nkoch/model_mutations_2022
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Added a few more comments to code

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nkoch1 2022-11-12 00:11:53 -05:00
parent 9037e1a016
commit 93ab5c1792
2 changed files with 15 additions and 16 deletions
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29
Code/csv_generation/Plotting_data_collection.py
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@ -15,8 +15,8 @@ from ast import literal_eval
import string import string
import matplotlib.cm as cm import matplotlib.cm as cm
# %% rheo_{}_ex.csv, AUC_{}_ex.csv # %% rheo_{}_ex.csv, AUC_{}_ex.csv #####################################################################################
# Collect examples of effects of a shift, a slope change and a change in g on AUC and rheobase
## AUC ################### ## AUC ###################
AUC_shift = pd.DataFrame(columns=['alteration', 'RS Pyramidal', 'RS Inhibitory', 'FS', 'IB', AUC_shift = pd.DataFrame(columns=['alteration', 'RS Pyramidal', 'RS Inhibitory', 'FS', 'IB',
'RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$', 'FS +$K_V1.1$','Cb stellate', 'RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$', 'FS +$K_V1.1$','Cb stellate',
@ -35,16 +35,12 @@ AUC_g = pd.DataFrame(columns=['alteration', 'RS Pyramidal', 'RS Inhibitory', 'FS
script_dir = os.path.dirname(os.path.realpath("__file__")) script_dir = os.path.dirname(os.path.realpath("__file__"))
fname = os.path.join(script_dir, ) fname = os.path.join(script_dir, )
# f = h5py.File(fname, "r")
models = ['RS_pyramidal', 'RS_inhib', 'FS','RS_pyramidal_Kv', 'RS_inhib_Kv', 'FS_Kv', 'Cb_stellate','Cb_stellate_Kv', models = ['RS_pyramidal', 'RS_inhib', 'FS','RS_pyramidal_Kv', 'RS_inhib_Kv', 'FS_Kv', 'Cb_stellate','Cb_stellate_Kv',
'Cb_stellate_Kv_only','STN','STN_Kv', 'STN_Kv_only'] 'Cb_stellate_Kv_only','STN','STN_Kv', 'STN_Kv_only']
model_labels = ['RS Pyramidal','RS Inhibitory', 'FS','RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$', model_labels = ['RS Pyramidal','RS Inhibitory', 'FS','RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$',
'FS +$K_V1.1$','Cb stellate','Cb stellate +$K_V1.1$', 'FS +$K_V1.1$','Cb stellate','Cb stellate +$K_V1.1$',
'Cb stellate $\Delta$$K_V1.1$','STN','STN +$K_V1.1$', 'STN $\Delta$$K_V1.1$'] 'Cb stellate $\Delta$$K_V1.1$','STN','STN +$K_V1.1$', 'STN $\Delta$$K_V1.1$']
shift_interest = 'n' shift_interest = 'n'
for i in range(len(models)): for i in range(len(models)):
with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_shift_AUC.json'.format(models[i])) as json_file: with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_shift_AUC.json'.format(models[i])) as json_file:
@ -56,7 +52,6 @@ for i in range(len(models)):
AUC_shift['alteration'] = AUC_shift.index AUC_shift['alteration'] = AUC_shift.index
slope_interest = 's' slope_interest = 's'
for i in range(len(models)): for i in range(len(models)):
with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_slope_AUC.json'.format(models[i])) as json_file: with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_slope_AUC.json'.format(models[i])) as json_file:
@ -70,6 +65,7 @@ for i in range(len(models)):
pass pass
AUC_slope['alteration'] = AUC_slope.index AUC_slope['alteration'] = AUC_slope.index
g_interest = 'Kd' g_interest = 'Kd'
for i in range(len(models)): for i in range(len(models)):
with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_g_AUC.json'.format(models[i])) as json_file: with open('../Sensitivity_Analysis/Data/SA_summary_df/{}_g_AUC.json'.format(models[i])) as json_file:
@ -86,7 +82,6 @@ AUC_g.to_csv('AUC_g_ex.csv')
## rheobase ################### ## rheobase ###################
rheo_shift = pd.DataFrame(columns=['alteration', 'RS Pyramidal', 'RS Inhibitory', 'FS', 'IB', rheo_shift = pd.DataFrame(columns=['alteration', 'RS Pyramidal', 'RS Inhibitory', 'FS', 'IB',
'RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$', 'FS +$K_V1.1$','Cb stellate', 'RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$', 'FS +$K_V1.1$','Cb stellate',
'Cb stellate +$K_V1.1$', 'Cb stellate $\Delta$$K_V1.1$', 'STN', 'STN +$K_V1.1$', 'Cb stellate +$K_V1.1$', 'Cb stellate $\Delta$$K_V1.1$', 'STN', 'STN +$K_V1.1$',
@ -148,14 +143,13 @@ for i in range(len(models)):
rheo_g[model_labels[i]] = data[g_interest] rheo_g[model_labels[i]] = data[g_interest]
rheo_g['alteration'] = rheo_g.index rheo_g['alteration'] = rheo_g.index
rheo_shift.to_csv('rheo_shift_ex.csv') rheo_shift.to_csv('rheo_shift_ex.csv')
rheo_slope.to_csv('rheo_slope_ex.csv') rheo_slope.to_csv('rheo_slope_ex.csv')
rheo_g.to_csv('rheo_g_ex.csv') rheo_g.to_csv('rheo_g_ex.csv')
# %% Model fI # %% Model fI ##########################################################################################################
# for each model # for each model generate summary csv of sensitivity analysis results on AUC and rheobase
# | (index) | mag | alt | type | F | I | # | (index) | mag | alt | type | F | I |
# | 0 | -10 | m | shift | array | array | # | 0 | -10 | m | shift | array | array |
@ -230,7 +224,10 @@ for m in models:
# %% firing_values.csv, model_spiking.csv, model_F_inf.csv # %% firing_values.csv, model_spiking.csv, model_F_inf.csv #############################################################
# generate firing_values.csv with values for hysteresis from ramp current input
# generate model_spiking.csv with example model response to step current
# generate model_F_inf.csv with model fI curve data
import numpy as np import numpy as np
import pandas as pd import pandas as pd
@ -272,7 +269,8 @@ for model_name in models:
firing_values.to_csv('firing_values.csv') firing_values.to_csv('firing_values.csv')
spiking.to_csv('model_spiking.csv') spiking.to_csv('model_spiking.csv')
model_F_inf.to_csv('model_F_inf.csv') model_F_inf.to_csv('model_F_inf.csv')
# %% model_ramp.csv # %% model_ramp.csv ####################################################################################################
# generate model_ramp.csv with model responses to ramp input
# | (index) | t | models .... # | (index) | t | models ....
import numpy as np import numpy as np
import pandas as pd import pandas as pd
@ -298,8 +296,9 @@ for model_name in models:
model_ramp.to_csv('model_ramp.csv') model_ramp.to_csv('model_ramp.csv')
#%% sim_mut_AUC.csv, sim_mut_rheo.csv # #%% sim_mut_AUC.csv, sim_mut_rheo.csv ##################################################################################
# generate mutation plot data # generate mutation plot data in sim_mut_AUC.csv and sim_mut_rheo.csv for the AUC and rheobase effects respectively for
# each mutation in each model
mutations = json.load(open("../KCNA1_mutations/mutations_effects_dict.json")) mutations = json.load(open("../KCNA1_mutations/mutations_effects_dict.json"))
keys_to_remove = ['V408L', 'T226R', 'R239S', 'R324T'] keys_to_remove = ['V408L', 'T226R', 'R239S', 'R324T']
for key in keys_to_remove: for key in keys_to_remove:

2
Code/csv_generation/SA_collection.py
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@ -285,7 +285,7 @@ shift_df.to_json('./Sensitivity_analysis/rheo_shift_box_kendall_corr.json')
slope_df.to_json('./Sensitivity_analysis/rheo_slope_box_kendall_corr.json') slope_df.to_json('./Sensitivity_analysis/rheo_slope_box_kendall_corr.json')
g_df.to_json('./Sensitivity_analysis/rheo_g_kendall_corr.json') g_df.to_json('./Sensitivity_analysis/rheo_g_kendall_corr.json')
#%% create csv file #%% create csv files for plotting
# | (index) | model | corr | p_value | g | color # | (index) | model | corr | p_value | g | color
#% AUC #% AUC
AUC_shift_json = pd.read_json('./Sensitivity_analysis/shift_kendall_corr_rel.json', orient='records') AUC_shift_json = pd.read_json('./Sensitivity_analysis/shift_kendall_corr_rel.json', orient='records')