diff --git a/Figures/AUC_correlation.py b/Figures/AUC_correlation.py index 611b7eb..e5a4333 100644 --- a/Figures/AUC_correlation.py +++ b/Figures/AUC_correlation.py @@ -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 diff --git a/Figures/diversity_in_firing.py b/Figures/diversity_in_firing.py index 64bcb2e..ee4909c 100644 --- a/Figures/diversity_in_firing.py +++ b/Figures/diversity_in_firing.py @@ -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() diff --git a/Figures/firing_characterization.py b/Figures/firing_characterization.py index 6344fd0..67fcab8 100644 --- a/Figures/firing_characterization.py +++ b/Figures/firing_characterization.py @@ -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() diff --git a/Figures/ramp_examples.py b/Figures/ramp_examples.py index dcade0b..efe1f2a 100644 --- a/Figures/ramp_examples.py +++ b/Figures/ramp_examples.py @@ -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() \ No newline at end of file diff --git a/Figures/rheobase_correlation.py b/Figures/rheobase_correlation.py index b4d3125..7d74fbe 100644 --- a/Figures/rheobase_correlation.py +++ b/Figures/rheobase_correlation.py @@ -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 diff --git a/Figures/simulation_model_comparison.pdf b/Figures/simulation_model_comparison.pdf index 5c3c8f2..6369706 100644 Binary files a/Figures/simulation_model_comparison.pdf and b/Figures/simulation_model_comparison.pdf differ diff --git a/Figures/simulation_model_comparison.py b/Figures/simulation_model_comparison.py index e0fe9a2..7c25a8b 100644 --- a/Figures/simulation_model_comparison.py +++ b/Figures/simulation_model_comparison.py @@ -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() diff --git a/Figures/plotstyle.py b/plotstyle.py similarity index 100% rename from Figures/plotstyle.py rename to plotstyle.py