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 @author: nils
""" """
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd import pandas as pd
import numpy as np import numpy as np
import string import string
import textwrap import textwrap
import json import json
import matplotlib import matplotlib
import matplotlib.cm as cm
import matplotlib.lines as mlines import matplotlib.lines as mlines
from matplotlib import ticker from matplotlib import ticker
from matplotlib.collections import LineCollection from matplotlib.ticker import NullFormatter
from matplotlib.ticker import StrMethodFormatter, NullFormatter
from plotstyle import boxplot_style
#%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ## #%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ##
# to change marker types in seaborn swarmplot # to change marker types in seaborn swarmplot
@ -28,7 +23,6 @@ import matplotlib.pyplot as plt
############## Begin hack ############## ############## Begin hack ##############
from matplotlib.axes._axes import Axes from matplotlib.axes._axes import Axes
from matplotlib.markers import MarkerStyle from matplotlib.markers import MarkerStyle
from seaborn import color_palette
from numpy import ndarray from numpy import ndarray
def GetColor2Marker(markers): 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') plot_AUC_alt(ax2_ex, model='STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1='lightgrey', color2='k', alteration='g')
#save #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() plt.show()
# #%% alternative layout # #%% 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') spike_axs[i].text(-0.18, 1.08, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=16, weight='bold')
# save # save
fig.savefig('diversity_in_firing.pdf', bbox_inches='tight') fig.savefig('./Figures/diversity_in_firing.pdf', bbox_inches='tight')
plt.show() 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]) ax3_BR = ax3.inset_axes([0.7, 0, 0.3, 0.2])
plot_diff_sqrt(ax3_BR, b2=0.4, c2=75) plot_diff_sqrt(ax3_BR, b2=0.4, c2=75)
ax3_BR.set_ylim(inset_ylim) 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() 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)): 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') 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() 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 @author: nils
""" """
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd import pandas as pd
import numpy as np import numpy as np
import string import string
import textwrap import textwrap
import json import json
import matplotlib import matplotlib
import matplotlib.cm as cm
import matplotlib.lines as mlines import matplotlib.lines as mlines
from matplotlib import ticker from matplotlib import ticker
from matplotlib.collections import LineCollection from matplotlib.ticker import NullFormatter
from matplotlib.ticker import StrMethodFormatter, NullFormatter
from plotstyle import boxplot_style
#%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ## #%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ##
# to change marker types in seaborn swarmplot # to change marker types in seaborn swarmplot
@ -28,7 +23,6 @@ import matplotlib.pyplot as plt
############## Begin hack ############## ############## Begin hack ##############
from matplotlib.axes._axes import Axes from matplotlib.axes._axes import Axes
from matplotlib.markers import MarkerStyle from matplotlib.markers import MarkerStyle
from seaborn import color_palette
from numpy import ndarray from numpy import ndarray
def GetColor2Marker(markers): 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') plot_rheo_alt(ax2_ex, model='Cb stellate', color1='lightgrey', color2='k', alteration='g')
# save # save
fig.savefig('rheobase_correlation.pdf', bbox_inches='tight') fig.savefig('./Figures/rheobase_correlation.pdf', bbox_inches='tight')
plt.show() plt.show()
# #%% alternative layout # #%% alternative layout

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Figures/simulation_model_comparison.pdf
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20
Figures/simulation_model_comparison.py
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@ -1,14 +1,9 @@
import numpy as np import numpy as np
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
import os
import json
import matplotlib.cm as cm
import pandas as pd import pandas as pd
import os import os
import string import string
from plotstyle import plot_style from plotstyle import plot_style
from adjustText import adjust_text
import seaborn as sns import seaborn as sns
import scipy.stats as stats import scipy.stats as stats
import matplotlib.lines as mlines import matplotlib.lines as mlines
@ -27,7 +22,13 @@ def Kendall_tau(df):
def correlation_plot(ax, df='AUC', title='', cbar=False): def correlation_plot(ax, df='AUC', title='', cbar=False):
cbar_ax = fig.add_axes([0.94, .25, .03, .4]) 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': if df == 'AUC':
df = pd.read_csv(os.path.join('./Figures/Data/sim_mut_AUC.csv'), index_col='Unnamed: 0') df = pd.read_csv(os.path.join('./Figures/Data/sim_mut_AUC.csv'), index_col='Unnamed: 0')
elif df == 'rheo': 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') 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', V404I = mlines.Line2D([], [], color=colors[5], marker=Markers[3], markersize=marker_s_leg, linestyle='None',
label='V404I') 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 marker_s_leg = 4
pos = (0.25, -0.45) pos = (0.25, -0.45)
ncol = 4 ncol = 5
mutation_legend(ax21, marker_s_leg, pos, ncol) mutation_legend(ax21, marker_s_leg, pos, ncol)
# plot correlation matrices # 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') axr1.text(-0.38, 1.2, string.ascii_uppercase[j+1], transform=axr1.transAxes, size=16, weight='bold')
# save # save
fig.savefig('simulation_model_comparison.pdf', bbox_inches='tight') fig.savefig('./Figures/simulation_model_comparison.pdf', bbox_inches='tight')
plt.show() plt.show()

0
Figures/plotstyle.py → plotstyle.py
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