From 907c6fbd4bdbca6c0310c56db3f0bd6b8476356a Mon Sep 17 00:00:00 2001 From: nkoch1 Date: Wed, 18 May 2022 10:38:26 -0400 Subject: [PATCH] Changes with Jan's comments, altered tables and added plotstyle.py --- Figures/plotstyle.py | 59 ++++++++++++++++++++++++++++++++++++++++++++ g_table.tex | 22 ++++++++--------- gating_table.tex | 16 ++++++------ manuscript.tex | 7 +++--- 4 files changed, 81 insertions(+), 23 deletions(-) create mode 100644 Figures/plotstyle.py diff --git a/Figures/plotstyle.py b/Figures/plotstyle.py new file mode 100644 index 0000000..543e191 --- /dev/null +++ b/Figures/plotstyle.py @@ -0,0 +1,59 @@ +import matplotlib.pyplot as plt + + +def scheme_style(): + plt.rcParams['xtick.direction'] = 'out' + plt.rcParams['ytick.direction'] = 'out' + plt.rcParams['axes.titlesize'] = 20 + plt.rcParams['axes.labelsize'] = 8 + plt.rcParams['lines.linewidth'] = 2 + plt.rcParams['lines.markersize'] = 10 + plt.rcParams['xtick.labelsize'] = 10 + plt.rcParams['ytick.labelsize'] = 10 + plt.rcParams['savefig.bbox'] = 'tight' + # plt.rcParams['figure.figsize'] = [8.0, 8.0] + plt.rcParams['figure.dpi'] = 300 + + +def plot_style(): + plt.rcParams['xtick.direction'] = 'out' + plt.rcParams['ytick.direction'] = 'out' + plt.rcParams['axes.titlesize'] = 20 + plt.rcParams['axes.labelsize'] = 12 + plt.rcParams['lines.linewidth'] = 2 + plt.rcParams['lines.markersize'] = 10 + plt.rcParams['xtick.labelsize'] = 10 + plt.rcParams['ytick.labelsize'] = 10 + plt.rcParams['savefig.bbox'] = 'tight' + plt.rcParams['figure.dpi'] = 300 + +def boxplot_style(): + plt.rcParams['xtick.direction'] = 'out' + plt.rcParams['ytick.direction'] = 'out' + plt.rcParams['lines.linewidth'] = 1 + plt.rcParams['lines.markersize'] = 0.5 + plt.rcParams['xtick.labelsize'] = 4 + plt.rcParams['ytick.labelsize'] = 4 + plt.rcParams['savefig.bbox'] = 'tight' + plt.rcParams['axes.titlesize'] = 5 + plt.rcParams['axes.labelsize'] = 4 + plt.rcParams['legend.fontsize']= 4 + plt.rcParams['xtick.labelsize'] = 3 + plt.rcParams['ytick.labelsize']= 3 + plt.rcParams['mathtext.default'] = 'regular' + plt.rcParams['figure.dpi'] = 300 + + + +def sim_style(): + plt.rcParams['xtick.direction'] = 'out' + plt.rcParams['ytick.direction'] = 'out' + plt.rcParams['axes.titlesize'] = 6 + plt.rcParams['axes.labelsize'] = 4 + plt.rcParams['lines.linewidth'] = 1 + plt.rcParams['lines.markersize'] = 4 + plt.rcParams['xtick.labelsize'] = 4 + plt.rcParams['ytick.labelsize'] = 4 + plt.rcParams['savefig.bbox'] = 'tight' + plt.rcParams.update({'font.size': 4}) + plt.rcParams['figure.dpi'] = 300 \ No newline at end of file diff --git a/g_table.tex b/g_table.tex index dc00ce2..34870b1 100644 --- a/g_table.tex +++ b/g_table.tex @@ -12,17 +12,17 @@ \Xhline{1\arrayrulewidth} & \begin{tabular}[x]{@{}c@{}} RS\\Pyra-\\midal \end{tabular} & \begin{tabular}[x]{@{}c@{}} RS\\Inhib-\\itory\end{tabular} & FS & \begin{tabular}[x]{@{}c@{}} Cb\\Stellate \end{tabular}& \begin{tabular}[x]{@{}c@{}}Cb\\Stellate\\+\Kv \end{tabular} & \begin{tabular}[x]{@{}c@{}}Cb\\Stellate\\\(\Delta\)\Kv \end{tabular} & STN &\begin{tabular}[x]{@{}c@{}} STN\\+\Kv \end{tabular} &\begin{tabular}[x]{@{}c@{}} STN\\\(\Delta\)\Kv \end{tabular} \\ \Xhline{1\arrayrulewidth} - \(g_{Na}\) & 56 & 10 & 58 & 3.4 & 3.4 & 3.4 & 49 & 49 & 49 \\ - \(g_{K}\) & 5.4 & 1.89 & 3.51 & 9.0556 & 8.15 &9.0556 & 57 & 56.43 & 57 \\ - \(g_{K_V1.1}\) & 0.6 & 0.21 & 0.39 & --- & 0.90556 & 1.50159 & --- & 0.57 & 0.5 \\ - \(g_{A}\) & --- & --- & --- & 15.0159 & 15.0159 & --- & 5 & 5 & --- \\ - \(g_{M}\) & 0.075 & 0.0098 &0.075 & --- & --- & --- & --- & --- & --- \\ - \(g_{L}\) & --- & --- & --- & --- & --- & --- & 5 & 5 & 5 \\ - \(g_{T}\) & --- & --- & --- & 0.45045 & 0.45045 & 0.45045 & 5 & 5 & 5 \\ - \(g_{Ca,K}\) & --- & --- & --- & --- & --- & --- & 1 & 1 & 1 \\ - \(g_{Leak}\) &0.0205 & 0.0205 & 0.038 & 0.07407 & 0.07407 & 0.07407 & 0.035 & 0.035 & 0.035 \\%\Xhline{1\arrayrulewidth} - \(\tau_{max, M}\)& 608 & 934 & 502 & --- & --- & --- & --- & --- & --- \\ - \(C_m\) & 118.44 & 119.99 & 101.71& 177.83 & 177.83 & 177.83 & 118.44& 118.44& 118.44 \\ + \(g_{Na}\) & \(56\) & \(10\) & \(58\) & \(3.4\) & \(3.4\) & \(3.4\) & \(49\) & \(49\) & \(49\) \\ + \(g_{K}\) & \(5.4\) & \(1.89\) & \(3.51\) & \(9.0556\) & \(8.15\) &\(9.0556\) & \(57\) & \(56.43\) & \(57\) \\ + \(g_{K_V1.1}\) & \(0.6\) & \(0.21\) & \(0.39\) & --- & \(0.90556\) & \(1.50159\) & --- & \(0.57\) & \(0.5\) \\ + \(g_{A}\) & --- & --- & --- & \(15.0159\) & \(15.0159\) & --- & \(5\) & \(5\) & --- \\ + \(g_{M}\) & \(0.075\) & \(0.0098\) &\(0.075\) & --- & --- & --- & --- & --- & --- \\ + \(g_{L}\) & --- & --- & --- & --- & --- & --- & \(5\) & \(5 \) & \(5\) \\ + \(g_{T}\) & --- & --- & --- & \(0.45045\) & \(0.45045\) & \(0.45045\) & \(5\) & \(5\) & \(5\) \\ + \(g_{Ca,K}\) & --- & --- & --- & --- & --- & --- & \(1\) & \(1\) & \(1\) \\ + \(g_{Leak}\) &\(0.0205\) & \(0.0205\) & \(0.038\) & \(0.07407\) & \(0.07407\) & \(0.07407\) & \(0.035\) & \(0.035\) & \(0.035\) \\%\Xhline{1\arrayrulewidth} + \(\tau_{max, M}\)& \(608\) & \(934\) & \(502\) & --- & --- & --- & --- & --- & --- \\ + \(C_m\) & \(118.44\) & \(119.99\) & \(101.71\)& \(177.83\) & \(177.83\) & \(177.83\) & \(118.44\)& \(118.44\)& \(118.44\) \\ \Xhline{1\arrayrulewidth} \end{tabular}} diff --git a/gating_table.tex b/gating_table.tex index eb5c536..e424cf7 100644 --- a/gating_table.tex +++ b/gating_table.tex @@ -8,16 +8,16 @@ & Gating & \(V_{1/2}\) [mV]& \(k\) & \(j\) & \(a\) \\ \Xhline{1\arrayrulewidth} %Pospischil - & \(\textrm{I}_{\textrm{Na}}\) activation &$-34.33054521$ & $-8.21450277$ & $1.42295686$ & --- \\ -RS pyramidal, & \(\textrm{I}_{\textrm{Na}}\) inactivation &$-34.51951036$ & $4.04059373$ & $1$ & $0.05$ \\ - RS inhibitory, & \(\textrm{I}_{\textrm{Kd}}\) activation &$-63.76096946$ & $-13.83488194$ & $7.35347425$ & --- \\ - FS & \(\textrm{I}_{\textrm{L}}\) activation &$-39.03684525$ & $-5.57756176$ & $2.25190197$ & --- \\ - & \(\textrm{I}_{\textrm{L}}\) inactivation &$-57.37$ & $20.98$ & $1$ & --- \\ - & \(\textrm{I}_{\textrm{M}}\) activation &$-45$ & $-9.9998807337$ & $1$ & --- \\ %-45 with 10 mV shift to contributes to resting potential + & \(\textrm{I}_{\textrm{Na}}\) activation &\(-34.33054521\) & \(-8.21450277\) & \(1.42295686\) & --- \\ +RS pyramidal, & \(\textrm{I}_{\textrm{Na}}\) inactivation &\(-34.51951036\) & \(4.04059373\) & \(1\) & \(0.05\) \\ + RS inhibitory, & \(\textrm{I}_{\textrm{Kd}}\) activation &\(-63.76096946\) & \(-13.83488194\) & \(7.35347425\) & --- \\ + FS & \(\textrm{I}_{\textrm{L}}\) activation &\(-39.03684525\) & \(-5.57756176\) & \(2.25190197\) & --- \\ + & \(\textrm{I}_{\textrm{L}}\) inactivation &\(-57.37\) & \(20.98\) & \(1\) & --- \\ + & \(\textrm{I}_{\textrm{M}}\) activation &\(-45\) & \(-9.9998807337\) & \(1\) & --- \\ %-45 with 10 mV shift to contributes to resting potential % & & & & &\\ \Xhline{1\arrayrulewidth} - \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) & \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) activation &$-30.01851852$ & $-7.73333333$ & $1$ & --- \\ - & \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) Inactivation &$-46.85851852$ & $7.67266667$ & $1$ & $0.245$ \\ + \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) & \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) activation &\(-30.01851852\) & \(-7.73333333\) & \(1\) & --- \\ + & \(\textrm{I}_{\textrm{K}_{\textrm{V}}\textrm{1.1}}\ \) Inactivation &\(-46.85851852\) & \(7.67266667\) & \(1\) & \(0.245\) \\ \Xhline{1\arrayrulewidth} diff --git a/manuscript.tex b/manuscript.tex index 2f69158..7b2827d 100644 --- a/manuscript.tex +++ b/manuscript.tex @@ -276,8 +276,7 @@ To examine the role of cell-type specific ionic current environments on the impa \begin{figure}[tp] \centering \includegraphics[width=0.5\linewidth]{Figures/firing_characterization.pdf} - \\\notejb{Nils, can you put the python script of this figure into the git? I have some ideas I would like to try.} - \notenk{Should already be in \path{./Figures}, specifically file: \path{./Figures/firing_characterization.py}}\notejb{Ok, thanks. plotstyle.py is missing in the repository. Can you please add it?} + \\\notejb{Ok, thanks. plotstyle.py is missing in the repository. Can you please add it?}\notenk{Sorry it should now be in \path{./Figures},} \linespread{1.}\selectfont \caption[]{Characterization of firing with AUC and rheobase. (A) The area under the curve (AUC) of the repetitive firing frequency-current (fI) curve. (B) Changes in firing as characterized by \(\Delta\)AUC and \(\Delta\)rheobase occupy 4 quadrants separated by no changes in AUC and rheobase. Representative schematic fI curves in blue with respect to a reference fI curve (black) depict the general changes associated with each quadrant.} @@ -298,12 +297,12 @@ Neuronal firing is a complex phenomenon and a quantification of firing propertie Neuronal firing is heterogenous across the CNS and a set of neuronal models with heterogenous firing due to different ionic currents is desirable to reflect this heterogeneity. The set of neuronal models used here has considerable diversity as evident in the variability seen across neuronal models both in spike trains and their fI curves (\Cref{fig:diversity_in_firing}). The models chosen all fire tonically and do not exhibit bursting. Some models, such as Cb stellate and RS inhibitory models, display type I firing whereas others such as Cb stellate \(\Delta\)\Kv and STN models have type II firing. Type I firing is characterized by continuous fI curve (i.e. firing rate increases from 0 in a continuous fashion) generated through a saddle-node on invariant cycle bifurcation. Type II firing is characterized by a discontinuity in the fI curve (i.e. a jump occurs from no firing to firing at a certain frequency) due to sub-critical Hopf bifurcation \cite{ERMENTROUT2002, ermentrout_type_1996}. The other models used here lie on a continuum between these prototypical firing classifications. Most neuronal models exhibit hysteresis with ascending and descending ramps eliciting spikes with different thresholds, however the STN +\Kv, STN \(\Delta\)\Kv, and Cb stellate \(\Delta\)\Kv models have large hysteresis (\Cref{fig:diversity_in_firing}, \Cref{fig:ramp_firing}). \subsection*{Sensitivity Analysis} -Sensitivity analyses are used to understand how input model parameters contribute to determining the output of a model \citep{Saltelli2002}. In other words, sensitivity analyses are used to understand how sensitive the output of a model is to a change in input or model parameters. One-factor-a-time sensitivity analyses involve altering one parameter at a time and assessing the impact of this parameter on the output. This approach enables the comparison of given alterations in parameters of ionic currents across models. Changes in gating \(V_{1/2}\) and slope factor \(k\) as well as the maximum conductance affect AUC (\Cref{fig:AUC_correlation} A, B and C). Heterogeneity in the correlation between gating and conductance changes and AUC occurs across models for most ionic currents. In these cases some of the models display non-monotonic relationships or no relationship (\( |\text{Kendall} \tau | \approx 0\)). However, shifts in A-current activation \(V_{1/2}\), changes in \Kv activation \(V_{1/2}\) and slope factor \(k\), and changes in A-current conductance display consistent monotonic relationships across models (\( |\text{Kendall} \tau | \ne 0\)). The impact of a similar change in \(V_{1/2}\), slope factor \(k\), or conductance of different currents will impact firing behaviour differently not just within and between models \notejb{something is wrong with `` not just within and between models'', I do not understand what the message should be}. +Sensitivity analyses are used to understand how input model parameters contribute to determining the output of a model \citep{Saltelli2002}. In other words, sensitivity analyses are used to understand how sensitive the output of a model is to a change in input or model parameters. One-factor-a-time sensitivity analyses involve altering one parameter at a time and assessing the impact of this parameter on the output. This approach enables the comparison of given alterations in parameters of ionic currents across models. Changes in gating \(V_{1/2}\) and slope factor \(k\) as well as the maximum conductance affect AUC (\Cref{fig:AUC_correlation} A, B and C). Heterogeneity in the correlation between gating and conductance changes and AUC occurs across models for most ionic currents. In these cases some of the models display non-monotonic relationships or no relationship (\( |\text{Kendall} \tau | \approx 0\)). However, shifts in A-current activation \(V_{1/2}\), changes in \Kv activation \(V_{1/2}\) and slope factor \(k\), and changes in A-current conductance display consistent monotonic relationships across models (\( |\text{Kendall} \tau | \ne 0\)). The impact of a similar change in \(V_{1/2}\), slope factor \(k\), or conductance of different currents will impact firing behaviour differently not just within but also between models \notejb{something is wrong with `` not just within and between models'', I do not understand what the message should be} \notenk{change to `` not just within but also between models''}. \begin{figure}[tp] \centering \includegraphics[width=\linewidth]{Figures/AUC_correlation.pdf} - \\\notejb{tick labels too small!} + \\\notejb{tick labels too small!}\notenk{I will fix this tongiht or tomorrow} \linespread{1.}\selectfont \caption[]{The Kendall rank correlation (Kendall \(\tau\)) coefficients between shifts in \(V_{1/2}\) and AUC, slope factor k and AUC as well as current conductances and AUC for each model are shown on the right in (A), (B) and (C) respectively. The relationships between AUC and \(\Delta V_{1/2}\), slope (k) and conductance (g) for the Kendall \(\tau\) coefficients highlights by the black box are depicted in the middle panel. The fI curves corresponding to one of the models are shown in the left panels.} \label{fig:AUC_correlation}