add summary_fig.py as a tenative summary figure

Figures/AUC_correlation_letters.py

@@ -538,6 +538,6 @@ 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) #pdf #eps
-# fig.savefig('./Figures/AUC_correlation.png', dpi=fig.dpi) #pdf #eps
+# fig.savefig('./Figures/AUC_correlation.pdf', dpi=fig.dpi) #pdf #eps
+fig.savefig('./Figures/AUC_correlation.jpg', dpi=fig.dpi) #pdf #eps
 plt.show()

Figures/diversity_in_firing.py

@@ -188,7 +188,7 @@ for i in range(0,len(models)):
     spike_axs[i].text(-0.18, 1.2, string.ascii_uppercase[i], transform=spike_axs[i].transAxes, size=10, weight='bold')
 # save
 fig.set_size_inches(cm2inch(17.6,20))
-fig.savefig('./Figures/diversity_in_firing.pdf', dpi=fig.dpi) #pdf # eps
+fig.savefig('./Figures/diversity_in_firing.jpg', dpi=fig.dpi) #pdf # eps
 # fig.savefig('./Figures/diversity_in_firing.png', dpi=fig.dpi) #pdf # eps
 plt.show()
 

Figures/firing_characterization.py

@@ -365,5 +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.png', dpi=fig.dpi, bbox_inches='tight') #, dpi=fig.dpi #pdf #eps
+fig.savefig('./Figures/firing_characterization_arrows.jpg', dpi=300, bbox_inches='tight') #, dpi=fig.dpi #pdf #eps
 plt.show()

Figures/ramp_firing_letters.py

@@ -317,6 +317,6 @@ for i in range(0,len(models)):
 
 #save
 fig.set_size_inches(cm2inch(17.6,22))
-fig.savefig('./Figures/ramp_firing.png', dpi=fig.dpi)#pdf #eps
+fig.savefig('./Figures/ramp_firing.jpg', dpi=fig.dpi)#pdf #eps
 plt.show()
 

Figures/rheobase_correlation_letters.py

@@ -608,8 +608,8 @@ 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)
-# fig.savefig('./Figures/rheobase_correlation.png', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi # eps # pdf
+# fig.savefig('./Figures/rheobase_correlation.pdf', dpi=fig.dpi)
+fig.savefig('./Figures/rheobase_correlation.jpg', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi # eps # pdf
 plt.show()
 
 

Figures/simulation_model_comparison_letters.py

@@ -269,7 +269,7 @@ axr1.text(-0.27, 1.075, string.ascii_uppercase[j+1], transform=axr1.transAxes, s
 
 # save
 fig.set_size_inches(cm2inch(22.2,15))
-fig.savefig('./Figures/simulation_model_comparison.pdf', dpi=fig.dpi) #eps
-# fig.savefig('./Figures/simulation_model_comparison.png', dpi=fig.dpi) #eps
+# fig.savefig('./Figures/simulation_model_comparison.pdf', dpi=fig.dpi) #eps
+fig.savefig('./Figures/simulation_model_comparison.jpg', dpi=fig.dpi) #eps
 plt.show()
 

Figures/summary_fig.py

@@ -0,0 +1,387 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+import matplotlib.ticker as ticker
+from matplotlib.colors import colorConverter as cc
+from matplotlib.colors import to_hex
+import string
+from plotstyle import scheme_style
+
+colorslist = ['#40A787',  # cyan'#
+              '#F0D730',  # yellow
+              '#C02717',  # red
+              '#007030',  # dark green
+              '#AAB71B',  # lightgreen
+              '#008797',  # light blue
+              '#F78017',  # orange
+              '#478010',  # green
+              '#53379B',  # purple
+              '#2060A7',  # blue
+              '#873770',  # magenta
+              '#D03050'  # pink
+              ]
+
+
+def cm2inch(*tupl):
+    inch = 2.54
+    if isinstance(tupl[0], tuple):
+        return tuple(i / inch for i in tupl[0])
+    else:
+        return tuple(i / inch for i in tupl)
+
+
+def show_spines(ax, spines='lrtb'):
+    """ Show and hide spines.
+
+    From github.com/janscience/plottools.git  spines.py
+
+    Parameters
+    ----------
+    ax: matplotlib figure, matplotlib axis, or list of matplotlib axes
+        Axis on which spine and ticks visibility is manipulated.
+        If figure, then apply manipulations on all axes of the figure.
+        If list of axes, apply manipulations on each of the given axes.
+    spines: string
+        Specify which spines and ticks should be shown.
+        All other ones or hidden.
+        'l' is the left spine, 'r' the right spine,
+        't' the top one and 'b' the bottom one.
+        E.g. 'lb' shows the left and bottom spine, and hides the top
+        and and right spines, as well as their tick marks and labels.
+        '' shows no spines at all.
+        'lrtb' shows all spines and tick marks.
+
+    Examples
+    --------
+    ```py
+    import matplotlib.pyplot as plt
+    import plottools.spines
+
+    fig, (ax0, ax1, ax2) = plt.subplots(1, 3)
+    ax0.show_spines('lb')
+    ax1.show_spines('bt')
+    ax2.show_spines('tr')
+    ```
+    ![show](figures/spines-show.png)
+    """
+    # collect spine visibility:
+    xspines = []
+    if 't' in spines:
+        xspines.append('top')
+    if 'b' in spines:
+        xspines.append('bottom')
+    yspines = []
+    if 'l' in spines:
+        yspines.append('left')
+    if 'r' in spines:
+        yspines.append('right')
+    # collect axes:
+    if isinstance(ax, (list, tuple, np.ndarray)):
+        axs = ax
+    elif hasattr(ax, 'get_axes'):
+        # ax is figure:
+        axs = ax.get_axes()
+    else:
+        axs = [ax]
+    if not isinstance(axs, (list, tuple)):
+        axs = [axs]
+    for ax in axs:
+        # hide spines:
+        ax.spines['top'].set_visible('top' in xspines)
+        ax.spines['bottom'].set_visible('bottom' in xspines)
+        ax.spines['left'].set_visible('left' in yspines)
+        ax.spines['right'].set_visible('right' in yspines)
+        # ticks:
+        if len(xspines) == 0:
+            ax.xaxis.set_ticks_position('none')
+            ax.xaxis.label.set_visible(False)
+            ax.xaxis._orig_major_locator = ax.xaxis.get_major_locator()
+            ax.xaxis.set_major_locator(ticker.NullLocator())
+        else:
+            if hasattr(ax.xaxis, '_orig_major_locator'):
+                ax.xaxis.set_major_locator(ax.xaxis._orig_major_locator)
+                delattr(ax.xaxis, '_orig_major_locator')
+            elif isinstance(ax.xaxis.get_major_locator(), ticker.NullLocator):
+                ax.xaxis.set_major_locator(ticker.AutoLocator())
+            if len(xspines) == 1:
+                ax.xaxis.set_ticks_position(xspines[0])
+                ax.xaxis.set_label_position(xspines[0])
+            else:
+                ax.xaxis.set_ticks_position('both')
+                ax.xaxis.set_label_position('bottom')
+        if len(yspines) == 0:
+            ax.yaxis.set_ticks_position('none')
+            ax.yaxis.label.set_visible(False)
+            ax.yaxis._orig_major_locator = ax.yaxis.get_major_locator()
+            ax.yaxis.set_major_locator(ticker.NullLocator())
+        else:
+            if hasattr(ax.yaxis, '_orig_major_locator'):
+                ax.yaxis.set_major_locator(ax.yaxis._orig_major_locator)
+                delattr(ax.yaxis, '_orig_major_locator')
+            elif isinstance(ax.yaxis.get_major_locator(), ticker.NullLocator):
+                ax.yaxis.set_major_locator(ticker.AutoLocator())
+            if len(yspines) == 1:
+                ax.yaxis.set_ticks_position(yspines[0])
+                ax.yaxis.set_label_position(yspines[0])
+            else:
+                ax.yaxis.set_ticks_position('both')
+                ax.yaxis.set_label_position('left')
+
+
+def lighter(color, lightness):
+    """ Make a color lighter.
+
+    From github.com/janscience/plottools.git  colors.py
+
+    ![lighter](figures/colors-lighter.png)
+
+    Parameters
+    ----------
+    color: dict or matplotlib color spec
+        A matplotlib color (hex string, name color string, rgb tuple)
+        or a dictionary with an 'color' or 'facecolor' key.
+    lightness: float
+        The smaller the lightness, the lighter the returned color.
+        A lightness of 0 returns white.
+        A lightness of 1 leaves the color untouched.
+        A lightness of 2 returns black.
+
+    Returns
+    -------
+    color: string or dict
+        The lighter color as a hexadecimal RGB string (e.g. '#rrggbb').
+        If `color` is a dictionary, a copy of the dictionary is returned
+        with the value of 'color' or 'facecolor' set to the lighter color.
+
+    Examples
+    --------
+    For 40% lightness of blue do
+    ```py
+    import plottools.colors as c
+    colors = c.palettes['muted']
+    lightblue = c.lighter(colors['blue'], 0.4)
+    ```
+    """
+    try:
+        c = color['color']
+        cd = dict(**color)
+        cd['color'] = lighter(c, lightness)
+        return cd
+    except (KeyError, TypeError):
+        try:
+            c = color['facecolor']
+            cd = dict(**color)
+            cd['facecolor'] = lighter(c, lightness)
+            return cd
+        except (KeyError, TypeError):
+            if lightness > 2:
+                lightness = 2
+            if lightness > 1:
+                return darker(color, 2.0 - lightness)
+            if lightness < 0:
+                lightness = 0
+            r, g, b = cc.to_rgb(color)
+            rl = r + (1.0 - lightness) * (1.0 - r)
+            gl = g + (1.0 - lightness) * (1.0 - g)
+            bl = b + (1.0 - lightness) * (1.0 - b)
+            return to_hex((rl, gl, bl)).upper()
+
+
+def plot_sqrt(ax, a=1, b=0.2, c=100, d=0):
+    x = np.linspace(0, 1, 10000)
+    y = c * np.sqrt(a * (x - b)) + d
+    ax.plot(x, y)
+    ax.set_xlabel('Current [nA]')
+    ax.set_ylabel('Frequency [Hz]')
+    ax.set_xlim(0, 1)
+    ax.set_ylim(0, ax.get_ylim()[1])
+
+
+def plot_AUC(ax, a=1, b=0.2, c=180, d=0, width=0.2):
+    x = np.linspace(0, 1, 1000)
+    y = c * np.sqrt(a * (x - b)) + d
+    ax.plot(x, y, colorslist[9])
+    ax.set_xlabel('Current [nA]')
+    ax.set_ylabel('Frequency [Hz]')
+    ax.fill_between(x, y, where=(x <= b + width), color=lighter(colorslist[9], 0.3))
+    ax.text(0.3, 15, 'AUC', ha='center')
+    ax.annotate('', (0.2, 10), (0, 10), arrowprops=dict(arrowstyle="<->"))
+    ax.text(0.1, 20, 'rheobase', ha='center')
+    ax.set_xlim(0, 0.5)
+    ax.set_ylim(0, 100)
+    ax.yaxis.set_major_locator(ticker.MultipleLocator(50))
+
+
+def plot_diff_sqrt(ax, a=1, b=0.2, c=100, d=0, a2=1, b2=0.2, c2=100, d2=0):
+    show_spines(ax, 'lb')
+    x = np.linspace(0, 1, 10000)
+    y = c * np.sqrt(a * (x - b)) + d
+    y2 = c2 * np.sqrt(a2 * (x - b2)) + d2
+    ax.plot(x, y, colorslist[9])
+    ax.plot(x, y2, colorslist[2])
+    ax.set_xlim(0, 1)
+    ax.set_ylim(0, ax.get_ylim()[1])
+    ax.set_xticks([])
+    ax.set_yticks([])
+    ax.set_xlabel('Current')
+    ax.set_ylabel('Frequency')
+
+
+def plot_quadrant(ax):
+    ax.spines['left'].set_position('zero')
+    ax.spines['bottom'].set_position('zero')
+    ax.text(1.2, -0.15, '$\\Delta$ rheobase', ha='right')
+    ax.text(-0.03, 0.7, '$\\Delta$ AUC', ha='right', rotation=90)
+    ax.tick_params(length=0)
+    ax.set_xlim(-1, 1)
+    ax.set_ylim(-1, 1)
+    ax.annotate('', (1, 0), (-1, 0), arrowprops=dict(arrowstyle="->"))
+    ax.annotate('', (0, 1), (0, -1), arrowprops=dict(arrowstyle="->"))
+    ax.set_xticks([-0.5, 0.5])
+    a = ax.get_xticks().tolist()
+    a[0] = '\u2212'
+    a[1] = '+'
+    ax.set_xticklabels(a)
+    ax.set_yticks([-0.5, 0.5])
+    b = ax.get_xticks().tolist()
+    b[0] = '\u2212'
+    b[1] = '+'
+    ax.set_yticklabels(b)
+#
+# #%%
+#
+# imgplot = plt.imshow(img)
+# plt.show()
+
+
+
+# %% with legend
+scheme_style()
+import matplotlib.image as mpimg
+img = mpimg.imread('./Figures/summary_diagram.png')
+inset_ylim = (0, 100)
+lfsize = 8
+fig = plt.figure(figsize=cm2inch(17.2, 12))
+gs = gridspec.GridSpec(14, 3, top=0.95, bottom=0.1, left=0.15, right=0.95, hspace=0.4, wspace=0.2)
+
+# 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],
+ax1 = fig.add_subplot(gs[1:4,2])
+ax2 = fig.add_subplot(gs[6:9,2])
+ax3 = fig.add_subplot(gs[11:14,2])
+
+ax0 = fig.add_subplot(gs[:, :2])
+# ax1 = fig.add_subplot(gs0[0])
+# ax2 = fig.add_subplot(gs0[1])
+# ax3 = fig.add_subplot(gs0[2])
+
+ax0.imshow(img)
+show_spines(ax0, '')
+
+
+# ax1.text(-0.95, -0.55, 'GOF/\nLOF?', ha='right')
+plot_diff_sqrt(ax1, b2=0.06, c2=65)
+ax1.set_ylim(inset_ylim)
+ax1.annotate('', (0.225, 7), (0.07, 7),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax1.annotate('', (0.8, 80), (0.85, 55),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax1.text(x=0.05, y=95, s='$\\downarrow$ AUC $\downarrow$ rheobase', fontsize=lfsize)
+
+
+
+# ax2.text(0.95, 0.35, 'LOF/\nGOF?')
+plot_diff_sqrt(ax2, b2=0.4, c2=200)
+ax2.set_ylim(inset_ylim)
+ax2.annotate('', (0.19, 7), (0.41, 7),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax2.annotate('', (0.75, 70), (0.6, 90),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax2.text(x=0.05, y=110, s='$\\uparrow$ AUC $\\uparrow$ rheobase', fontsize=lfsize)
+#
+
+
+
+
+plot_diff_sqrt(ax3, b2=0.09, c2=200)
+
+# ax3.text(x=-0.9, y=0.7, s='$\\uparrow$ AUC\n$\\downarrow$ rheobase', fontsize=lfsize)
+# ax3.text(-0.95, 0.35, 'GOF', ha='right')
+ax3.set_ylim(inset_ylim)
+ax3.annotate('', (0.225, 7), (0.085, 7),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax3.annotate('', (0.55, 55), (0.3, 90),
+                arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+ax3.text(x=0.05, y=110, s='$\\uparrow$ AUC $\\downarrow$ rheobase', fontsize=lfsize)
+
+# fig.set_size_inches(cm2inch(17, 12))
+fig.savefig('./Figures/summary_fig.pdf', dpi=300, bbox_inches='tight')  # , 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=0.9, 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)
+# ax3 = fig.add_subplot(gs[1:, :])
+#
+# # add panel letter labels
+# ax1.text(-0.4, 1.2, string.ascii_uppercase[0], transform=ax1.transAxes, size=16, weight='bold')
+# ax3.text(-0.15, 1.05, string.ascii_uppercase[1], transform=ax3.transAxes, size=16, weight='bold')
+#
+# show_spines(ax3, '')
+# plot_quadrant(ax3)  # plot delineation into quadrants
+#
+# inset_ylim = (0, 100)
+# # top left
+# lfsize = 8
+# ax3.text(x=-0.9, y=0.7, s='$\\uparrow$ AUC\n$\\downarrow$ rheobase', fontsize=lfsize)
+# ax3.text(-0.95, 0.35, 'GOF', ha='right')
+# ax3_TL = ax3.inset_axes([0.07, 0.6, 0.3, 0.2])
+# plot_diff_sqrt(ax3_TL, b2=0.09, c2=200)
+# ax3_TL.set_ylim(inset_ylim)
+# ax3_TL.annotate('', (0.25, 7), (0.085, 7),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+# ax3_TL.annotate('', (0.55, 55), (0.3, 90),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+# # top right
+# ax3.text(x=0.22, y=0.7, s='$\\uparrow$ AUC\n$\\uparrow$ rheobase', fontsize=lfsize)
+# ax3.text(0.95, 0.35, 'LOF/\nGOF?')
+# ax3_TR = ax3.inset_axes([0.63, 0.6, 0.3, 0.2])
+# plot_diff_sqrt(ax3_TR, b2=0.4, c2=200)
+# ax3_TR.set_ylim(inset_ylim)
+# ax3_TR.annotate('', (0.17, 7), (0.41, 7),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+# ax3_TR.annotate('', (0.8, 70), (0.6, 90),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+#
+# # bottom left
+# ax3.text(x=-0.9, y=-0.95, s='$\\downarrow$ AUC\n$\downarrow$ rheobase', fontsize=lfsize)
+# ax3.text(-0.95, -0.55, 'GOF/\nLOF?', ha='right')
+# ax3_BL = ax3.inset_axes([0.07, 0.15, 0.3, 0.2])
+# plot_diff_sqrt(ax3_BL, b2=0.06, c2=65)
+# ax3_BL.set_ylim(inset_ylim)
+# ax3_BL.annotate('', (0.25, 7), (0.07, 7),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+# ax3_BL.annotate('', (0.8, 80), (0.85, 55),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+#
+# # bottom right
+# ax3.text(x=0.22, y=-0.95, s='$\\downarrow$ AUC\n$\\uparrow$ rheobase', fontsize=lfsize)
+# ax3.text(0.95, -0.55, 'LOF')
+# ax3_BR = ax3.inset_axes([0.63, 0.15, 0.3, 0.2])
+# plot_diff_sqrt(ax3_BR, b2=0.4, c2=60)
+# ax3_BR.set_ylim(inset_ylim)
+# ax3_BR.annotate('', (0.18, 7), (0.42, 7),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+# ax3_BR.annotate('', (0.7, 75), (0.8, 37.5),
+#                 arrowprops=dict(arrowstyle="<|-", color=colorslist[2], lw=0.5, mutation_scale=5), zorder=-10)  #
+#
+# fig.set_size_inches(cm2inch(8.5, 12))
+# fig.savefig('./Figures/firing_characterization_arrows.jpg', dpi=300, bbox_inches='tight')  # , dpi=fig.dpi #pdf #eps
+# plt.show()
+

Frontiers_manuscript/For_Submission/Koch_reviewer_comments.tex

@@ -106,7 +106,16 @@ Although hysteresis is important both from a dynamical systems perspective and i
 
 \textit{A final outline summarizing the main results of the main models and the general limitations of this approach could be included.}
 
-Todo?
+Something like this?
+
+\begin{figure}[!h]
+        \centering
+        \includegraphics[width=\linewidth]{summary_fig.jpg}
+        \linespread{1.}\selectfont
+	\caption[]{Something like this?}
+\end{figure}
+
+\FloatBarrier
 
 \section{Reviewer 3}