modified AUC_correlation, rheobase_correlation, ramp_firing
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nkoch1
parent
f21c5be832
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@ -13,7 +13,7 @@ import matplotlib
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import matplotlib.lines as mlines
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from matplotlib import ticker
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from matplotlib.ticker import NullFormatter
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from plotstyle import boxplot_style
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from Figures.plotstyle import boxplot_style
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def cm2inch(*tupl):
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inch = 2.54
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@ -99,6 +99,7 @@ Axes.scatter = new_scatter
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#%%
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def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
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# size =4
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hlinewidth = 0.5
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# ax.tick_params(axis='x', rotation=90)
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model_names = ['RS pyramidal','RS inhibitory','FS',
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'RS pyramidal +$K_V1.1$','RS inhibitory +$K_V1.1$',
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@ -120,20 +121,6 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
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'#873770', # magenta
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]
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# colorslist = ['#40A787', # cyan'#
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# '#F0D730', # yellow
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# 'C02717', # red
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# '#007030', # dark green
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# '#AAB71B', # lightgreen
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# '#008797', # light blue
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# '#F78017', # orange
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# '#478010', # green
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# '#53379B', # purple
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# '#2060A7', # blue
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# '#873770', # magenta
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# '#D03050' # pink
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# ]
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hlinewidth =0.5
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import matplotlib.colors
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colors = [matplotlib.colors.to_rgb(c) for c in colorslist] # sns.color_palette("hls", 14, desat=0.75)#[cm.tab20(i) for i in range(20)]
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@ -158,6 +145,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
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# sns.despine(trim=True, bottom=True, ax=ax)
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# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
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ax.set_title("Shift ($\Delta V_{1/2}$)", y=1.05)
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ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
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'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
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elif alteration=='slope':
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i = 3 # Kv1.1 act
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ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
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@ -183,6 +172,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
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# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
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ax.set_title("Slope (k)", y=1.05)
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# sns.despine(trim=True, bottom=True, ax=ax)
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ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
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'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
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elif alteration=='g':
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i = 1 # Kd
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ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
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@ -203,14 +194,15 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
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# sns.despine(trim=True, bottom=True, ax=ax)
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# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
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ax.set_title("Conductance (g)", y=1.05)
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# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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else:
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print('Please chose "shift", "slope" or "g"')
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ax.get_legend().remove()
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ax.xaxis.grid(False)
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sns.despine(trim=True, bottom=True, ax=ax)
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ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
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ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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# fixlegend(ax, Markers)
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def model_legend(ax, marker_s_leg, pos, ncol):
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@ -363,7 +355,7 @@ def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color
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c += 1
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ax.set_ylabel('Frequency [Hz]')
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ax.set_xlabel('Current [nA]')
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ax.set_title(model)
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ax.set_title(model, x=0.2, y=1.0)
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ax.spines["right"].set_visible(False)
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ax.spines["top"].set_visible(False)
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L = ax.get_ylim()
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@ -390,15 +382,15 @@ color_dict = {'Cb stellate': '#40A787', # cyan'#
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# plot setup
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marker_s_leg = 2
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max_width = 20
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pad_x = 0.65
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pad_y= 0.4
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pad_w = 0.85
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pad_x = 0.8
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pad_y= 0.45
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pad_w = 1
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pad_h = 0.7
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fig = plt.figure()
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# fig = plt.figure()
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# fig.set_size_inches(cm2inch(17.6,10))
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gs = fig.add_gridspec(3, 6, wspace=1., hspace=0.8)
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gs = fig.add_gridspec(3, 6, wspace=1.2, hspace=1.)
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# plt.subplots_adjust(hspace=0.8) #, wspace=0.6
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ax0 = fig.add_subplot(gs[0,2:6])
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ax0_ex = fig.add_subplot(gs[0,1])
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@ -428,9 +420,9 @@ rec = ax2_fI.add_patch(rec)
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rec.set_clip_on(False)
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# label subplots with letters
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ax0_fI.text(-0.95, 1.12, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold') #-0.09
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ax1_fI.text(-0.95, 1.12, string.ascii_uppercase[1], transform=ax1_fI.transAxes,size=10, weight='bold')
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ax2_fI.text(-0.95, 1.12, string.ascii_uppercase[2], transform=ax2_fI.transAxes,size=10, weight='bold')
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ax0_fI.text(-0.825, 1.3, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold') #-0.09
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ax1_fI.text(-0.825, 1.3, string.ascii_uppercase[1], transform=ax1_fI.transAxes,size=10, weight='bold')
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ax2_fI.text(-0.825, 1.3, string.ascii_uppercase[2], transform=ax2_fI.transAxes,size=10, weight='bold')
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# plot boxplots
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boxplot_with_markers(ax0,max_width, alteration='shift')
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@ -438,8 +430,8 @@ boxplot_with_markers(ax1,max_width, alteration='slope')
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boxplot_with_markers(ax2,max_width, alteration='g')
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# plot legend
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pos = (0.25, -0.6)
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ncol = 6
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pos = (0.15, -0.9)
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ncol = 5
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model_legend(ax2, marker_s_leg, pos, ncol)
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# plot examples
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@ -450,7 +442,7 @@ plot_AUC_alt(ax2_ex, model='STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1=
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#save
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# plt.tight_layout(pad=0)
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print(fig.dpi)
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fig.set_size_inches(cm2inch(21,10))
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fig.set_size_inches(cm2inch(20.6,12))
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fig.savefig('./Figures/AUC_correlation.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
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plt.show()
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@ -299,6 +299,6 @@ ax3.text(0.95, -0.55, 'LOF')
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ax3_BR = ax3.inset_axes([0.63, 0.15, 0.3, 0.2])
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plot_diff_sqrt(ax3_BR, b2=0.4, c2=75)
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ax3_BR.set_ylim(inset_ylim)
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fig.set_size_inches(cm2inch(8.17,12))
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fig.set_size_inches(cm2inch(8.5,12))
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fig.savefig('./Figures/firing_characterization.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
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plt.show()
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@ -28,18 +28,18 @@ def plot_style():
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plt.rcParams['figure.dpi'] = 300
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def boxplot_style():
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plt.rcParams['xtick.direction'] = 'out'
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plt.rcParams['ytick.direction'] = 'out'
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plt.rcParams['xtick.direction'] = 'in'
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plt.rcParams['ytick.direction'] = 'in'
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plt.rcParams['lines.linewidth'] = 1
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plt.rcParams['lines.markersize'] = 0.5
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plt.rcParams['xtick.labelsize'] = 4
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plt.rcParams['ytick.labelsize'] = 4
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plt.rcParams['xtick.labelsize'] = 7
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plt.rcParams['ytick.labelsize'] = 7
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plt.rcParams['savefig.bbox'] = 'tight'
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plt.rcParams['axes.titlesize'] = 5
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plt.rcParams['axes.labelsize'] = 4
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plt.rcParams['legend.fontsize']= 4
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plt.rcParams['xtick.labelsize'] = 3
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plt.rcParams['ytick.labelsize']= 3
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plt.rcParams['axes.titlesize'] = 7
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plt.rcParams['axes.labelsize'] = 7
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plt.rcParams['legend.fontsize']= 6
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plt.rcParams['xtick.labelsize'] = 6
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plt.rcParams['ytick.labelsize']= 6
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plt.rcParams['mathtext.default'] = 'regular'
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plt.rcParams['figure.dpi'] = 300
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@ -239,11 +239,40 @@ def plot_ramp_V(ax, model='RS Pyramidal'): # , stop=750
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ax.axis('off')
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ax.set_title(model, fontsize=8)
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def plot_I_ramp(ax):
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dt = 0.01
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I_low = 0
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I_high = 0.001
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initial_period = 1000
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sec = 4
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ramp_len = int(4 * 1000 * 1 / dt)
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stim_time = ramp_len * 2
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I_amp = np.array([0])
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I_amp = np.reshape(I_amp, (1, I_amp.shape[0]))
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I_ramp = np.zeros((stim_time, 1)) @ I_amp
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I_ramp[:, :] = np.ones((stim_time, 1)) @ I_amp
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stim_num_step = I_ramp.shape[1]
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# start = np.int(initial_period * 1 / dt)
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start=0
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I_ramp[start:int(start + ramp_len), 0] = np.linspace(0, I_high, ramp_len)
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I_ramp[int(start + ramp_len):int(start + ramp_len * 2), 0] = np.linspace(I_high, 0, ramp_len)
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t = np.arange(0, 4000 * 2, dt)
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ax.plot(t, I_ramp)
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# ax.plot(model_ramp['t'], model_ramp[model], 'k', linewidth=0.0025)
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ax.set_ylabel('I')
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ax.set_xlabel('Time [s]')
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# ax.set_ylim(-80, 60)
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ax.axis('off')
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ax.set_title('Ramp Current', fontsize=8, x=0.5, y=-0.5)
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return ax
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#% plot setup
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fig = plt.figure(figsize=cm2inch(17.6,25))
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gs0 = fig.add_gridspec(2, 1, wspace=0.)
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gs00 = gs0[:].subgridspec(12, 1, wspace=0.7, hspace=1.0)
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gs00 = gs0[:].subgridspec(13, 1, wspace=0.7, hspace=1.0)
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# gs01 = gs0[1:].subgridspec(7, 2, wspace=0.6, hspace=1)
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ax1_ramp = fig.add_subplot(gs00[0])
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@ -258,7 +287,7 @@ ax9_ramp = fig.add_subplot(gs00[8])
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ax10_ramp = fig.add_subplot(gs00[9])
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ax11_ramp = fig.add_subplot(gs00[10])
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ax12_ramp = fig.add_subplot(gs00[11])
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ax13_I = fig.add_subplot(gs00[12])
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ramp_axs = [ax1_ramp, ax2_ramp, ax3_ramp, ax4_ramp, ax5_ramp,ax6_ramp, ax7_ramp, ax8_ramp,
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ax9_ramp, ax10_ramp, ax11_ramp, ax12_ramp]
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@ -282,6 +311,10 @@ add_scalebar(ax12_ramp, matchx=False, matchy=False, hidex=True, hidey=True, size
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# add_scalebar(ax12_ramp, matchx=False, matchy=False, hidex=True, hidey=True, sizex=1000, sizey=25, labelx='1 s',
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# labely='25 mV', loc=3, pad=-2, borderpad=0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.05, 0.1, 1, 1),
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# bbox_transform=ax12_ramp.transAxes)
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ax13_I = plot_I_ramp(ax13_I)
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add_scalebar(ax13_I, matchx=False, matchy=False, hidex=True, hidey=True, sizex=1000, sizey=0.0005, labelx='1 s',
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labely='0.5 $I_{max}$', loc=3, pad=-2, borderpad=0, barwidth=1,
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bbox_to_anchor=Bbox.from_bounds(0.0, -0.01, 1, 1), bbox_transform=ax13_I.transAxes)
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# add subplot labels
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for i in range(0,len(models)):
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@ -289,7 +322,7 @@ for i in range(0,len(models)):
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# fig.savefig('./Figures/ramp_firing.pdf') #, bbox_inches='tight'
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print(fig.dpi)
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fig.set_size_inches(cm2inch(17.6,20))
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fig.set_size_inches(cm2inch(17.6,22))
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fig.savefig('./Figures/ramp_firing.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
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plt.show()
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Binary file not shown.
Binary file not shown.
@ -13,7 +13,7 @@ import matplotlib
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import matplotlib.lines as mlines
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from matplotlib import ticker
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from matplotlib.ticker import NullFormatter
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from plotstyle import boxplot_style
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from Figures.plotstyle import boxplot_style
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def cm2inch(*tupl):
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@ -132,7 +132,6 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
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i = 3 # Kv1.1 act
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ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
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df = pd.read_csv('./Figures/Data/rheo_shift_corr.csv')
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sns.swarmplot(y="corr", x="$\Delta V_{1/2}$", hue="model", data=df, #dodge=True,
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palette=clr_dict, linewidth=0, orient='v', ax=ax, size=msize,
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order=['Na activation', 'Na inactivation', 'K activation', '$K_V1.1$ activation',
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@ -143,6 +142,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
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ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
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ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
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ax.set_title("Shift ($\Delta V_{1/2}$)", y=1.05)
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ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
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'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
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elif alteration=='slope':
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i = 4 # Kv1.1 inact
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ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
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@ -159,6 +160,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
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ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
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ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
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ax.set_title("Slope (k)", y=1.05)
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ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
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'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
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elif alteration=='g':
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i = 4 # Leak
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ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
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@ -174,13 +177,14 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
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ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
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ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
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ax.set_title("Conductance (g)", y=1.05)
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ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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else:
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print('Please chose "shift", "slope" or "g"')
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ax.get_legend().remove()
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ax.xaxis.grid(False)
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sns.despine(trim=True, bottom=True, ax=ax)
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ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
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ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
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def model_legend(ax, marker_s_leg, pos, ncol):
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colorslist = [ '#40A787', # cyan'#
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@ -298,11 +302,12 @@ def plot_rheo_alt(ax, model='FS', color1='red', color2='dodgerblue', alteration=
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else:
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ax.plot(df['alteration'], df[mod], color=clr_dict[mod], alpha=1, zorder=1, linewidth=1)
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ax.set_ylabel('$\Delta$ Rheobase (nA)')
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ax.set_ylabel('$\Delta$ Rheobase (nA)', labelpad=0)
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x = df['alteration']
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y = df[model_name_dict[model]]
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ax.set_xlim(x.min(), x.max())
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ax.set_ylim(df[model_names].min().min(), df[model_names].max().max())
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return ax
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def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color2='dodgerblue'):
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@ -335,7 +340,7 @@ def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color
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c += 1
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ax.set_ylabel('Frequency [Hz]')
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ax.set_xlabel('Current [nA]')
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ax.set_title(model)
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ax.set_title(model, x=0.2, y=1.025)
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ax.spines["right"].set_visible(False)
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ax.spines["top"].set_visible(False)
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L = ax.get_ylim()
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@ -362,21 +367,22 @@ color_dict = {'Cb stellate': '#40A787', # cyan'#
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# plot setup
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marker_s_leg = 2
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max_width = 20
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pad_x = 0.65
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pad_x = 0.85
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pad_y= 0.4
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pad_w = 0.85
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pad_w = 1.1
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pad_h = 0.7
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fig = plt.figure(figsize=cm2inch(17.6,10))
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gs = fig.add_gridspec(3, 6, wspace=1., hspace=0.8)
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fig = plt.figure()
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# fig = plt.figure(figsize=cm2inch(17.6,10))
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gs = fig.add_gridspec(3, 7, wspace=1.2, hspace=1.)
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# plt.subplots_adjust(hspace=0.8) #, wspace=0.6
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ax0 = fig.add_subplot(gs[0,2:6])
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ax0 = fig.add_subplot(gs[0,2:7])
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ax0_ex = fig.add_subplot(gs[0,1])
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ax0_fI = fig.add_subplot(gs[0,0])
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ax1 = fig.add_subplot(gs[1,2:6])
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ax1 = fig.add_subplot(gs[1,2:7])
|
||||
ax1_ex = fig.add_subplot(gs[1,1])
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ax1_fI = fig.add_subplot(gs[1,0])
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||||
ax2 = fig.add_subplot(gs[2,2:6])
|
||||
ax2 = fig.add_subplot(gs[2,2:7])
|
||||
ax2_ex = fig.add_subplot(gs[2,1])
|
||||
ax2_fI = fig.add_subplot(gs[2,0])
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||||
|
||||
@ -398,9 +404,9 @@ rec = ax2_fI.add_patch(rec)
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||||
rec.set_clip_on(False)
|
||||
|
||||
# label fI subplots with letters
|
||||
ax0_fI.text(-0.95, 1.12, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold') #-0.09
|
||||
ax1_fI.text(-0.95, 1.12, string.ascii_uppercase[1], transform=ax1_fI.transAxes,size=10, weight='bold')
|
||||
ax2_fI.text(-0.95, 1.12, string.ascii_uppercase[2], transform=ax2_fI.transAxes,size=10, weight='bold')
|
||||
ax0_fI.text(-0.875, 1.35, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold') #-0.09
|
||||
ax1_fI.text(-0.875, 1.35, string.ascii_uppercase[1], transform=ax1_fI.transAxes,size=10, weight='bold')
|
||||
ax2_fI.text(-0.875, 1.35, string.ascii_uppercase[2], transform=ax2_fI.transAxes,size=10, weight='bold')
|
||||
|
||||
# plot boxplots
|
||||
boxplot_with_markers(ax0,max_width, alteration='shift')
|
||||
@ -408,8 +414,8 @@ boxplot_with_markers(ax1,max_width, alteration='slope')
|
||||
boxplot_with_markers(ax2,max_width, alteration='g')
|
||||
|
||||
# plot legend
|
||||
pos = (0.25, -0.6)
|
||||
ncol = 6
|
||||
pos = (0.225, -0.9)
|
||||
ncol = 5
|
||||
model_legend(ax2, marker_s_leg, pos, ncol)
|
||||
|
||||
# plot rheo across model for example alteration
|
||||
@ -420,7 +426,7 @@ plot_rheo_alt(ax2_ex, model='Cb stellate', color1='lightgrey', color2='k', alter
|
||||
# save
|
||||
# fig.savefig('./Figures/rheobase_correlation.pdf', bbox_inches='tight')
|
||||
print(fig.dpi)
|
||||
fig.set_size_inches(cm2inch(20.3,10))
|
||||
fig.set_size_inches(cm2inch(20.75,12))
|
||||
fig.savefig('./Figures/rheobase_correlation.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
|
||||
plt.show()
|
||||
|
||||
|
||||
@ -310,7 +310,7 @@ Qualitative differences can be found, for example, when increasing the conductan
|
||||
\begin{figure}[tp]
|
||||
\centering
|
||||
\includegraphics[width=\linewidth]{Figures/AUC_correlation.pdf}
|
||||
\\\notejb{tick labels too small!}\notenk{I will fix this tongiht or tomorrow}
|
||||
\\\notejb{tick labels too small!}\notenk{Is this better?}
|
||||
\linespread{1.}\selectfont
|
||||
\caption[]{Effects of altered channel kinetics on AUC in various neuron models. 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}
|
||||
@ -456,7 +456,7 @@ Accordingly, for accurate modelling and predictions of the effects of mutations
|
||||
\centering
|
||||
\includegraphics[width=\linewidth]{Figures/ramp_firing.pdf}
|
||||
\linespread{1.}\selectfont
|
||||
\\\notejb{You should add the ramp stimulus at the bottom. To be able to see the hysteresis one needs to know where the symmetry axis is. (I gues it is in the center, but better is to see that.}
|
||||
\\\notejb{You should add the ramp stimulus at the bottom. To be able to see the hysteresis one needs to know where the symmetry axis is. (I gues it is in the center, but better is to see that.}\notenk{like this?}
|
||||
\caption[]{Diversity in Neuronal Model Firing Responses to a Current Ramp. Spike trains for Cb stellate (A), RS inhibitory (B), FS (C), RS pyramidal (D), RS inhibitory +\Kv (E), Cb stellate +\Kv (F), FS +\Kv (G), RS pyramidal +\Kv (H), STN +\Kv (I), Cb stellate \(\Delta\)\Kv (J), STN \(\Delta\)\Kv (K), and STN (L) neuron models in response to a slow ascending current ramp followed by the descending version of the current ramp. The current at which firing begins in response to an ascending current ramp and the current at which firing ceases in response to a descending current ramp are depicted on the frequency current (fI) curves in \Cref{fig:diversity_in_firing} for each model.}
|
||||
\label{fig:ramp_firing}
|
||||
\end{figure}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user