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figure_properties.py
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figure_properties.py
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import numpy as np
from gates import minisog_inf, aox_inf, rotenone_inf
import matplotlib.pyplot as plt
from matplotlib import colors
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
from matplotlib.ticker import LogLocator, NullFormatter
from palettable.cartocolors.sequential import Burg_5
from palettable.colorbrewer.qualitative import Set2_8, Set1_8, Set3_12
from palettable.colorbrewer.sequential import RdPu_5, BuPu_5, YlGn_5
style_dict = {
'font.family': 'sans-serif',
'font.sans-serif': 'Arial',
'xtick.labelsize': 6,
'xtick.major.size': 2,
'xtick.major.width': 0.5,
'xtick.major.pad': 1,
'xtick.minor.size': 1,
'xtick.minor.width': 0.5,
'ytick.labelsize': 6,
'ytick.major.size': 2,
'ytick.major.width': 0.5,
'ytick.major.pad': 1,
'ytick.minor.size': 1,
'ytick.minor.width': 0.5,
'font.size': 7,
'axes.labelsize': 7,
'axes.labelpad': 1,
'axes.titlesize': 7,
'axes.titlepad': 2,
'legend.fontsize': 7,
'axes.linewidth': 0.5
}
plt.rcParams.update(style_dict)
def add_arrow(line, position=None, direction='right', size=15,
color=None, arrowstyle='->', num=1):
"""
add an arrow to a line.
line: Line2D object
position: (x,y)-position of the arrow. If None, min*1.007 of xdata is taken
direction: 'left' or 'right'
size: size of the arrow in fontsize points
color: if None, line color is taken.
"""
if color is None:
color = line.get_color()
xdata = line.get_xdata()
ydata = line.get_ydata()
if position is None:
position = np.min(xdata)
# find closest index
# start_ind = np.argmin(np.absolute(xdata - position)) # - 1500
start_ind = np.argmin(np.linalg.norm(np.stack((xdata, ydata)) -
np.array(position).reshape(2, 1),
axis=0))
print('Verify that this has changed since, offset?')
if direction == 'right':
end_ind = start_ind + 1
else:
end_ind = start_ind - 1
for ii in range(num):
strt_ = start_ind + int(ii*750)
end_ = end_ind + int(ii*750)
line.axes.annotate('',
xytext=(xdata[strt_], ydata[strt_]),
xy=(xdata[end_], ydata[end_]),
arrowprops=dict(arrowstyle=arrowstyle, color=color),
size=size)
def cm_to_inches(vals):
return [0.393701*ii for ii in vals]
def add_sizebar(ax, size, loc=8, size_vertical=2, text=None):
if not text:
text = str(size) + ' ms'
asb = AnchoredSizeBar(ax.transData,
int(size),
text,
loc=loc,
pad=0.5, borderpad=.4, sep=5,
frameon=False,
size_vertical=size_vertical)
ax.add_artist(asb)
return ax
def align_axis_labels(ax_list, axis='x', value=-0.25):
for ax in ax_list:
if axis == 'x':
ax.get_xaxis().set_label_coords(0.5, value)
else:
ax.get_yaxis().set_label_coords(value, 0.5)
def add_logticks(axx, xax=True, ticks=[1, 10, 100, 1000]):
if xax:
axx.set_xticks(ticks)
x_minor = LogLocator(base=10.0, subs=np.arange(1.0, 10.0)*0.1,
numticks=10)
axx.xaxis.set_minor_locator(x_minor)
axx.xaxis.set_minor_formatter(NullFormatter())
else:
axx.set_yticks(ticks)
y_minor = LogLocator(base=10.0, subs=np.arange(1.0, 10.0)*0.1,
numticks=10)
axx.yaxis.set_minor_locator(y_minor)
axx.yaxis.set_minor_formatter(NullFormatter())
return axx
def truncate_colormap(cmap, minval=0.0, maxval=1.0, n=100):
new_cmap = colors.LinearSegmentedColormap.from_list(
'trunc({n},{a:.2f},{b:.2f})'.format(n=cmap.name, a=minval, b=maxval),
cmap(np.linspace(minval, maxval, n)))
return new_cmap
snc = {'ros': rotenone_inf, 'atp_bl': 25, 'Q': 30}
dfb = {'ros_sog': minisog_inf, 'atp_bl': [30], 'Q': 20, 'ros_aox': aox_inf}
def_colors = {'nad': Set2_8.hex_colors[6],
'pyr': Set2_8.hex_colors[7],
'atp': Set2_8.hex_colors[0],
'psi': Set2_8.hex_colors[1],
'ln1': Set1_8.hex_colors[1],
'ln2': Set1_8.hex_colors[3],
'ln3': Set1_8.hex_colors[7],
'ln4': '#1f77b4',
'ln5': '#ff7f0e',
'ln6': '#e377c2',
'ln7': Set3_12.hex_colors[4],
'ln8': Set3_12.hex_colors[5],
'ln9': Set3_12.hex_colors[6],
'ln10': BuPu_5.hex_colors[1],
'ln11': BuPu_5.hex_colors[2],
'ln12': BuPu_5.hex_colors[3],
'ln13': RdPu_5.hex_colors[1],
'ln14': RdPu_5.hex_colors[2],
'ln15': RdPu_5.hex_colors[3],
'ln16': Burg_5.hex_colors[0],
'ln17': Burg_5.hex_colors[2],
'ln18': Burg_5.hex_colors[4],
'ln19': YlGn_5.hex_colors[1],
'ln20': YlGn_5.hex_colors[2],
'ln21': YlGn_5.hex_colors[3],
'ros': '#1f77b4',
'hyp': '#ca0020',
'teri': '#008000',
'aox': '#f04e4d',
'ret': '#4d9221',
'fet': '#c51b7d',
'SD': '#62a73b',
'minisog': '#3589d6',
'park1': '#ff0000',
'park2': '#0000ff'}
colormap_dict = {'Continuous': '#f4cae4', # Pastel2_8 cb2
'Bursting': '#f1e2cc',
'Regular': '#cccccc',
'Silent': '#fdcdac',
'Adapting': '#e6f5c9'}
ln_cols_mcu = [def_colors['ln1'], def_colors['ln2'], def_colors['ln3']]
ln_cols_ros2 = [def_colors['ln7'], def_colors['ln8'], def_colors['ln9']]
ln_cols_ros = [def_colors['ln16'], def_colors['ln17'], def_colors['ln18']]
# ln_cols_ros2 = [def_colors['ln19'], def_colors['ln20'], def_colors['ln21']]
ln_cols_tau = [def_colors['ln13'], def_colors['ln14'], def_colors['ln15']]
ln_cols_q = [def_colors['ln10'], def_colors['ln11'], def_colors['ln12']]
ln_cols_fet = ['#a6761d', '#e6ab02']
# ln_cols_ret = ['#1f78b4', '#a6cee3', 'k']
ln_cols_ret = ['#1f78b4', '#38baff', 'k']
ln_cols_rise = [def_colors['ln1'], def_colors['ln2'], def_colors['ln3']]