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modified AUC_correlation, rheobase_correlation, ramp_firing

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nkoch1
2022-05-20 00:21:14 -04:00
parent f21c5be832
commit 4497aaf4af
10 changed files with 92 additions and 61 deletions
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Figures/AUC_correlation.pdf
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48
Figures/AUC_correlation.py
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@@ -13,7 +13,7 @@ import matplotlib
import matplotlib.lines as mlines
from matplotlib import ticker
from matplotlib.ticker import NullFormatter
from plotstyle import boxplot_style
from Figures.plotstyle import boxplot_style
def cm2inch(*tupl):
inch = 2.54
@@ -99,6 +99,7 @@ Axes.scatter = new_scatter
#%%
def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
# size =4
hlinewidth = 0.5
# ax.tick_params(axis='x', rotation=90)
model_names = ['RS pyramidal','RS inhibitory','FS',
'RS pyramidal +$K_V1.1$','RS inhibitory +$K_V1.1$',
@@ -120,20 +121,6 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
'#873770', # magenta
]
# 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
# ]
hlinewidth =0.5
import matplotlib.colors
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)]
@@ -158,6 +145,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
# sns.despine(trim=True, bottom=True, ax=ax)
# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
ax.set_title("Shift ($\Delta V_{1/2}$)", y=1.05)
ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
elif alteration=='slope':
i = 3 # Kv1.1 act
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
@@ -183,6 +172,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
ax.set_title("Slope (k)", y=1.05)
# sns.despine(trim=True, bottom=True, ax=ax)
ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
elif alteration=='g':
i = 1 # Kd
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
@@ -203,14 +194,15 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=3):
# sns.despine(trim=True, bottom=True, ax=ax)
# ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
ax.set_title("Conductance (g)", y=1.05)
# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
else:
print('Please chose "shift", "slope" or "g"')
ax.get_legend().remove()
ax.xaxis.grid(False)
sns.despine(trim=True, bottom=True, ax=ax)
ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
# fixlegend(ax, Markers)
def model_legend(ax, marker_s_leg, pos, ncol):
@@ -363,7 +355,7 @@ def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color
c += 1
ax.set_ylabel('Frequency [Hz]')
ax.set_xlabel('Current [nA]')
ax.set_title(model)
ax.set_title(model, x=0.2, y=1.0)
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
L = ax.get_ylim()
@@ -390,15 +382,15 @@ color_dict = {'Cb stellate': '#40A787', # cyan'#
# plot setup
marker_s_leg = 2
max_width = 20
pad_x = 0.65
pad_y= 0.4
pad_w = 0.85
pad_x = 0.8
pad_y= 0.45
pad_w = 1
pad_h = 0.7
fig = plt.figure()
# fig = plt.figure()
# fig.set_size_inches(cm2inch(17.6,10))
gs = fig.add_gridspec(3, 6, wspace=1., hspace=0.8)
gs = fig.add_gridspec(3, 6, wspace=1.2, hspace=1.)
# plt.subplots_adjust(hspace=0.8) #, wspace=0.6
ax0 = fig.add_subplot(gs[0,2:6])
ax0_ex = fig.add_subplot(gs[0,1])
@@ -428,9 +420,9 @@ rec = ax2_fI.add_patch(rec)
rec.set_clip_on(False)
# label 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(-0.825, 1.3, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold') #-0.09
ax1_fI.text(-0.825, 1.3, string.ascii_uppercase[1], transform=ax1_fI.transAxes,size=10, weight='bold')
ax2_fI.text(-0.825, 1.3, string.ascii_uppercase[2], transform=ax2_fI.transAxes,size=10, weight='bold')
# plot boxplots
boxplot_with_markers(ax0,max_width, alteration='shift')
@@ -438,8 +430,8 @@ 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 = (0.15, -0.9)
ncol = 5
model_legend(ax2, marker_s_leg, pos, ncol)
# plot examples
@@ -450,7 +442,7 @@ plot_AUC_alt(ax2_ex, model='STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1=
#save
# plt.tight_layout(pad=0)
print(fig.dpi)
fig.set_size_inches(cm2inch(21,10))
fig.set_size_inches(cm2inch(20.6,12))
fig.savefig('./Figures/AUC_correlation.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
plt.show()

2
Figures/firing_characterization-jb.py
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@@ -299,6 +299,6 @@ 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=75)
ax3_BR.set_ylim(inset_ylim)
fig.set_size_inches(cm2inch(8.17,12))
fig.set_size_inches(cm2inch(8.5,12))
fig.savefig('./Figures/firing_characterization.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
plt.show()

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Figures/plotstyle.py
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@@ -28,18 +28,18 @@ def plot_style():
plt.rcParams['figure.dpi'] = 300
def boxplot_style():
plt.rcParams['xtick.direction'] = 'out'
plt.rcParams['ytick.direction'] = 'out'
plt.rcParams['xtick.direction'] = 'in'
plt.rcParams['ytick.direction'] = 'in'
plt.rcParams['lines.linewidth'] = 1
plt.rcParams['lines.markersize'] = 0.5
plt.rcParams['xtick.labelsize'] = 4
plt.rcParams['ytick.labelsize'] = 4
plt.rcParams['xtick.labelsize'] = 7
plt.rcParams['ytick.labelsize'] = 7
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['axes.titlesize'] = 7
plt.rcParams['axes.labelsize'] = 7
plt.rcParams['legend.fontsize']= 6
plt.rcParams['xtick.labelsize'] = 6
plt.rcParams['ytick.labelsize']= 6
plt.rcParams['mathtext.default'] = 'regular'
plt.rcParams['figure.dpi'] = 300

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Figures/ramp_examples.py
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@@ -239,11 +239,40 @@ def plot_ramp_V(ax, model='RS Pyramidal'): # , stop=750
ax.axis('off')
ax.set_title(model, fontsize=8)
def plot_I_ramp(ax):
dt = 0.01
I_low = 0
I_high = 0.001
initial_period = 1000
sec = 4
ramp_len = int(4 * 1000 * 1 / dt)
stim_time = ramp_len * 2
I_amp = np.array([0])
I_amp = np.reshape(I_amp, (1, I_amp.shape[0]))
I_ramp = np.zeros((stim_time, 1)) @ I_amp
I_ramp[:, :] = np.ones((stim_time, 1)) @ I_amp
stim_num_step = I_ramp.shape[1]
# start = np.int(initial_period * 1 / dt)
start=0
I_ramp[start:int(start + ramp_len), 0] = np.linspace(0, I_high, ramp_len)
I_ramp[int(start + ramp_len):int(start + ramp_len * 2), 0] = np.linspace(I_high, 0, ramp_len)
t = np.arange(0, 4000 * 2, dt)
ax.plot(t, I_ramp)
# ax.plot(model_ramp['t'], model_ramp[model], 'k', linewidth=0.0025)
ax.set_ylabel('I')
ax.set_xlabel('Time [s]')
# ax.set_ylim(-80, 60)
ax.axis('off')
ax.set_title('Ramp Current', fontsize=8, x=0.5, y=-0.5)
return ax
#% plot setup
fig = plt.figure(figsize=cm2inch(17.6,25))
gs0 = fig.add_gridspec(2, 1, wspace=0.)
gs00 = gs0[:].subgridspec(12, 1, wspace=0.7, hspace=1.0)
gs00 = gs0[:].subgridspec(13, 1, wspace=0.7, hspace=1.0)
# gs01 = gs0[1:].subgridspec(7, 2, wspace=0.6, hspace=1)
ax1_ramp = fig.add_subplot(gs00[0])
@@ -258,7 +287,7 @@ ax9_ramp = fig.add_subplot(gs00[8])
ax10_ramp = fig.add_subplot(gs00[9])
ax11_ramp = fig.add_subplot(gs00[10])
ax12_ramp = fig.add_subplot(gs00[11])
ax13_I = fig.add_subplot(gs00[12])
ramp_axs = [ax1_ramp, ax2_ramp, ax3_ramp, ax4_ramp, ax5_ramp,ax6_ramp, ax7_ramp, ax8_ramp,
ax9_ramp, ax10_ramp, ax11_ramp, ax12_ramp]
@@ -282,6 +311,10 @@ add_scalebar(ax12_ramp, matchx=False, matchy=False, hidex=True, hidey=True, size
# add_scalebar(ax12_ramp, matchx=False, matchy=False, hidex=True, hidey=True, sizex=1000, sizey=25, labelx='1 s',
# labely='25 mV', loc=3, pad=-2, borderpad=0, barwidth=2, bbox_to_anchor=Bbox.from_bounds(-0.05, 0.1, 1, 1),
# bbox_transform=ax12_ramp.transAxes)
ax13_I = plot_I_ramp(ax13_I)
add_scalebar(ax13_I, matchx=False, matchy=False, hidex=True, hidey=True, sizex=1000, sizey=0.0005, labelx='1 s',
labely='0.5 $I_{max}$', loc=3, pad=-2, borderpad=0, barwidth=1,
bbox_to_anchor=Bbox.from_bounds(0.0, -0.01, 1, 1), bbox_transform=ax13_I.transAxes)
# add subplot labels
for i in range(0,len(models)):
@@ -289,7 +322,7 @@ for i in range(0,len(models)):
# fig.savefig('./Figures/ramp_firing.pdf') #, bbox_inches='tight'
print(fig.dpi)
fig.set_size_inches(cm2inch(17.6,20))
fig.set_size_inches(cm2inch(17.6,22))
fig.savefig('./Figures/ramp_firing.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
plt.show()

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Figures/rheobase_correlation.pdf
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Figures/rheobase_correlation.py
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@@ -13,7 +13,7 @@ import matplotlib
import matplotlib.lines as mlines
from matplotlib import ticker
from matplotlib.ticker import NullFormatter
from plotstyle import boxplot_style
from Figures.plotstyle import boxplot_style
def cm2inch(*tupl):
@@ -132,7 +132,6 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
i = 3 # Kv1.1 act
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
df = pd.read_csv('./Figures/Data/rheo_shift_corr.csv')
sns.swarmplot(y="corr", x="$\Delta V_{1/2}$", hue="model", data=df, #dodge=True,
palette=clr_dict, linewidth=0, orient='v', ax=ax, size=msize,
order=['Na activation', 'Na inactivation', 'K activation', '$K_V1.1$ activation',
@@ -143,6 +142,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
ax.set_title("Shift ($\Delta V_{1/2}$)", y=1.05)
ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
elif alteration=='slope':
i = 4 # Kv1.1 inact
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
@@ -159,6 +160,8 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
ax.set_title("Slope (k)", y=1.05)
ax.set_xticklabels(['Na \nactivation', 'Na \ninactivation', 'K \nactivation', '$K_V1.1$ \nactivation',
'$K_V1.1$ \ninactivation', 'A \nactivation', 'A \ninactivation'])
elif alteration=='g':
i = 4 # Leak
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
@@ -174,13 +177,14 @@ def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
ax.plot([lim[0], lim[1]], [1, 1], ':k',linewidth=hlinewidth)
ax.plot([lim[0], lim[1]], [-1, -1], ':k',linewidth=hlinewidth)
ax.set_title("Conductance (g)", y=1.05)
ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
else:
print('Please chose "shift", "slope" or "g"')
ax.get_legend().remove()
ax.xaxis.grid(False)
sns.despine(trim=True, bottom=True, ax=ax)
ax.set(xlabel=None, ylabel=r'Kendall $\it{\tau}$')
ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
# ax.set_xticklabels(textwrap.fill(x.get_text(), max_width) for x in ax.get_xticklabels())
def model_legend(ax, marker_s_leg, pos, ncol):
colorslist = [ '#40A787', # cyan'#
@@ -298,11 +302,12 @@ def plot_rheo_alt(ax, model='FS', color1='red', color2='dodgerblue', alteration=
else:
ax.plot(df['alteration'], df[mod], color=clr_dict[mod], alpha=1, zorder=1, linewidth=1)
ax.set_ylabel('$\Delta$ Rheobase (nA)')
ax.set_ylabel('$\Delta$ Rheobase (nA)', labelpad=0)
x = df['alteration']
y = df[model_name_dict[model]]
ax.set_xlim(x.min(), x.max())
ax.set_ylim(df[model_names].min().min(), df[model_names].max().max())
return ax
def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color2='dodgerblue'):
@@ -335,7 +340,7 @@ def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color
c += 1
ax.set_ylabel('Frequency [Hz]')
ax.set_xlabel('Current [nA]')
ax.set_title(model)
ax.set_title(model, x=0.2, y=1.025)
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
L = ax.get_ylim()
@@ -362,21 +367,22 @@ color_dict = {'Cb stellate': '#40A787', # cyan'#
# plot setup
marker_s_leg = 2
max_width = 20
pad_x = 0.65
pad_x = 0.85
pad_y= 0.4
pad_w = 0.85
pad_w = 1.1
pad_h = 0.7
fig = plt.figure(figsize=cm2inch(17.6,10))
gs = fig.add_gridspec(3, 6, wspace=1., hspace=0.8)
fig = plt.figure()
# fig = plt.figure(figsize=cm2inch(17.6,10))
gs = fig.add_gridspec(3, 7, wspace=1.2, hspace=1.)
# plt.subplots_adjust(hspace=0.8) #, wspace=0.6
ax0 = fig.add_subplot(gs[0,2:6])
ax0 = fig.add_subplot(gs[0,2:7])
ax0_ex = fig.add_subplot(gs[0,1])
ax0_fI = fig.add_subplot(gs[0,0])
ax1 = fig.add_subplot(gs[1,2:6])
ax1 = fig.add_subplot(gs[1,2:7])
ax1_ex = fig.add_subplot(gs[1,1])
ax1_fI = fig.add_subplot(gs[1,0])
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])
@@ -398,9 +404,9 @@ rec = ax2_fI.add_patch(rec)
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()