From ea759e49fe2afb06083afc1b3d223a753f450548 Mon Sep 17 00:00:00 2001
From: nkoch1 <nils@ualberta.ca>
Date: Wed, 20 Jul 2022 22:52:34 -0400
Subject: [PATCH] small changes observed during word file preparation

---
 Figures/AUC_correlation.py                 |   2 +-
 Figures/diversity_in_firing.py             |   2 +-
 Figures/firing_characterization.py         |   7 ++++---
 Figures/firing_characterization_arrows.pdf | Bin 23038 -> 22427 bytes
 Figures/ramp_firing.py                     |   5 +++--
 Figures/rheobase_correlation.py            |   2 +-
 Figures/simulation_model_comparison.py     |   2 +-
 g_table.tex                                |   5 +++--
 manuscript.tex                             |   2 +-
 9 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/Figures/AUC_correlation.py b/Figures/AUC_correlation.py
index ba9ea18..99a0c5b 100644
--- a/Figures/AUC_correlation.py
+++ b/Figures/AUC_correlation.py
@@ -427,5 +427,5 @@ ax2.text(-0.075, 1.35, string.ascii_uppercase[8], transform=ax2.transAxes, size=
 
 #save
 fig.set_size_inches(cm2inch(20.75,12))
-fig.savefig('./Figures/AUC_correlation.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/AUC_correlation.png', dpi=fig.dpi) #pdf #eps
 plt.show()
diff --git a/Figures/diversity_in_firing.py b/Figures/diversity_in_firing.py
index f48646a..6469494 100644
--- a/Figures/diversity_in_firing.py
+++ b/Figures/diversity_in_firing.py
@@ -188,7 +188,7 @@ for i in range(0,len(models)):
 
 # save
 fig.set_size_inches(cm2inch(17.6,20))
-fig.savefig('./Figures/diversity_in_firing.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/diversity_in_firing.png', dpi=fig.dpi) #pdf # eps
 plt.show()
 
 
diff --git a/Figures/firing_characterization.py b/Figures/firing_characterization.py
index cf5a33e..a02f8dd 100644
--- a/Figures/firing_characterization.py
+++ b/Figures/firing_characterization.py
@@ -303,14 +303,15 @@ ncol = 2
 fig.legend(handles=[wt, mut], loc='center', bbox_to_anchor=pos, ncol=ncol, frameon=False, fontsize=8)
 
 fig.set_size_inches(cm2inch(8.5,12))
-fig.savefig('./Figures/firing_characterization.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/firing_characterization.png', dpi=fig.dpi) #pdf #eps
 plt.show()
 
 
 
 #%% with arrows
 fig = plt.figure(figsize=cm2inch(7, 12))
-gs = gridspec.GridSpec(3,6, top=0.95, bottom=0.1, left=0.15, right = 0.95, hspace=0.8, wspace=0.6)
+# gs = gridspec.GridSpec(3,6, top=0.95, bottom=0.1, left=0.15, right = 0.95, hspace=0.8, wspace=0.6)
+gs = gridspec.GridSpec(3,6, top=0.9, bottom=0.05, left=0.15, right = 0.9, hspace=0.8, wspace=0.6)
 ax1 = fig.add_subplot(gs[0,1:])
 show_spines(ax1, 'lb')
 plot_AUC(ax1, width=0.2)
@@ -364,5 +365,5 @@ ax3_BR.annotate('', (0.7, 75), (0.8, 37.5), arrowprops=dict(arrowstyle="<|-", co
 
 
 fig.set_size_inches(cm2inch(8.5,12))
-fig.savefig('./Figures/firing_characterization_arrows.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
+fig.savefig('./Figures/firing_characterization_arrows.png', dpi=fig.dpi, bbox_inches='tight') #, dpi=fig.dpi #pdf #eps
 plt.show()
diff --git a/Figures/firing_characterization_arrows.pdf b/Figures/firing_characterization_arrows.pdf
index d77050cf4ecc6b7b5391f73b5cc3e68773be7947..eeb20212dd8ae3b6a6e9041d246ffdd33895bed7 100644
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diff --git a/Figures/ramp_firing.py b/Figures/ramp_firing.py
index 1812b05..9888ec9 100644
--- a/Figures/ramp_firing.py
+++ b/Figures/ramp_firing.py
@@ -232,7 +232,8 @@ def add_scalebar(ax, matchx=True, matchy=True, hidex=True, hidey=True, **kwargs)
 
 def plot_ramp_V(ax, model='RS Pyramidal'):  # , stop=750
     model_ramp = pd.read_csv('./Figures/Data/model_ramp.csv')
-    ax.plot(model_ramp['t'], model_ramp[model], 'k', linewidth=0.0025)
+    # ax.plot(model_ramp['t'], model_ramp[model], 'k', linewidth=0.0025)
+    ax.plot(model_ramp['t'], model_ramp[model], 'k', linewidth=0.1)
     ax.set_ylabel('V')
     ax.set_xlabel('Time [s]')
     ax.set_ylim(-80, 60)
@@ -316,6 +317,6 @@ for i in range(0,len(models)):
 
 #save
 fig.set_size_inches(cm2inch(17.6,22))
-fig.savefig('./Figures/ramp_firing.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/ramp_firing.png', dpi=fig.dpi)#pdf #eps
 plt.show()
 
diff --git a/Figures/rheobase_correlation.py b/Figures/rheobase_correlation.py
index c22ec7d..cea6168 100644
--- a/Figures/rheobase_correlation.py
+++ b/Figures/rheobase_correlation.py
@@ -424,5 +424,5 @@ ax2.text(-0.075, 1.35, string.ascii_uppercase[8], transform=ax2.transAxes, size=
 
 # save
 fig.set_size_inches(cm2inch(20.75,12))
-fig.savefig('./Figures/rheobase_correlation.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
+fig.savefig('./Figures/rheobase_correlation.png', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi # eps # pdf
 plt.show()
diff --git a/Figures/simulation_model_comparison.py b/Figures/simulation_model_comparison.py
index f84d6be..84d95eb 100644
--- a/Figures/simulation_model_comparison.py
+++ b/Figures/simulation_model_comparison.py
@@ -241,6 +241,6 @@ axr1.text(-0.77, 1.1, string.ascii_uppercase[j+1], transform=axr1.transAxes, siz
 
 # save
 fig.set_size_inches(cm2inch(22.2,15))
-fig.savefig('./Figures/simulation_model_comparison.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/simulation_model_comparison.png', dpi=fig.dpi) #eps
 plt.show()
 
diff --git a/g_table.tex b/g_table.tex
index 52b2411..3bc5c48 100644
--- a/g_table.tex
+++ b/g_table.tex
@@ -26,6 +26,7 @@
         \Xhline{1\arrayrulewidth}
     \end{tabular}}
     
-	    \caption[Cell properties and conductances of neuronal models]{Cell properties and conductances of regular spiking pyramidal neuron (RS Pyramidal), regular spiking inhibitory neuron (RS Inhibitory), fast spiking neuron (FS), cerebellar stellate cell (Cb Stellate), with additional \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) (Cb Stellate \(\Delta\)\Kv) and with \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) replacement of \(\textrm{I}_\textrm{A}\) (Cb Stellate \(\Delta\)\Kv), and subthalamic nucleus neuron (STN), with additional \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) (STN \(\Delta\)\Kv) and with \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) replacement of \(\textrm{I}_{\textrm{A}}\) (STN \Kv) models. All conductances are given in \(\textrm{mS}/\textrm{cm}^2\). Capacitances (\(C_m\)) and \(\tau_{max, M}\) are given in pF and ms respectively.}
+	    \caption[Cell properties and conductances of neuronal models]{Cell properties and conductances of regular spiking pyramidal neuron (RS Pyramidal), regular spiking inhibitory neuron (RS Inhibitory), fast spiking neuron (FS) each with additional \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) (RS Pyramidal +\Kv, RS Inhibitory +\Kv, FS +\Kv respectively), cerebellar stellate cell (Cb Stellate), with additional \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) (Cb Stellate +\Kv) and with \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) replacement of \(\textrm{I}_\textrm{A}\) (Cb Stellate \(\Delta\)\Kv), and subthalamic nucleus neuron (STN), with additional \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) (STN +\Kv) and with \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\) replacement of \(\textrm{I}_{\textrm{A}}\) (STN \Kv) models. All conductances are given in \(\textrm{mS}/\textrm{cm}^2\). Capacitances (\(C_m\)) and \(\tau_{max, M}\) are given in pF and ms respectively.}
     \label{tab:g}
-\end{table}
\ No newline at end of file
+\end{table}
+
diff --git a/manuscript.tex b/manuscript.tex
index bdd087b..d32e3e9 100644
--- a/manuscript.tex
+++ b/manuscript.tex
@@ -338,7 +338,7 @@ Qualitative differences can be found, for example, when increasing the maximal c
         \label{fig:AUC_correlation}
 \end{figure}
 
-Changes in gating half activation potential \(V_{1/2}\) and slope factor \(k\) as well as the maximum conductance \(g\) affect rheobase (\Cref{fig:rheobase_correlation}), however, in contrast to AUC, qualitatively consistent effects on rheobase across models are observed. Increasing, for example, the maximal conductance of the leak current in the Cb stellate model increases the rheobase (\Cref{fig:rheobase_correlation}~G). When these changes are plotted against the change in maximal conductance a monontonically increasing relationship is evident (thick teal line in \Cref{fig:AUC_correlation}~H). This monotonically increasing relationship is evident in all models (\( \text{Kendall} \ \tau \approx +1\)), but with different slopes (thin lines in \Cref{fig:rheobase_correlation}~H). Similarily, positive correlations are consistently found across models for maximal conductances of delayed rectifier K, \Kv, and A type currents, whereas the maximal conductance of the sodium current consistently is associated with negative correlations (\( \text{Kendall} \ \tau \approx -1\); \Cref{fig:rheobase_correlation}~I), i.e. rheobase is decreased with increasing maximum conductance in all models.
+Changes in gating half activation potential \(V_{1/2}\) and slope factor \(k\) as well as the maximum conductance \(g\) affect rheobase (\Cref{fig:rheobase_correlation}), however, in contrast to AUC, qualitatively consistent effects on rheobase across models are observed. Increasing, for example, the maximal conductance of the leak current in the Cb stellate model increases the rheobase (\Cref{fig:rheobase_correlation}~G). When these changes are plotted against the change in maximal conductance a monontonically increasing relationship is evident (thick teal line in \Cref{fig:rheobase_correlation}~H). This monotonically increasing relationship is evident in all models (\( \text{Kendall} \ \tau \approx +1\)), but with different slopes (thin lines in \Cref{fig:rheobase_correlation}~H). Similarily, positive correlations are consistently found across models for maximal conductances of delayed rectifier K, \Kv, and A type currents, whereas the maximal conductance of the sodium current consistently is associated with negative correlations (\( \text{Kendall} \ \tau \approx -1\); \Cref{fig:rheobase_correlation}~I), i.e. rheobase is decreased with increasing maximum conductance in all models.
 
 Although changes in half maximal potential \(V_{1/2}\) and slope factor \(k\) generally correlate with rheobase similarly across model there are some exceptions. Changing the slope factor of Na-current inactivation, \Kv-current inactivation, and A-current activation affect rheobase both with positive and negative correlations in different models (\Cref{fig:rheobase_correlation}~F). Departures from monotonic relationships also occur in some models as a result of K-current activation  \(V_{1/2}\) and slope factor \(k\), \Kv-current inactivation slope factor \(k\), and A-current activation slope factor \(k\) in some models. Thus, identical changes in current gating properties such as the half maximal potential \(V_{1/2}\) or slope factor \(k\) can have differing effects on firing depending on the model in which they occur.