This document outlines the steps necessary to generate the figures for the manuscript Neurovascular coupling and bilateral connectivity during NREM and REM sleep by K.L. Turner, K.W. Gheres, E.A. Proctor and P.J. Drew.
This data and code generates all main and supplemental figures and tables that involved data analysis.
Begin by downloading the entire code repository and the data from the following locations:
- Code repository location: https://github.com/KL-Turner/Turner-eLife2020
- Data repository location: https://doi.org/10.5061/dryad.6hdr7sqz5
The Dryad link contains a pre-analyzed AnalysisResults.mat structure that can be used to immediately generate the figures without re-analyzing any data. Download this file (~1.2 GB) as well as the entire github code repository. Add the AnalysisResults.mat file to the MATLAB file path by dragging it into the folder containing the code. Open the MATLAB function MainScript_eLife2020.m and run.
Software/System Requirements: Code was tested with MATLAB 2019b. Running MainScript_eLife2020.m took < 5 minutes to run on a 2018 Macbook Pro (2.6 Ghz 6-Core Intel i7 with 16 Gb 2400 MHz DDR4 RAM, Radeon Pro 560X GPU).
If you would like to automatically save the MATLAB figures and statistical read-outs, change line 29 of MainScript_eLife2020.m to saveFigs = 'y'; This will increase the analysis time to create a new folder /Summary Figures and Structures/MATLAB Analysis Figures/.
LabVIEW code used to acquire the data can be found at: https://github.com/DrewLab/LabVIEW-DAQ
- multiWaitbar.m Author: Ben Tordoff https://www.mathworks.com/matlabcentral/fileexchange/26589-multiwaitbar-label-varargin
- colors.m Author: John Kitchin http://matlab.cheme.cmu.edu/cmu-matlab-package.html
- Chronux subfunctions http://chronux.org/
- Ternary plot subfunctions: Uli Theune https://www.mathworks.com/matlabcentral/fileexchange/7210-ternary-plots
- Several functions utilize code written by Dr. Patrick J. Drew and Dr. Aaron T. Winder https://github.com/DrewLab