diff --git a/figures/Schmidt2018/README.md b/figures/Schmidt2018/README.md index a591dbfd6845d83580f70ed310e8551e775586ef..5780f29e49d8aff8c30c4fc0ee252bcdf287f524 100644 --- a/figures/Schmidt2018/README.md +++ b/figures/Schmidt2018/README.md @@ -4,12 +4,14 @@ This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R  -Please note: Figures 2, 5, and 8 show slight deviations from the published figures in the paper. Published Figures 2 and 5 miss a few data points. This error slipped in during the review process. Importantly, the presented fits are identical in the (correct) figures in this repository and in the manuscript. These deviations thus do not affect the scientific conclusions. - Please note that the placement of areas in Figure 7 will deviate from the published figure, because their location depends on the force-directed algorithm implemented in `igraph` and `python-igraph` does not allow manual setting of the random seed for the algorithm. This is a mere visual issue and does not affect the scientific content. Please note that, since we currently cannot publish the data on Neuronal Densities, Figures 2 and 5 can currently not be produced and executing it throws an error. +Reproducing the figures requires some additional Python packages listed in `additional_requirements.txt`. They can be installed using pip by executing: + +`pip install -r additional_requirements.txt` + If snakemake is installed, the figures can be produced by executing `snakemake` diff --git a/figures/Schmidt2018_dyn/README.md b/figures/Schmidt2018_dyn/README.md index bc6bd073da0a5e21dd4a96697cbabf7083aead6c..64fdd94d3c9e8efd07ae52b73641fe50b7187763 100644 --- a/figures/Schmidt2018_dyn/README.md +++ b/figures/Schmidt2018_dyn/README.md @@ -22,6 +22,12 @@ and responses to parametric stimuli in macaque V1, available in the crcns.org da Figure 8 requires the experimental fMRI data (described by Babapoor-Farrokhran et al. (2013), see Methods section of Schmidt et al. 2018 for more details) that are contained in this repository in `Fig8_exp_func_conn.csv`. +### Requirements + +Reproducing the figures requires some additional Python packages listed in `additional_requirements.txt`. They can be installed using pip by executing: + +`pip install -r additional_requirements.txt` + ### Snakemake workflow The entire workflow from raw spike files till the final figures is defined in `Snakefile` and `Snakefile_preprocessing`. If snakemake is installed, the figures can be produced by executing `snakemake`.