Martin Spacek fd9ef83f69 Clarify R/README.md a little 2 years ago
..
README.md fd9ef83f69 Clarify R/README.md a little 2 years ago
figure_1.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_1_S2.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_1_S3.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_1_S4.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_1_S5.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_1_S6.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_2.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_3.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_3_S1.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_4.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_4_S1.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_5.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_5_S1.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_5_S2.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_6.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
figure_6_S1.Rmd 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago
get_data.R 50117c3582 Copy new R folder from main natfeedback_code repo 2 years ago

README.md

The R markdown files (.Rmd) contain code for all statistical analyses in R, separately for each figure in the manuscript. The output created by fitting linear mixed-effects models is saved in the corresponding .pdf files in the parent folder's stats folder.

For easy programmatic access when plotting in Python, coefficients of the linear models are also saved in .csv files in the parent folder's stats folder.

The data exported from Python for use as input to the R analyses are stored in .csv files in the parent folder's csv folder. The .csv input files are parsed by a helper function, get_data.R, which creates unique IDs for mice, series, experiments, and neurons, required to fit the models.

datacite.yml
Title Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN
Authors Spacek,Martin;LMU Munich;0000-0002-9519-3284
Crombie,Davide;LMU Munich;0000-0003-3424-3249
Bauer,Yannik;LMU Munich;0000-0003-2613-6443
Born,Gergory;LMU Munich;0000-0003-0430-3052
Liu,Xinyu;LMU Munich;0000-0002-3527-6168
Katzner,Steffen;LMU Munich;0000-0002-4424-2197
Busse,Laura;LMU Munich;0000-0002-6127-7754
Description Data and Python code for regenerating plots in Spacek et. al., 2022, published in eLife (https://doi.org/10.7554/eLife.70469). Use `main.py` to load data for all LGN optogenetic experiments as a function of stimulus type (movies, gratings), run state, and opto state. Data are loaded from pandas DataFrames, which are saved as Python pickles. Statistics are computed using the included R code.
License Creative Commons Attribution 4.0 International Public License (https://creativecommons.org/licenses/by/4.0/)
References Spacek, M. A., Crombie, D., Bauer, Y., Born, G., Liu, X., Katzner, S., Busse, L. Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN. eLife 11:e70469 (2022) [doi:10.7554/eLife.70469] (IsSupplementTo)
Funding DFG, SFB 1233 TP 13, project number 276693517
DFG, SFB 870 TP 19, project number 118803580
DFG, BU 1808/5-1
Joachim Herz Stiftung (Joachim Herz Foundation)
Keywords lateral geniculate nucleus
corticothalamic feedback
naturalistic movies
locomotion
pupil dilation
firing mode
Resource Type Dataset