9 to PATH when you install it

2. Download a coding application/IDE (i.e. VisualStudio, VSCode, PyCharm)

3. Clone the software repo (2 ways)

   1. sign into your github through the IDE
   2. paste the repo address: https://github.com/ramseylab/vgrampy.git

4. Change to the correct branch- for running for one experiment use user-friendly

   1. for VisualStudio- on the right side click Git Changes and change the drop-down menu

5. Open the command prompt and change your directory to the software repo cd vgrampy

   1. if you open the command prompt within your IDE, it should already be in the right directory

6. Install all of the required packages:

pip install numpy

• depending on your computer, it may be pip or pip3
• most packages will be installed when creating the virtual environment

7. Run the program by typing in

python groupvg2.py

• depending on your computer, it may be python or python3 or py

Options for groupvg2.py:

There are default parameters applied to the code, but you can change them if needed

• Log-Transformation: log-transform or not (default = log)
• Peak Feature: peak curvature, height or area (default = peak curvature)
• Smoothing Parameter: amount of smoothing the voltammogram (default = 0.006)
• Stiffness Parameter: how strictly the spline passes through the data points (default = 0)
• Window Width: voltage width to window out when making the spline (default = 0.15)

Plotting In groupvg2.py:

You can choose whether or not to plot, and whether to separate those plots by concentration

The plots saved will be the smoothed and detilted voltammograms, more options are in plotseparate.py

Output Files

There are 3 files created by running groupvg2.py

The naming convention for each file is: [filename]_[log or no log]_[smoothing parameter]_[stiffness parameter]_[window width]

For example dataframe_log_curvature_0.006_0_0.15.xlsx

1. A dataframe excel file that has each replicates' data:

conc	replicate	V	I	logI	smoothed	detilted
0	1	0.504	0.08379	-0.25515	-0.24431	0
0	1	0.508	0.8375	-0.25584	-0.23192	0
0	1	0.512	0.8564	-0.21048	-0.21048	0
0	1	0.516	0.8797	-0.18492	-0.18001	0
0	1	0.520	0.9069	-0.14098	-0.14420	0

2. A signal excel file that has the signal, peak voltage, and voltage center for each replicate:

In the file, the vcenter column contains the voltage value, for each voltammogram, of the inflection point identified by the "shoulder getter" function; and the peak V column contains the voltage value, for each voltammogram, at which the background-subtracted voltammogram has a critical point within the censoring window.

file	signal	peak V	vcenter
2024_01_02_cbz00_01.txt	23.9020	1.083	1.012
2024_01_02_cbz15_01.txt	324.8372	1.074	1.076
2024_01_02_cbz15_02.txt	236.3741	1.061	1.064

3. A stats excel file that has the signal, peak voltage, and voltage center for each replicate:

conc	average	std	CV	T-Statistic	avg peak	std peak
0.0μM	28.9	20.11	0	0	1.02	0.04
5.0μM	84.11	14.19	0.169	6.34	1.06	0.01
10.0μM	9.80	29.8	0.206	5.19	1.07	0
15.0μM	227.97	42.43	0.186	4.54	1.07	0

Troubleshooting:

1. Problem: When I try to switch my branch to user-friendly I get the error:

Exception of type 'Microsoft.TeamFoundation.Git.Contracts.GitCheckoutConflictException' was thrown`"

This means that the destination branch has more exclusions in .gitignore than the original branch.

Solution: in the Git changes, 'ignore' the .suo (or .wsuo) file and then do a force checkout to get to your desired branch.

2. Problem: When I am installing the packages, I get an error with scikit-fda

This means that you are not using Python 3.9

Solution:

• Uninstall the Python version you have on your computer (make sure it is no longer in PATH).
• Install Python 3.9 and change your interpreter to the correct version

3. Problem: I cannot access the vgrampy github

You need to be added by an admin in order to access the code (currently Noel)

Solution: email the admin to get your github account added to the repo