a0f64fd365
and old firing_characterization file to firing_characterization_old.py also renamed ramp_examples.py as ramp_firing.py; cleaned up comments and code for rheobase_correlation.py, AUC_correlation.py, diversity_in_firing.py, ramp_firing.py, simulation_model_comparison.py
429 lines
21 KiB
Python
429 lines
21 KiB
Python
# -*- coding: utf-8 -*-
|
|
"""
|
|
Created on Sat Jul 3 19:52:04 2021
|
|
|
|
@author: nils
|
|
"""
|
|
import pandas as pd
|
|
import numpy as np
|
|
import string
|
|
import textwrap
|
|
import json
|
|
import matplotlib
|
|
import matplotlib.lines as mlines
|
|
from matplotlib import ticker
|
|
from matplotlib.ticker import NullFormatter
|
|
from Figures.plotstyle import boxplot_style
|
|
|
|
|
|
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)
|
|
#%% ##################### From https://stackoverflow.com/questions/52878845/swarmplot-with-hue-affecting-marker-beyond-color ##
|
|
# to change marker types in seaborn swarmplot
|
|
|
|
import seaborn as sns
|
|
import matplotlib.pyplot as plt
|
|
|
|
############## Begin hack ##############
|
|
from matplotlib.axes._axes import Axes
|
|
from matplotlib.markers import MarkerStyle
|
|
from numpy import ndarray
|
|
|
|
def GetColor2Marker(markers):
|
|
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
|
|
]
|
|
import matplotlib.colors
|
|
palette = [matplotlib.colors.to_rgb(c) for c in colorslist] #
|
|
mkcolors = [(palette[i]) for i in range(len(markers))]
|
|
return dict(zip(mkcolors,markers))
|
|
|
|
def fixlegend(ax,markers,markersize=3,**kwargs):
|
|
# Fix Legend
|
|
legtitle = ax.get_legend().get_title().get_text()
|
|
_,l = ax.get_legend_handles_labels()
|
|
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
|
|
]
|
|
import matplotlib.colors
|
|
palette = [matplotlib.colors.to_rgb(c) for c in colorslist]
|
|
mkcolors = [(palette[i]) for i in range(len(markers))]
|
|
newHandles = [plt.Line2D([0],[0], ls="none", marker=m, color=c, mec="none", markersize=markersize,**kwargs) \
|
|
for m,c in zip(markers, mkcolors)]
|
|
ax.legend(newHandles,l)
|
|
leg = ax.get_legend()
|
|
leg.set_title(legtitle)
|
|
|
|
old_scatter = Axes.scatter
|
|
def new_scatter(self, *args, **kwargs):
|
|
colors = kwargs.get("c", None)
|
|
co2mk = kwargs.pop("co2mk",None)
|
|
FinalCollection = old_scatter(self, *args, **kwargs)
|
|
if co2mk is not None and isinstance(colors, ndarray):
|
|
Color2Marker = GetColor2Marker(co2mk)
|
|
paths=[]
|
|
for col in colors:
|
|
mk=Color2Marker[tuple(col)]
|
|
marker_obj = MarkerStyle(mk)
|
|
paths.append(marker_obj.get_path().transformed(marker_obj.get_transform()))
|
|
FinalCollection.set_paths(paths)
|
|
return FinalCollection
|
|
Axes.scatter = new_scatter
|
|
############## End hack. ##############
|
|
########################################################################################################################
|
|
|
|
#%%
|
|
def boxplot_with_markers(ax,max_width, alteration='shift', msize=2.2):
|
|
hlinewidth = 0.5
|
|
model_names = ['RS pyramidal','RS inhibitory','FS',
|
|
'RS pyramidal +$K_V1.1$','RS inhibitory +$K_V1.1$',
|
|
'FS +$K_V1.1$','Cb stellate','Cb stellate +$K_V1.1$',
|
|
'Cb stellate $\Delta$$K_V1.1$','STN','STN +$K_V1.1$',
|
|
'STN $\Delta$$K_V1.1$']
|
|
|
|
colorslist = ['#007030', # dark green
|
|
'#F0D730', # yellow
|
|
'#C02717', # red
|
|
'#478010', # green
|
|
'#AAB71B', # lightgreen
|
|
'#F78017', # orange
|
|
'#40A787', # cyan'#
|
|
'#008797', # light blue
|
|
'#2060A7', # blue
|
|
'#D03050', # pink
|
|
'#53379B', # purple
|
|
'#873770', # magenta
|
|
]
|
|
|
|
import matplotlib.colors
|
|
colors = [matplotlib.colors.to_rgb(c) for c in colorslist]
|
|
clr_dict = {}
|
|
for m in range(len(model_names)):
|
|
clr_dict[model_names[m]] = colors[m]
|
|
Markers = ["o", "o", "o", "^", "^", "^", "D", "D", "D", "s", "s", "s"]
|
|
if alteration=='shift':
|
|
i = 3 # Kv1.1 act
|
|
ax.axvspan(i - 0.4, i + 0.4, fill=False, edgecolor='k')
|
|
df = pd.read_csv('./Figures/Data/rheo_shift_corr.csv')
|
|
sns.swarmplot(y="corr", x="$\Delta V_{1/2}$", hue="model", data=df,
|
|
palette=clr_dict, linewidth=0, orient='v', ax=ax, size=msize,
|
|
order=['Na activation', 'Na inactivation', 'K activation', '$K_V1.1$ activation',
|
|
'$K_V1.1$ inactivation', 'A activation', 'A inactivation'],
|
|
hue_order=model_names, co2mk=Markers)
|
|
lim = ax.get_xlim()
|
|
ax.plot([lim[0], lim[1]], [0, 0], ':r',linewidth=hlinewidth)
|
|
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')
|
|
df = pd.read_csv('./Figures/Data/rheo_scale_corr.csv')
|
|
|
|
# Add in points to show each observation
|
|
sns.swarmplot(y="corr", x="Slope (k)", hue="model", data=df,
|
|
palette=clr_dict, linewidth=0, orient='v', ax=ax, size=msize,
|
|
order=['Na activation', 'Na inactivation', 'K activation', '$K_V1.1$ activation',
|
|
'$K_V1.1$ inactivation', 'A activation', 'A inactivation'],
|
|
hue_order=model_names, co2mk=Markers)
|
|
lim = ax.get_xlim()
|
|
ax.plot([lim[0], lim[1]], [0, 0], ':r',linewidth=hlinewidth)
|
|
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')
|
|
df = pd.read_csv('./Figures/Data/rheo_g_corr.csv')
|
|
|
|
# Add in points to show each observation
|
|
sns.swarmplot(y="corr", x="g", hue="model", data=df,
|
|
palette=clr_dict, linewidth=0, orient='v', ax=ax, size=msize,
|
|
order=['Na', 'K', '$K_V1.1$', 'A', 'Leak'],
|
|
hue_order=model_names, co2mk=Markers)
|
|
lim = ax.get_xlim()
|
|
ax.plot([lim[0], lim[1]], [0, 0], ':r',linewidth=hlinewidth)
|
|
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 $\it{\tau}$')
|
|
|
|
|
|
def model_legend(ax, marker_s_leg, pos, ncol):
|
|
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
|
|
]
|
|
import matplotlib.colors
|
|
colors = [matplotlib.colors.to_rgb(c) for c in colorslist]
|
|
model_pos = {'Cb stellate':0, 'RS Inhibitory':1, 'FS':2, 'RS Pyramidal':3,
|
|
'RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':4,
|
|
'Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':5, 'FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':6,
|
|
'RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':7, 'STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':8,
|
|
'Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':9,
|
|
'STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$':10, 'STN':11}
|
|
Markers = ["o", "o", "o", "^", "^", "^", "D", "D", "D", "s", "s", "s"]
|
|
RS_p = mlines.Line2D([], [], color=colors[model_pos['RS Pyramidal']], marker=Markers[model_pos['RS Pyramidal']], markersize=marker_s_leg, linestyle='None',
|
|
label='RS pyramidal')
|
|
RS_i = mlines.Line2D([], [], color=colors[model_pos['RS Inhibitory']], marker=Markers[model_pos['RS Inhibitory']], markersize=marker_s_leg, linestyle='None',
|
|
label='RS inhibitory')
|
|
FS = mlines.Line2D([], [], color=colors[model_pos['FS']], marker=Markers[model_pos['FS']], markersize=marker_s_leg, linestyle='None', label='FS')
|
|
RS_p_Kv = mlines.Line2D([], [], color=colors[model_pos['RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
RS_i_Kv = mlines.Line2D([], [], color=colors[model_pos['RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
FS_Kv = mlines.Line2D([], [], color=colors[model_pos['Cb stellate']], marker=Markers[model_pos['Cb stellate']], markersize=marker_s_leg, linestyle='None', label='FS +$K_V1.1$')
|
|
Cb = mlines.Line2D([], [], color=colors[8], marker=Markers[8], markersize=marker_s_leg, linestyle='None',
|
|
label='Cb stellate')
|
|
Cb_pl = mlines.Line2D([], [], color=colors[model_pos['Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
Cb_sw = mlines.Line2D([], [], color=colors[model_pos['Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
STN = mlines.Line2D([], [], color=colors[model_pos['STN']], marker=Markers[model_pos['STN']], markersize=marker_s_leg, linestyle='None', label='STN')
|
|
STN_pl = mlines.Line2D([], [], color=colors[model_pos['STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
STN_sw = mlines.Line2D([], [], color=colors[model_pos['STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], marker=Markers[model_pos['STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$']], markersize=marker_s_leg, linestyle='None',
|
|
label='STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$')
|
|
ax.legend(handles=[RS_p, RS_i, FS, RS_p_Kv, RS_i_Kv, FS_Kv, Cb, Cb_pl, Cb_sw, STN, STN_pl, STN_sw], loc='center',
|
|
bbox_to_anchor=pos, ncol=ncol, frameon=False)
|
|
|
|
def plot_rheo_alt(ax, model='FS', color1='red', color2='dodgerblue', alteration='shift'):
|
|
ax.spines["right"].set_visible(False)
|
|
ax.spines["top"].set_visible(False)
|
|
model_names = ['RS Pyramidal','RS Inhibitory','FS',
|
|
'RS Pyramidal +$K_V1.1$','RS Inhibitory +$K_V1.1$',
|
|
'FS +$K_V1.1$','Cb stellate','Cb stellate +$K_V1.1$',
|
|
'Cb stellate $\Delta$$K_V1.1$','STN','STN +$K_V1.1$',
|
|
'STN $\Delta$$K_V1.1$']
|
|
|
|
model_name_dict = {'RS Pyramidal': 'RS Pyramidal',
|
|
'RS Inhibitory': 'RS Inhibitory',
|
|
'FS': 'FS',
|
|
'RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'RS Pyramidal +$K_V1.1$',
|
|
'RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'RS Inhibitory +$K_V1.1$',
|
|
'FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'FS +$K_V1.1$',
|
|
'Cb stellate': 'Cb stellate',
|
|
'Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'Cb stellate +$K_V1.1$',
|
|
'Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'Cb stellate $\Delta$$K_V1.1$',
|
|
'STN': 'STN',
|
|
'STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'STN +$K_V1.1$',
|
|
'STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'STN $\Delta$$K_V1.1$'}
|
|
|
|
colorslist = ['#007030', # dark green
|
|
'#F0D730', # yellow
|
|
'#C02717', # red
|
|
'#478010', # green
|
|
'#AAB71B', # lightgreen
|
|
'#F78017', # orange
|
|
'#40A787', # cyan'#
|
|
'#008797', # light blue
|
|
'#2060A7', # blue
|
|
'#D03050', # pink
|
|
'#53379B', # purple
|
|
'#873770', # magenta
|
|
]
|
|
import matplotlib.colors
|
|
colors = [matplotlib.colors.to_rgb(c) for c in colorslist]
|
|
clr_dict = {}
|
|
for m in range(len(model_names)):
|
|
clr_dict[model_names[m]] = colors[m]
|
|
if alteration=='shift':
|
|
df = pd.read_csv('./Figures/Data/rheo_shift_ex.csv')
|
|
df = df.sort_values('alteration')
|
|
ax.set_xlabel('$\Delta$$V_{1/2}$')
|
|
elif alteration=='slope':
|
|
df = pd.read_csv('./Figures/Data/rheo_slope_ex.csv')
|
|
ax.set_xscale("log")
|
|
ax.set_xticks([0.5, 1, 2])
|
|
ax.xaxis.set_major_formatter(ticker.ScalarFormatter())
|
|
ax.xaxis.set_minor_formatter(NullFormatter())
|
|
ax.set_xlabel('$k$/$k_{WT}$')
|
|
elif alteration=='g':
|
|
df = pd.read_csv('./Figures/Data/rheo_g_ex.csv')
|
|
ax.set_xscale("log")
|
|
ax.set_xticks([0.5, 1, 2])
|
|
ax.xaxis.set_major_formatter(ticker.ScalarFormatter())
|
|
ax.xaxis.set_minor_formatter(NullFormatter())
|
|
ax.set_xlabel('$g$/$g_{WT}$')
|
|
for mod in model_names:
|
|
if mod == model_name_dict[model]:
|
|
ax.plot(df['alteration'], df[mod], color=clr_dict[mod], alpha=1, zorder=10, linewidth=2)
|
|
else:
|
|
ax.plot(df['alteration'], df[mod], color=clr_dict[mod], alpha=1, zorder=1, linewidth=1)
|
|
|
|
ax.set_ylabel('$\Delta$ Rheobase (nA)', labelpad=0)
|
|
x = df['alteration']
|
|
y = df[model_name_dict[model]]
|
|
ax.set_xlim(x.min(), x.max())
|
|
ax.set_ylim(df[model_names].min().min(), df[model_names].max().max())
|
|
|
|
return ax
|
|
|
|
def plot_fI(ax, model='RS Pyramidal', type='shift', alt='m', color1='red', color2='dodgerblue'):
|
|
model_save_name = {'RS Pyramidal': 'RS_pyr_posp',
|
|
'RS Inhibitory': 'RS_inhib_posp',
|
|
'FS': 'FS_posp',
|
|
'RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'RS_pyr_Kv',
|
|
'RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'RS_inhib_Kv',
|
|
'FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'FS_Kv',
|
|
'Cb stellate': 'Cb_stellate',
|
|
'Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'Cb_stellate_Kv',
|
|
'Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'Cb_stellate_Kv_only',
|
|
'STN': 'STN',
|
|
'STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'STN_Kv',
|
|
'STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': 'STN_Kv_only'}
|
|
cvals = [-2., 2]
|
|
colors = [color1, color2]
|
|
norm = plt.Normalize(min(cvals), max(cvals))
|
|
tuples = list(zip(map(norm, cvals), colors))
|
|
cmap = matplotlib.colors.LinearSegmentedColormap.from_list("", tuples)
|
|
colors = cmap(np.linspace(0, 1, 22))
|
|
df = pd.read_csv('./Figures/Data/Model_fI/{}_fI.csv'.format(model_save_name[model]))
|
|
df.drop(['Unnamed: 0'], axis=1)
|
|
newdf = df.loc[df.index[(df['alt'] == alt) & (df['type'] == type)], :]
|
|
newdf['mag'] = newdf['mag'].astype('float')
|
|
newdf = newdf.sort_values('mag').reset_index()
|
|
c = 0
|
|
for i in newdf.index:
|
|
ax.plot(json.loads(newdf.loc[i, 'I']), json.loads(newdf.loc[i, 'F']), color=colors[c])
|
|
c += 1
|
|
ax.set_ylabel('Frequency [Hz]')
|
|
ax.set_xlabel('Current [nA]')
|
|
ax.set_title(model, x=0.2, y=1.025)
|
|
ax.spines["right"].set_visible(False)
|
|
ax.spines["top"].set_visible(False)
|
|
L = ax.get_ylim()
|
|
ax.set_ylim([0, L[1]])
|
|
return ax
|
|
|
|
|
|
#%%
|
|
boxplot_style()
|
|
color_dict = {'Cb stellate': '#40A787', # cyan'#
|
|
'RS Inhibitory': '#F0D730', # yellow
|
|
'FS': '#C02717', # red
|
|
'RS Pyramidal': '#007030', # dark green
|
|
'RS Inhibitory +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#AAB71B', # lightgreen
|
|
'Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#008797', # light blue
|
|
'FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#F78017', # orange
|
|
'RS Pyramidal +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#478010', # green
|
|
'STN +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#53379B', # purple
|
|
'Cb stellate $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#2060A7', # blue
|
|
'STN $\Delta$$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$': '#873770', # magenta
|
|
'STN': '#D03050' # pink
|
|
}
|
|
|
|
# plot setup
|
|
marker_s_leg = 2
|
|
max_width = 20
|
|
pad_x = 0.85
|
|
pad_y= 0.4
|
|
pad_w = 1.1
|
|
pad_h = 0.7
|
|
|
|
fig = plt.figure()
|
|
gs = fig.add_gridspec(3, 7, wspace=1.2, hspace=1.)
|
|
ax0 = fig.add_subplot(gs[0,2:7])
|
|
ax0_ex = fig.add_subplot(gs[0,1])
|
|
ax0_fI = fig.add_subplot(gs[0,0])
|
|
ax1 = fig.add_subplot(gs[1,2:7])
|
|
ax1_ex = fig.add_subplot(gs[1,1])
|
|
ax1_fI = fig.add_subplot(gs[1,0])
|
|
ax2 = fig.add_subplot(gs[2,2:7])
|
|
ax2_ex = fig.add_subplot(gs[2,1])
|
|
ax2_fI = fig.add_subplot(gs[2,0])
|
|
|
|
line_width = 1
|
|
# plot fI curves
|
|
ax0_fI = plot_fI(ax0_fI, model='FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', type='shift', alt='s', color1='lightgrey', color2='k')
|
|
rec = plt.Rectangle((-pad_x, -pad_y), 1 + pad_w, 1 + pad_h, fill=False, lw=line_width,transform=ax0_fI.transAxes, color=color_dict['FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$'], alpha=1, zorder=-1)
|
|
rec = ax0_fI.add_patch(rec)
|
|
rec.set_clip_on(False)
|
|
|
|
ax1_fI = plot_fI(ax1_fI, model='Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', type='slope', alt='u', color1='lightgrey', color2='k')
|
|
rec = plt.Rectangle((-pad_x, -pad_y), 1 + pad_w, 1 + pad_h, fill=False, lw=line_width,transform=ax1_fI.transAxes, color=color_dict['Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$'], alpha=1, zorder=-1)
|
|
rec = ax1_fI.add_patch(rec)
|
|
rec.set_clip_on(False)
|
|
|
|
ax2_fI = plot_fI(ax2_fI, model='Cb stellate', type='g', alt='Leak', color1='lightgrey', color2='k')
|
|
rec = plt.Rectangle((-pad_x, -pad_y), 1 + pad_w, 1 + pad_h, fill=False, lw=line_width,transform=ax2_fI.transAxes, color=color_dict['Cb stellate'], alpha=1, zorder=-1)
|
|
rec = ax2_fI.add_patch(rec)
|
|
rec.set_clip_on(False)
|
|
|
|
|
|
# plot boxplots
|
|
boxplot_with_markers(ax0,max_width, alteration='shift')
|
|
boxplot_with_markers(ax1,max_width, alteration='slope')
|
|
boxplot_with_markers(ax2,max_width, alteration='g')
|
|
|
|
# plot legend
|
|
pos = (0.225, -0.9)
|
|
ncol = 5
|
|
model_legend(ax2, marker_s_leg, pos, ncol)
|
|
|
|
# plot rheo across model for example alteration
|
|
plot_rheo_alt(ax0_ex,model='FS +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1='lightgrey', color2='k', alteration='shift')
|
|
plot_rheo_alt(ax1_ex,model='Cb stellate +$\mathrm{K}_{\mathrm{V}}\mathrm{1.1}$', color1='lightgrey', color2='k',alteration='slope')
|
|
plot_rheo_alt(ax2_ex, model='Cb stellate', color1='lightgrey', color2='k', alteration='g')
|
|
|
|
# label subplots with letters
|
|
ax0_fI.text(-0.875, 1.35, string.ascii_uppercase[0], transform=ax0_fI.transAxes, size=10, weight='bold')
|
|
ax0_ex.text(-0.8, 1.35, string.ascii_uppercase[1], transform=ax0_ex.transAxes, size=10, weight='bold')
|
|
ax0.text(-0.075, 1.35, string.ascii_uppercase[2], transform=ax0.transAxes, size=10, weight='bold')
|
|
|
|
ax1_fI.text(-0.875, 1.35, string.ascii_uppercase[3], transform=ax1_fI.transAxes,size=10, weight='bold')
|
|
ax1_ex.text(-0.8, 1.35, string.ascii_uppercase[4], transform=ax1_ex.transAxes, size=10, weight='bold')
|
|
ax1.text(-0.075, 1.35, string.ascii_uppercase[5], transform=ax1.transAxes, size=10, weight='bold')
|
|
|
|
ax2_fI.text(-0.875, 1.35, string.ascii_uppercase[6], transform=ax2_fI.transAxes,size=10, weight='bold')
|
|
ax2_ex.text(-0.8, 1.35, string.ascii_uppercase[7], transform=ax2_ex.transAxes, size=10, weight='bold')
|
|
ax2.text(-0.075, 1.35, string.ascii_uppercase[8], transform=ax2.transAxes, size=10, weight='bold')
|
|
|
|
# save
|
|
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()
|