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Project title

Sodium salicylate improves detection of amplitude-modulated sound in mice

Description

This is the code to generate Figure panels for the manuscript "Sodium salicylate improves detection of amplitude-modulated sound in mice" by Van den Berg et al, 2024.

Authors

* equal contributions

Last updated

12 Mar 2024

BUILD INSTRUCTIONS

  1. Dependencies
  • Obtain raw data files and extract the folder /Data/ in the root directory of this repository
  • Matlab (version 2019a or later) for the vast majority of figures
  • Igor Pro 9 for Figure S3
  • R and RStudio (3.6.x) for statistics in Figures 4 and 5.
    • Install the following R packages ("here","lme4","nlme","plyr","multcomp") or run the following code in the R console:
    packages <- c("here","lme4","nlme","plyr","multcomp")
install.packages(packages)
  1. Directory structure
  • \Data\ Stores raw and analyzed data.
  • \Figures\ Stores illustrator files to assemble final figures.
  • \src\paper\ Stores codes to generate figure panels and illustrations.
  • \src\statistics\ Stores codes for statistics related to linear mixed models (Fig .
  • \functions\ Stores miscellaneous functions needed to run the code
  1. How to run the project
  • Fig S3:
    • Open the Igor packaged experiment (.pxp) file src\paper\FigS3_Unit_Salicylate_effect_proportions.pxp in Igor Pro.
    • In the command window, type saveAllPics() and press enter.
  • All other figures:
    • Extract the folder \Data\ from source data into the root directory
    • Run the script run_me_AllFigures.m in Matlab, with the root directory as the working directory.
  • All figures subpanels will be stored under \Figures\Links\. This ensures all .ai files under \Figures\ can find them as linked files.
  • Linear mixed-effect model statistics: Run the R markdown file src\statistics\StatisticsSalicylate_2022-09-15.rmd in R-studio.