new firing_characterization-jb figure
This commit is contained in:
parent
907c6fbd4b
commit
adb408e945
297
Figures/firing_characterization-jb.py
Normal file
297
Figures/firing_characterization-jb.py
Normal file
@ -0,0 +1,297 @@
|
|||||||
|
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 plot_style
|
||||||
|
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')
|
||||||
|
```
|
||||||
|
|
||||||
|
"""
|
||||||
|
# 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
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
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[2])
|
||||||
|
ax.set_xlabel('Current [nA]')
|
||||||
|
ax.set_ylabel('Frequency [Hz]')
|
||||||
|
ax.fill_between(x, y, where=(x<=b+width), color=lighter(colorslist[2], 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([])
|
||||||
|
|
||||||
|
def plot_quadrant(ax):
|
||||||
|
ax.spines['left'].set_position('zero')
|
||||||
|
ax.spines['bottom'].set_position('zero')
|
||||||
|
ax.text(1.15, -0.15, '$\\Delta$ rheobase', ha='right')
|
||||||
|
ax.text(-0.05, 0.9, '$\\Delta$ AUC', ha='right')
|
||||||
|
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([-0.4, 0.4])
|
||||||
|
a = ax.get_xticks().tolist()
|
||||||
|
a[0] = '\u2212'
|
||||||
|
a[1] = '+'
|
||||||
|
ax.set_xticklabels(a)
|
||||||
|
ax.set_yticks([-0.4, 0.4])
|
||||||
|
b = ax.get_xticks().tolist()
|
||||||
|
b[0] = '\u2212'
|
||||||
|
b[1] = '+'
|
||||||
|
ax.set_yticklabels(b)
|
||||||
|
|
||||||
|
# ax.tick_params(labelsize=16)
|
||||||
|
# ax.set_yticks([0])
|
||||||
|
# ax.axis('off')
|
||||||
|
|
||||||
|
|
||||||
|
scheme_style()
|
||||||
|
|
||||||
|
fig = plt.figure(figsize=cm2inch(7, 12))
|
||||||
|
gs = gridspec.GridSpec(3,2, top=0.95, bottom=0.1, left=0.15, right = 0.95, hspace=0.8, wspace=0.6)
|
||||||
|
ax1 = fig.add_subplot(gs[0,:])
|
||||||
|
show_spines(ax1, 'lb')
|
||||||
|
plot_AUC(ax1, width=0.2)
|
||||||
|
ax3 = fig.add_subplot(gs[1:, :])
|
||||||
|
|
||||||
|
# add panel letter labels
|
||||||
|
ax_list = fig.axes
|
||||||
|
i =0
|
||||||
|
for a in ax_list:
|
||||||
|
a.text(-0.25, 1.08, string.ascii_uppercase[i], transform=a.transAxes,size=16, weight='bold')
|
||||||
|
i += 1
|
||||||
|
|
||||||
|
show_spines(ax3, '')
|
||||||
|
ax3.set_ylabel('$\Delta$ AUC')
|
||||||
|
ax3.set_xlabel('$\Delta$ rheobase')
|
||||||
|
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_TL = ax3.inset_axes([0.07, 0.6, 0.3, 0.2])
|
||||||
|
plot_diff_sqrt(ax3_TL, b2=0.1, c2=200)
|
||||||
|
ax3_TL.set_ylim(inset_ylim)
|
||||||
|
# top right
|
||||||
|
ax3.text(x=0.22, y=0.7, s='$\\uparrow$ AUC\n$\\uparrow$ rheobase', fontsize=lfsize)
|
||||||
|
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)
|
||||||
|
# bottom left
|
||||||
|
ax3.text(x=-0.9, y=-0.95, s='$\\downarrow$ AUC\n$\downarrow$ rheobase', fontsize=lfsize)
|
||||||
|
ax3_BL = ax3.inset_axes([0.07, 0.15, 0.3, 0.2])
|
||||||
|
plot_diff_sqrt(ax3_BL, b2=0.1, c2=75)
|
||||||
|
ax3_BL.set_ylim(inset_ylim)
|
||||||
|
# bottom right
|
||||||
|
ax3.text(x=0.22, y=-0.95, s='$\\downarrow$ AUC\n$\\uparrow$ rheobase', fontsize=lfsize)
|
||||||
|
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.savefig('./Figures/firing_characterization.pdf', dpi=fig.dpi) #bbox_inches='tight', dpi=fig.dpi
|
||||||
Binary file not shown.
@ -29,7 +29,8 @@ def plot_AUC(ax, a=1, b=0.2, c=100, d=0, width=0.2):
|
|||||||
ax.set_ylabel('Frequency [Hz]')
|
ax.set_ylabel('Frequency [Hz]')
|
||||||
ax.fill_between(x,y, where=(x<=b+width), color='c')
|
ax.fill_between(x,y, where=(x<=b+width), color='c')
|
||||||
ax.set_xlim(0,1)
|
ax.set_xlim(0,1)
|
||||||
ax.set_ylim(0, ax.get_ylim()[1])
|
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):
|
def plot_diff_sqrt(ax, a=1, b=0.2, c=100, d=0, a2=1, b2=0.2, c2=100, d2=0):
|
||||||
x = np.linspace(0, 1, 10000)
|
x = np.linspace(0, 1, 10000)
|
||||||
|
|||||||
@ -276,7 +276,6 @@ To examine the role of cell-type specific ionic current environments on the impa
|
|||||||
\begin{figure}[tp]
|
\begin{figure}[tp]
|
||||||
\centering
|
\centering
|
||||||
\includegraphics[width=0.5\linewidth]{Figures/firing_characterization.pdf}
|
\includegraphics[width=0.5\linewidth]{Figures/firing_characterization.pdf}
|
||||||
\\\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
|
\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)
|
\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.}
|
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.}
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user