Plots for Neuropixels Data

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These files assume the following hierarchy:

~/
  data/ (code and data go here) [in code, put path in DIRECTORY]
    plots/ [in code, put path in SUMMARY_PLOTS_DIRECTORY]
      cells/ (PSTH plots for every cell in every probe) [put path in CELL_PLOTS_DIRECTORY]
        probeA/ [ you just have to make these directories, with those exact names ]
        probeB/
        ...
        probeF/
      percentile/ (Plots for percentiles of every mouse)
      probes/ (PSTH plots averaged across all cells and trials) [put path in PROBE_PLOTS_DIRECTORY]
      variations/ (directories of class names) [in code, put path in VAR_DIREC]
    trial_data/ (data calculated for every trial)

Libraries Needed

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library >= version || pip install library

rpy2 >= 3.0.4 || pip install rpy2

numpy >= 1.14.2 || pip install numpy

pickle >= 4.0 || pip install pickle

h5py >= 2.8.0 || pip install h5py

matplotlib >= 3.0.2 || pip install matplotlib

Steps for Running

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1. Make sure you have all the directories and folders set up. Follow the [...put path in (VARIABLE_NAME_HERE)] comments to help you figure out where to put the paths in the code (Code could be written to automatically create the directories...).

2. Run nwb_plots.py. If everything goes well, the output before the program ends should be run again.

3. Run nwb_plots.py again. Repeat 2 and 3 for all mice (you can change the mouse you're working on by looking for the variable MOUSE_ID in the code). You should now see plots in SUMMARY_PLOTS_DIRECTORY and CELL_PLOTS_DIRECTORY. These two steps should take the longest.

4. Run nwb_plots_percentile.py for each mouse. These plots will be saved in percentile.

5. Run nwb_dropout.py for each mouse. These plots will be saved in probes.

NOTE: VAR_DIREC is no longer needed. Neither is nwb_trials.py