changes to Frontiers_manuscript/For_Submission/Koch_frontiers_revised and addition of Frontiers_manuscript/For_Submission/Koch_frontiers_diff for differences using Latexdiff
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nkoch1
@@ -87,12 +87,15 @@ def add_scalebar(ax, matchx=True, matchy=True, hidex=True, hidey=True, **kwargs)
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def plot_spike_train(ax, model='RS Pyramidal', stop=750):
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model_spiking = pd.read_csv('./Figures/Data/model_spiking.csv')
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stop_ind = int(np.argmin(np.abs(model_spiking['t'] - stop)))
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ax.plot(model_spiking['t'][0:stop_ind], model_spiking[model][0:stop_ind], 'k', linewidth=1.5)
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if model == 'STN':
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ax.plot(model_spiking['t'][0:stop_ind], model_spiking[model][0:stop_ind], 'k', linewidth=0.625)
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else:
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ax.plot(model_spiking['t'][0:stop_ind], model_spiking[model][0:stop_ind], 'k', linewidth=1.) #1.5
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ax.set_ylabel('V')
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ax.set_xlabel('Time [s]')
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ax.set_ylim(-85, 60)
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ax.axis('off')
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ax.set_title(model, fontsize=10)
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ax.set_title(model, fontsize=7)
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def plot_fI(ax, model='RS Pyramidal'):
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@@ -119,19 +122,35 @@ def plot_fI(ax, model='RS Pyramidal'):
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ax.plot(firing_values.loc['ramp_down', model],
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model_F_inf[model][int(np.argmin(np.abs(model_F_inf['I'] - firing_values.loc['ramp_down', model])))],
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'.', color='r', markersize=3)
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f = 8
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f = 6
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ax.set_ylabel('Frequency [Hz]', fontsize=f)
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ax.set_xlabel('Current [nA]', fontsize=f)
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.tick_params(axis='y', labelrotation=90)
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#%%
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# plot layout
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fig = plt.figure()
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gs0 = fig.add_gridspec(3, 2, wspace=0.3, hspace=0)
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gs00 = gs0[:,0].subgridspec(6, 3, wspace=1.5, hspace=1.5)
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gs01 = gs0[:,1].subgridspec(6, 3, wspace=1.2, hspace=1.3)
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gs0 = fig.add_gridspec(3, 3, wspace=0.4, hspace=0.2)
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gs00 = gs0[:,0].subgridspec(5, 3, wspace=1.8, hspace=1.5)
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gs01 = gs0[:,1].subgridspec(5, 3, wspace=1.8, hspace=1.5)
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gs02 = gs0[:,2].subgridspec(5, 3, wspace=1.8, hspace=1.5)
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ax_diag = fig.add_subplot(gs02[:3, :])
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import matplotlib.image as mpimg
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img = mpimg.imread('./Figures/model_diagram2.png')
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ax_diag.imshow(img)
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ax_diag.spines['top'].set_visible(False)
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ax_diag.spines['bottom'].set_visible(False)
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ax_diag.spines['left'].set_visible(False)
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ax_diag.spines['right'].set_visible(False)
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ax_diag.set_yticks([])
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ax_diag.set_xticks([])
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ax_diag.text(-0.12, 1.075, string.ascii_uppercase[12], transform=ax_diag.transAxes, size=10, weight='bold')
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ax1_spikes = fig.add_subplot(gs00[0,0:2])
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ax1_fI = fig.add_subplot(gs00[0, 2])
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@@ -153,15 +172,15 @@ ax9_spikes = fig.add_subplot(gs00[4,0:2])
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ax9_fI = fig.add_subplot(gs00[4, 2])
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ax10_spikes = fig.add_subplot(gs01[4,0:2])
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ax10_fI = fig.add_subplot(gs01[4, 2])
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ax11_spikes = fig.add_subplot(gs00[5,0:2])
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ax11_fI = fig.add_subplot(gs00[5, 2])
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ax12_spikes = fig.add_subplot(gs01[5,0:2])
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ax12_fI = fig.add_subplot(gs01[5, 2])
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ax11_spikes = fig.add_subplot(gs02[3,0:2])
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ax11_fI = fig.add_subplot(gs02[3, 2])
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ax12_spikes = fig.add_subplot(gs02[4,0:2])
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ax12_fI = fig.add_subplot(gs02[4, 2])
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spike_axs = [ax1_spikes, ax2_spikes, ax3_spikes, ax4_spikes, ax5_spikes,ax6_spikes, ax7_spikes, ax8_spikes,
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ax9_spikes, ax10_spikes, ax11_spikes, ax12_spikes]#, ax13_spikes, ax14_spikes]
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fI_axs = [ax1_fI, ax2_fI, ax3_fI, ax4_fI, ax5_fI,ax6_fI, ax7_fI, ax8_fI, ax9_fI, ax10_fI,
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ax11_fI, ax12_fI] #, ax13_fI, ax14_fI]
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ax11_spikes,ax9_spikes,ax10_spikes, ax12_spikes]#, ax13_spikes, ax14_spikes]
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fI_axs = [ax1_fI, ax2_fI, ax3_fI, ax4_fI, ax5_fI,ax6_fI, ax7_fI, ax8_fI, ax11_fI, ax9_fI, ax10_fI,
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ax12_fI] #, ax13_fI, ax14_fI]
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# model order
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models = ['Cb stellate','RS Inhibitory','FS', 'RS Pyramidal','RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
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@@ -176,20 +195,91 @@ for i in range(len(models)):
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plot_fI(fI_axs[i], model=models[i])
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# add scalebars
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add_scalebar(ax11_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.2, -0.05, 1, 1),
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bbox_transform=ax11_spikes.transAxes)
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add_scalebar(ax9_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.275, -0.05, 1, 1),
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bbox_transform=ax9_spikes.transAxes)
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add_scalebar(ax10_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.275, -0.05, 1, 1),
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bbox_transform=ax10_spikes.transAxes)
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add_scalebar(ax12_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.2, -0.05, 1, 1),
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labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.275, -0.05, 1, 1),
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bbox_transform=ax12_spikes.transAxes)
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# add subplot labels
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for i in range(0,len(models)):
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# spike_axs[i].text(-0.18, 1.08, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
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spike_axs[i].text(-0.18, 1.2, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
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spike_axs[i].text(-0.22, 1.2, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
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# save
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fig.set_size_inches(cm2inch(17.6,20))
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fig.savefig('./Figures/diversity_in_firing.jpg', dpi=fig.dpi) #pdf # eps
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# fig.savefig('./Figures/diversity_in_firing.png', dpi=fig.dpi) #pdf # eps
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fig.set_size_inches(cm2inch(21,15))
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fig.savefig('./Figures/diversity_in_firing_diagram.jpg', dpi=300, bbox_inches='tight') #pdf # eps
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plt.show()
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# #%%
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#
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# # plot layout
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# fig = plt.figure()
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# gs0 = fig.add_gridspec(3, 2, wspace=0.3, hspace=0)
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# gs00 = gs0[:,0].subgridspec(6, 3, wspace=1.5, hspace=1.5)
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# gs01 = gs0[:,1].subgridspec(6, 3, wspace=1.2, hspace=1.3)
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#
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# ax1_spikes = fig.add_subplot(gs00[0,0:2])
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# ax1_fI = fig.add_subplot(gs00[0, 2])
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# ax2_spikes = fig.add_subplot(gs01[0,0:2])
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# ax2_fI = fig.add_subplot(gs01[0, 2])
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# ax3_spikes = fig.add_subplot(gs00[1,0:2])
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# ax3_fI = fig.add_subplot(gs00[1, 2])
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# ax4_spikes = fig.add_subplot(gs01[1,0:2])
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# ax4_fI = fig.add_subplot(gs01[1, 2])
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# ax5_spikes = fig.add_subplot(gs00[2, 0:2])
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# ax5_fI = fig.add_subplot(gs00[2, 2])
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# ax6_spikes = fig.add_subplot(gs01[2, 0:2])
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# ax6_fI = fig.add_subplot(gs01[2, 2])
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# ax7_spikes = fig.add_subplot(gs00[3,0:2])
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# ax7_fI = fig.add_subplot(gs00[3, 2])
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# ax8_spikes = fig.add_subplot(gs01[3,0:2])
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# ax8_fI = fig.add_subplot(gs01[3, 2])
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# ax9_spikes = fig.add_subplot(gs00[4,0:2])
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# ax9_fI = fig.add_subplot(gs00[4, 2])
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# ax10_spikes = fig.add_subplot(gs01[4,0:2])
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# ax10_fI = fig.add_subplot(gs01[4, 2])
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# ax11_spikes = fig.add_subplot(gs00[5,0:2])
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# ax11_fI = fig.add_subplot(gs00[5, 2])
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# ax12_spikes = fig.add_subplot(gs01[5,0:2])
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# ax12_fI = fig.add_subplot(gs01[5, 2])
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#
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# spike_axs = [ax1_spikes, ax2_spikes, ax3_spikes, ax4_spikes, ax5_spikes,ax6_spikes, ax7_spikes, ax8_spikes,
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# ax9_spikes, ax10_spikes, ax11_spikes, ax12_spikes]#, ax13_spikes, ax14_spikes]
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# fI_axs = [ax1_fI, ax2_fI, ax3_fI, ax4_fI, ax5_fI,ax6_fI, ax7_fI, ax8_fI, ax9_fI, ax10_fI,
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# ax11_fI, ax12_fI] #, ax13_fI, ax14_fI]
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#
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# # model order
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# models = ['Cb stellate','RS Inhibitory','FS', 'RS Pyramidal','RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
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# 'Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', 'FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
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# 'RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', 'STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
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# 'Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$',
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# 'STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', 'STN']
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#
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# # plot spike train and fI for each model
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# for i in range(len(models)):
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# plot_spike_train(spike_axs[i], model=models[i])
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# plot_fI(fI_axs[i], model=models[i])
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#
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# # add scalebars
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# add_scalebar(ax11_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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# labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.2, -0.05, 1, 1),
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# bbox_transform=ax11_spikes.transAxes)
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# add_scalebar(ax12_spikes, matchx=False, matchy=False, hidex=True, hidey=True, sizex=100, sizey=50, labelx='100\u2009ms',
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# labely='50\u2009mV', loc=3, pad=-0.5, borderpad=-1.0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.2, -0.05, 1, 1),
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# bbox_transform=ax12_spikes.transAxes)
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# # add subplot labels
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# for i in range(0,len(models)):
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# # spike_axs[i].text(-0.18, 1.08, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
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# spike_axs[i].text(-0.18, 1.2, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
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# # save
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# fig.set_size_inches(cm2inch(17.6,20))
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# fig.savefig('./Figures/diversity_in_firing.jpg', dpi=fig.dpi) #pdf # eps
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# # fig.savefig('./Figures/diversity_in_firing.png', dpi=fig.dpi) #pdf # eps
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# plt.show()
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@@ -364,6 +364,6 @@ ax3_BR.annotate('', (0.7, 75), (0.8, 37.5), arrowprops=dict(arrowstyle="<|-", co
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fig.set_size_inches(cm2inch(8.5,12))
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fig.savefig('./Figures/firing_characterization_arrows.jpg', dpi=300, bbox_inches='tight') #, dpi=fig.dpi #pdf #eps
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fig.set_size_inches(cm2inch(8.3,12))
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fig.savefig('./Figures/firing_characterization_arrows.pdf', dpi=300, bbox_inches='tight') #, dpi=fig.dpi #pdf #eps
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plt.show()
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Binary file not shown.
@@ -262,12 +262,17 @@ img = mpimg.imread('./Figures/summary_diagram2.png')
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inset_ylim = (0, 100)
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lfsize = 8
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fig = plt.figure(figsize=cm2inch(17.2, 12))
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gs = gridspec.GridSpec(15, 3, top=0.95, bottom=0.1, left=0.15, right=0.95, hspace=0.4, wspace=0.2)
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gs = gridspec.GridSpec(14, 3, top=0.95, bottom=0.1, left=0.15, right=0.95, hspace=0.2, wspace=0.1)
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# gs0 = gs[1:13, 2].subgridspec(3, 1, hspace=0.9, wspace=0.25) # width_ratios=[0.3, 0.3,0.3], height_ratios=[0.35],
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ax1 = fig.add_subplot(gs[1:4,2])
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ax2 = fig.add_subplot(gs[6:9,2])
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ax3 = fig.add_subplot(gs[11:14,2])
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# ax1 = fig.add_subplot(gs[2:5,2])
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# ax2 = fig.add_subplot(gs[7:10,2])
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# ax3 = fig.add_subplot(gs[12:15,2])
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ax0 = fig.add_subplot(gs[:, :2])
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# ax1 = fig.add_subplot(gs0[0])
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@@ -314,7 +319,7 @@ ax3.annotate('', (0.55, 55), (0.3, 90),
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ax3.text(x=0.05, y=110, s='$\\uparrow$ AUC $\\downarrow$ rheobase', fontsize=lfsize)
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# fig.set_size_inches(cm2inch(17, 12))
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fig.savefig('./Figures/summary_fig.jpg', dpi=300, bbox_inches='tight') # , dpi=fig.dpi #pdf #eps
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# fig.savefig('./Figures/summary_fig.jpg', dpi=300, bbox_inches='tight') # , dpi=fig.dpi #pdf #eps
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#
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plt.show()
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