nkoch/model_mutations_2022
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Minor figure updates 02.03.2022

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nkoch1 2022-03-02 23:31:16 -05:00
parent 81599f7748
commit c8df08c34d
8 changed files with 18 additions and 28 deletions
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10
Figures/AUC_correlation.py
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@ -4,20 +4,15 @@ Created on Sat Jul 3 19:52:04 2021
@author: nils
"""
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import string
import textwrap
import json
import matplotlib
import matplotlib.cm as cm
import matplotlib.lines as mlines
from matplotlib import ticker
from matplotlib.collections import LineCollection
from matplotlib.ticker import StrMethodFormatter, NullFormatter
from plotstyle import boxplot_style
from matplotlib.ticker import NullFormatter
#%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ##
# to change marker types in seaborn swarmplot
@ -28,7 +23,6 @@ import matplotlib.pyplot as plt
############## Begin hack ##############
from matplotlib.axes._axes import Axes
from matplotlib.markers import MarkerStyle
from seaborn import color_palette
from numpy import ndarray
def GetColor2Marker(markers):
@ -444,7 +438,7 @@ plot_AUC_alt(ax1_ex,model='FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1='l
plot_AUC_alt(ax2_ex, model='STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1='lightgrey', color2='k', alteration='g')
#save
fig.savefig('AUC_correlation.pdf', bbox_inches='tight', dpi=fig.dpi)
fig.savefig('./Figures/AUC_correlation.pdf', bbox_inches='tight', dpi=fig.dpi)
plt.show()
# #%% alternative layout

2
Figures/diversity_in_firing.py
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@ -178,7 +178,7 @@ for i in range(0,len(models)):
spike_axs[i].text(-0.18, 1.08, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=16, weight='bold')
# save
fig.savefig('diversity_in_firing.pdf', bbox_inches='tight')
fig.savefig('./Figures/diversity_in_firing.pdf', bbox_inches='tight')
plt.show()

2
Figures/firing_characterization.py
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@ -103,7 +103,7 @@ $\uparrow$ rheobase''')
ax3_BR = ax3.inset_axes([0.7, 0, 0.3, 0.2])
plot_diff_sqrt(ax3_BR, b2=0.4, c2=75)
ax3_BR.set_ylim(inset_ylim)
fig.savefig('firing_characterization.pdf', bbox_inches='tight')
fig.savefig('./Figures/firing_characterization.pdf', bbox_inches='tight')
plt.show()

2
Figures/ramp_examples.py
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@ -131,5 +131,5 @@ add_scalebar(ax11_ramp, matchx=False, matchy=False, hidex=True, hidey=True, size
for i in range(0,len(models)):
ramp_axs[i].text(-0.05, 1.08, string.ascii_uppercase[i], transform=ramp_axs[i].transAxes, size=16, weight='bold')
fig.savefig('ramp_firing.pdf')
fig.savefig('./Figures/ramp_firing.pdf')
plt.show()

10
Figures/rheobase_correlation.py
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@ -4,20 +4,15 @@ Created on Sat Jul 3 19:52:04 2021
@author: nils
"""
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import string
import textwrap
import json
import matplotlib
import matplotlib.cm as cm
import matplotlib.lines as mlines
from matplotlib import ticker
from matplotlib.collections import LineCollection
from matplotlib.ticker import StrMethodFormatter, NullFormatter
from plotstyle import boxplot_style
from matplotlib.ticker import NullFormatter
#%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ##
# to change marker types in seaborn swarmplot
@ -28,7 +23,6 @@ import matplotlib.pyplot as plt
############## Begin hack ##############
from matplotlib.axes._axes import Axes
from matplotlib.markers import MarkerStyle
from seaborn import color_palette
from numpy import ndarray
def GetColor2Marker(markers):
@ -413,7 +407,7 @@ plot_rheo_alt(ax1_ex,model='Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
plot_rheo_alt(ax2_ex, model='Cb stellate', color1='lightgrey', color2='k', alteration='g')
# save
fig.savefig('rheobase_correlation.pdf', bbox_inches='tight')
fig.savefig('./Figures/rheobase_correlation.pdf', bbox_inches='tight')
plt.show()
# #%% alternative layout

BIN
Figures/simulation_model_comparison.pdf
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Binary file not shown.

20
Figures/simulation_model_comparison.py
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@ -1,14 +1,9 @@
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
import os
import json
import matplotlib.cm as cm
import pandas as pd
import os
import string
from plotstyle import plot_style
from adjustText import adjust_text
import seaborn as sns
import scipy.stats as stats
import matplotlib.lines as mlines
@ -27,7 +22,13 @@ def Kendall_tau(df):
def correlation_plot(ax, df='AUC', title='', cbar=False):
cbar_ax = fig.add_axes([0.94, .25, .03, .4])
cbar_ax.spines['left'].set_visible(False)
cbar_ax.spines['bottom'].set_visible(False)
cbar_ax.spines['right'].set_visible(False)
cbar_ax.spines['top'].set_visible(False)
# cbar_ax.axis('off')
cbar_ax.set_xticks([])
cbar_ax.set_yticks([])
if df == 'AUC':
df = pd.read_csv(os.path.join('./Figures/Data/sim_mut_AUC.csv'), index_col='Unnamed: 0')
elif df == 'rheo':
@ -168,8 +169,9 @@ def mutation_legend(ax, marker_s_leg, pos, ncol):
E283K = mlines.Line2D([], [], color=colors[2], marker=Markers[2], markersize=marker_s_leg, linestyle='None', label='E283K')
V404I = mlines.Line2D([], [], color=colors[5], marker=Markers[3], markersize=marker_s_leg, linestyle='None',
label='V404I')
WT = mlines.Line2D([], [], color='k', marker='s', markersize=marker_s_leg+5, linestyle='None', label='Wild type')
ax.legend(handles=[V174F, F414C, E283K, V404I], loc='center', bbox_to_anchor=pos, ncol=ncol, frameon=False)
ax.legend(handles=[WT, V174F, F414C, E283K, V404I], loc='center', bbox_to_anchor=pos, ncol=ncol, frameon=False)
@ -207,7 +209,7 @@ ax22 = mutation_plot2(ax22, model='STN_Kv_only')
marker_s_leg = 4
pos = (0.25, -0.45)
ncol = 4
ncol = 5
mutation_legend(ax21, marker_s_leg, pos, ncol)
# plot correlation matrices
@ -224,5 +226,5 @@ axr0.text(-0.38, 1.2, string.ascii_uppercase[j], transform=axr0.transAxes, size=
axr1.text(-0.38, 1.2, string.ascii_uppercase[j+1], transform=axr1.transAxes, size=16, weight='bold')
# save
fig.savefig('simulation_model_comparison.pdf', bbox_inches='tight')
fig.savefig('./Figures/simulation_model_comparison.pdf', bbox_inches='tight')
plt.show()

0
Figures/plotstyle.py → plotstyle.py
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