def ResidualsPlot(Figure, Time, Signal, FitSolution, Residuals, Noise):
cFig = Figure
gridSp = GridSpec(2, 2)
ax1 = cFig.add_subplot(gridSp[:, 0])
ax2 = cFig.add_subplot(gridSp[0, 1])
ax3 = cFig.add_subplot(gridSp[1, 1])
ax1.plot(Time, Signal, 'ro', label='Data')
ax1.plot(Time,
FitSolution,
label='Regression',
path_effects=[
path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()
])
ax1.legend(loc=0)
PlotStyle(ax1, 'Fitted Model')
ax2.plot(Residuals,
path_effects=[
path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()
])
PlotStyle(ax2, 'Residuals')
ax3.plot(Noise,
path_effects=[
path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()
])
PlotStyle(ax3, 'Noise')
plt.tight_layout()
def main():
gn = Granatum()
set1 = gn.get_import('set1')
set2 = gn.get_import('set2')
set3 = gn.get_import('set3')
maxScore = gn.get_arg('maxScore')
minScore = gn.get_arg('minScore')
labelSet1 = gn.get_arg("labelSet1")
labelSet2 = gn.get_arg("labelSet2")
labelSet3 = gn.get_arg("labelSet3")
wordcloud = gn.get_arg("wordcloud")
filtered_set1 = dict(filter(lambda elem: (isinstance(elem[1], numbers.Number) & (not isnan(elem[1]))) & (elem[1] >= minScore) & (elem[1] <= maxScore), set1.items()))
filtered_set2 = dict(filter(lambda elem: (isinstance(elem[1], numbers.Number) & (not isnan(elem[1]))) & (elem[1] >= minScore) & (elem[1] <= maxScore), set2.items()))
filtered_set3 = dict(filter(lambda elem: (isinstance(elem[1], numbers.Number) & (not isnan(elem[1]))) & (elem[1] >= minScore) & (elem[1] <= maxScore), set3.items()))
merged_frequencies = {**filtered_set1, **filtered_set2, **filtered_set3}
packedsets = [set(filtered_set1.keys()), set(filtered_set2.keys()), set(filtered_set3.keys())]
fig, ax = plt.subplots(1,1)
fig.set_size_inches(5,4)
caption = (
'The area weighted Venn diagram is shown for the gene sets matching the criteria'
)
if wordcloud:
out = venn3_wordcloud(packedsets, set_labels=(labelSet1, labelSet2, labelSet3), wordcloud_kwargs=dict(max_font_size=36), word_to_frequency=merged_frequencies, ax=ax)
for text in out.set_labels:
if text:
text.set_fontsize(18)
for text in out.subset_labels:
if text:
text.set_fontsize(16)
text.set_path_effects([path_effects.SimpleLineShadow(), path_effects.Normal()])
else:
out = venn3(packedsets, set_labels=(labelSet1, labelSet2, labelSet3))
venn3_circles(packedsets, linestyle='dashed', linewidth=1, color="black")
for text in out.set_labels:
if text:
text.set_fontsize(18)
for text in out.subset_labels:
if text:
text.set_fontsize(16)
text.set_path_effects([path_effects.SimpleLineShadow(), path_effects.Normal()])
gn.add_current_figure_to_results(caption)
gn.commit()
def test_PathEffect_points_to_pixels():
fig = plt.figure(dpi=150)
p1, = plt.plot(range(10))
p1.set_path_effects([path_effects.SimpleLineShadow(),
path_effects.Normal()])
renderer = fig.canvas.get_renderer()
pe_renderer = path_effects.SimpleLineShadow().get_proxy_renderer(renderer)
assert isinstance(pe_renderer, path_effects.PathEffectRenderer)
# Confirm that using a path effects renderer maintains point sizes
# appropriately. Otherwise rendered font would be the wrong size.
assert renderer.points_to_pixels(15) == pe_renderer.points_to_pixels(15)
def plotClose(dates, cl):
"""
produces a graph of the closing values for each day over 3 months.
Arguments:
dates: Datetime object list representing stock dates
# cl: List of floats representing closing values for each date
"""
plt.figure(1)
plt.plot(dates,
cl,
linewidth=2,
color='red',
path_effects=[
path_effects.SimpleLineShadow(),
path_effects.Normal(offset=(0.0, 5.0))
])
ax = plt.subplot(1, 1, 1)
ax.scatter(dates, cl)
ax.plot(dates, cl, "or")
plt.xlabel("Date (Month)")
plt.ylabel("Value ($)")
plt.title("Daily Closing Values")
plt.show()
def LollipopPlot(Fig, Time, Data, Regression):
cTime = Time
cData = Data
cRegression = Regression
ax = Fig.gca()
(markers, stemlines, baseline) = ax.stem(cTime,
cData,
bottom=-0.4,
label='Data',
basefmt=" ")
plt.setp(stemlines, linestyle="-", color="red", linewidth=0.5, alpha=0.5)
plt.setp(markers, color="red", alpha=0.75)
ax.plot(cTime,
cRegression,
'b-',
label='Model',
path_effects=[
path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()
])
ax.set_ylabel('Temperature', fontsize=16, fontweight='bold')
ax.set_xlabel('Time', fontsize=16, fontweight='bold')
ax.legend(loc=0, fontsize=14)
ax.set_ylim(-0.4, 110)
PlotStyle(ax, '')
def test_patheffect3():
p1, = plt.plot([1, 3, 5, 4, 3], 'o-b', lw=4)
p1.set_path_effects([path_effects.SimpleLineShadow(),
path_effects.Normal()])
plt.title(
r'testing$^{123}$',
path_effects=[path_effects.withStroke(linewidth=1, foreground="r")])
leg = plt.legend([p1], [r'Line 1$^2$'], fancybox=True, loc='upper left')
leg.legendPatch.set_path_effects([path_effects.withSimplePatchShadow()])
text = plt.text(2, 3, 'Drop test', color='white',
bbox={'boxstyle': 'circle,pad=0.1', 'color': 'red'})
pe = [path_effects.Stroke(linewidth=3.75, foreground='k'),
path_effects.withSimplePatchShadow((6, -3), shadow_rgbFace='blue')]
text.set_path_effects(pe)
text.get_bbox_patch().set_path_effects(pe)
pe = [path_effects.PathPatchEffect(offset=(4, -4), hatch='xxxx',
facecolor='gray'),
path_effects.PathPatchEffect(edgecolor='white', facecolor='black',
lw=1.1)]
t = plt.gcf().text(0.02, 0.1, 'Hatch shadow', fontsize=75, weight=1000,
va='center')
t.set_path_effects(pe)
def draw_timed_sequence(data_list, title, data_range):
# customize figure properties
scr_dpi, style = 96, 'seaborn-white'
mplt.figure(figsize=(800 / scr_dpi, 300 / scr_dpi), dpi=scr_dpi)
mplt.style.use(style)
# drow speed curves
time_seq = [i[0] for i in data_list]
data_seq = [i[1] for i in data_list]
mplt.plot(time_seq, data_seq, marker='', color='mediumvioletred', \
linewidth=3, alpha=1, \
path_effects=[mpe.SimpleLineShadow(shadow_color='b'), mpe.Normal()])
mplt.title(title, fontsize=10, fontweight=0, color='grey', loc='left')
mplt.grid(True)
# set x-axis properties
xmajorLocator = MultipleLocator(2)
xmajorFormatter = FormatStrFormatter('%1d')
ax = mplt.gca()
ax.xaxis.set_major_locator(xmajorLocator)
ax.xaxis.set_major_formatter(xmajorFormatter)
# set y-axis properties
mplt.ylim(data_range)
def draw_speedometer(speedometer_record):
# customize figure properties
scr_dpi, style = 96, 'seaborn-white'
mplt.figure(1, figsize=(1200 / scr_dpi, 300 / scr_dpi), dpi=scr_dpi)
mplt.style.use(style)
gs = gridspec.GridSpec(1, 2, width_ratios=[2, 1])
mplt.subplot(gs[0])
# drow speed curves
time = [i[0] for i in speedometer_record]
speed = [i[1] for i in speedometer_record]
mplt.plot(time, speed, marker='', color='mediumvioletred', \
linewidth=2, alpha=1, \
path_effects=[mpe.SimpleLineShadow(shadow_color='b'), mpe.Normal()])
# mplt.grid(True)
# mplt.ylim((-2, 2))
# mplt.legend(['sine'])
mplt.title("Speed (Kmph)",
fontsize=10,
fontweight=0,
color='grey',
loc='left')
# remove labels
mplt.xlabel('Time (Second)')
mplt.tick_params(labelbottom=True)
#mplt.ylabel('Speed (Km/H)')
mplt.tick_params(labelleft=True)
return
def plot_edges(self, axis, E, shadow=True, **kw):
kw['c'] = kw['c'] if 'c' in kw else 'black'
kw['alpha'] = kw['alpha'] if 'alpha' in kw else 0.6
kw['zorder'] = kw['zorder'] if 'zorder' in kw else 1
if shadow:
kw['path_effects'] = [pfx.SimpleLineShadow(), pfx.Normal()]
list(map(lambda e: axis.plot(e[:, 0], e[:, 1], **kw), E))
def lines(self, latlons, color, shadow=False, **kwargs):
if not latlons.any():
return
else:
use_kw = kwargs
ispoint = latlons.shape[0] == 1
if ispoint:
# a line plot will cause a singular point to vanish, so we force it to
# plot points here
use_kw = use_kw.copy()
use_kw.pop('linestyle', None)
size = use_kw.pop('linewidth', 2)
use_kw['marker'] = 'o'
use_kw['markersize'] = size
use_kw['markeredgewidth'] = 0.0
if shadow:
shadow_kw = dict(offset=(0.5, -0.5), alpha=0.6)
if ispoint:
shadow_effect = path_effects.SimplePatchShadow(**shadow_kw)
else:
shadow_effect = path_effects.SimpleLineShadow(**shadow_kw)
use_kw['path_effects'] = [shadow_effect, path_effects.Normal()]
self._bgmap.ax.plot(latlons[:, 1], latlons[:, 0],
color=color, transform=ccrs.PlateCarree(), **use_kw)
def send_pie(bot, update, data):
colors = ['yellowgreen', 'lightskyblue', 'gold', 'lightcoral', 'seagreen', 'lightsteelblue', 'lightpink']
explode = [0.01 for _ in range(7)]
print(data)
fig = plt.figure(figsize=[10, 10])
ax = fig.add_subplot(111)
plt.axis('off')
plt.title("Статистика по представителям 7 классов интеллекта")
patches, text, auto_texts = ax.pie(data.values(),
colors=colors,
explode=explode,
# labels=a.keys(),
autopct='%1.1f%%',
startangle=90,
radius=0.4,
wedgeprops={"linewidth": 6, },
shadow=True,
center=(0.5, 0.5),
frame=True,
pctdistance=1.125,
)
for patch in patches:
patch.set_path_effects([path_effects.SimpleLineShadow(),
path_effects.Normal()])
user_id = str(update.effective_user.id)
plt.legend(data.keys())
plt.savefig(user_id + ".png")
bot.send_photo(chat_id=user_id, photo=open(user_id + ".png", 'rb'))
os.remove(user_id + ".png")
def plotOpen(dates, op):
"""
produces a graph of the open values for each day over 3 months.
Arguments:
dates: Datetime object list representing stock dates
op: List of floats representing open values for each date
"""
plt.plot(dates,
op,
linewidth=2,
color='red',
path_effects=[
path_effects.SimpleLineShadow(),
path_effects.Normal(offset=(0.0, 5.0))
])
ax = plt.subplot(1, 1, 1)
ax.scatter(dates, op)
ax.plot(dates, op, "or")
plt.xlabel("Date (Month)")
plt.ylabel("Value ($)")
plt.title("Daily Open Values")
plt.show()
def updateCanvas(self):
self.ax.clear()
self.ax.set_facecolor('#828282')
self.ax.set_ylabel("Numbers inserted", family='sans-serif', size="13", weight="bold")
self.ax.set_xlabel("Time", family='sans-serif', size="13", weight="bold")
self.ax.set_title("Match stats", family='sans-serif', size="15", weight="bold")
self.ax.step(list(map(lambda x: x[0], self.moves)), list(map(lambda x: x[1], self.moves)), color="white", linewidth=5.0,
path_effects=[path_effects.SimpleLineShadow(shadow_color="white"),
path_effects.Normal()])
self.ax.figure.canvas.draw()
def plot_xmoc_tseries(time,
moc_t,
which_lat=['max'],
which_moc='amoc',
str_descript='',
str_time='',
figsize=[]):
import matplotlib.patheffects as path_effects
from matplotlib.ticker import AutoMinorLocator
if len(figsize) == 0: figsize = [13, 4]
fig, ax = plt.figure(figsize=figsize), plt.gca()
for ii in range(len(which_lat)):
if which_lat[ii] == 'max':
str_label = 'max {:s}: 30°N<=lat<=45°N'.format(
which_moc.upper(), which_lat[ii])
else:
str_label = 'max {:s} at: {:2.1f}°N'.format(
which_moc.upper(), which_lat[ii])
hp=ax.plot(time,moc_t[:,ii],\
linewidth=2,label=str_label,marker='o',markerfacecolor='w',\
path_effects=[path_effects.SimpleLineShadow(offset=(1.5,-1.5),alpha=0.3),path_effects.Normal()])
# plot mean value with trinagle
plt.plot(time[0]-(time[-1]-time[0])*0.015,moc_t[:,ii].mean(),\
marker='<',markersize=8,markeredgecolor='k',markeredgewidth=0.5,\
color=hp[0].get_color(),zorder=3,clip_box=False,clip_on=False)
# plot std. range
plt.plot(time[0]-(time[-1]-time[0])*0.015,moc_t[:,ii].mean()+moc_t[:,ii].std(),\
marker='^',markersize=6,markeredgecolor='k',markeredgewidth=0.5,\
color=hp[0].get_color(),zorder=3,clip_box=False,clip_on=False)
plt.plot(time[0]-(time[-1]-time[0])*0.015,moc_t[:,ii].mean()-moc_t[:,ii].std(),\
marker='v',markersize=6,markeredgecolor='k',markeredgewidth=0.5,\
color=hp[0].get_color(),zorder=3,clip_box=False,clip_on=False)
ax.legend(loc='lower right',
shadow=True,
fancybox=True,
frameon=True,
mode='None')
ax.set_xlabel('Time [years]', fontsize=12)
ax.set_ylabel('{:s} in [Sv]'.format(which_moc.upper()), fontsize=12)
minor_locator = AutoMinorLocator(5)
ax.yaxis.set_minor_locator(AutoMinorLocator(4))
ax.xaxis.set_minor_locator(minor_locator)
plt.grid(which='major')
plt.xticks(np.arange(1940, 2015, 5))
plt.xlim(time[0] - (time[-1] - time[0]) * 0.015,
time[-1] + (time[-1] - time[0]) * 0.015)
plt.show(block=False)
fig.canvas.draw()
return (fig, ax)
def plot_edge(self, axis, s, shadow=True, **kw):
p = self.data[list(s)]
if 'color' in kw:
kw['c'] = kw['color']
del kw['color']
kw['c'] = 'black' if not 'c' in kw else kw['c']
kw['alpha'] = 0.5 if not 'alpha' in kw else kw['alpha']
kw['zorder'] = 1 if not 'zorder' in kw else kw['zorder']
kw = {'color' : 'black', 'alpha' : 0.5, 'zorder' : 1}
if shadow:
kw['path_effects'] = [pfx.SimpleLineShadow(), pfx.Normal()]
return axis.plot(p[:,0], p[:,1], **kw)
def single_plot(robot,
p,
fig,
link_plot,
joint_plot,
eff_plot,
cfg_path_plots=None,
path_history=None,
save_dir=None,
ax=None):
from copy import copy
from matplotlib.lines import Line2D
points_traj = robot.fkine(p)
points_traj = torch.cat([torch.zeros(len(p), 1, 2), points_traj], dim=1)
traj_alpha = 0.3
ends_alpha = 0.5
lw = link_plot.get_lw()
link_traj = [
ax.plot(points[:, 0],
points[:, 1],
color='gray',
alpha=traj_alpha,
lw=lw,
solid_capstyle='round')[0] for points in points_traj
]
joint_traj = [
ax.plot(points[:-1, 0],
points[:-1, 1],
'o',
color='tab:red',
alpha=traj_alpha,
markersize=lw)[0] for points in points_traj
]
eff_traj = [
ax.plot(points[-1:, 0],
points[-1:, 1],
'o',
color='black',
alpha=traj_alpha,
markersize=lw)[0] for points in points_traj
]
for i in [0, -1]:
link_traj[i].set_alpha(ends_alpha)
link_traj[i].set_path_effects(
[path_effects.SimpleLineShadow(),
path_effects.Normal()])
joint_traj[i].set_alpha(ends_alpha)
eff_traj[i].set_alpha(ends_alpha)
link_traj[0].set_color('green')
link_traj[-1].set_color('orange')
def draw_scale_bar(ax,
X_bar=200,
Y_bar=150,
y_text=100,
scale=5 * u.arcmin,
pixel_scale=2.5,
lw=6,
fontsize=15,
color='w',
format='.1f',
border_color='k',
border_lw=0.5,
alpha=1):
""" Draw a scale bar """
import matplotlib.patheffects as PathEffects
L_bar = scale.to(u.arcsec).value / pixel_scale
ax.plot(
[X_bar - L_bar / 2, X_bar + L_bar / 2], [Y_bar, Y_bar],
color=color,
alpha=alpha,
lw=lw,
path_effects=[PathEffects.SimpleLineShadow(),
PathEffects.Normal()])
ax.text(X_bar,
y_text,
'{0:{1}} {2}'.format(scale.value, format, scale.unit),
color=color,
alpha=alpha,
fontsize=fontsize,
ha='center',
va='center',
fontweight='bold',
path_effects=[
PathEffects.SimpleLineShadow(),
PathEffects.withStroke(linewidth=border_lw,
foreground=border_color)
])
def plot_residuals(figure, time, signal, fit_solution, residuals, noise):
cFig = figure
gridSp = GridSpec(2, 2)
ax1 = cFig.add_subplot(gridSp[:, 0])
ax2 = cFig.add_subplot(gridSp[0, 1])
ax3 = cFig.add_subplot(gridSp[1, 1])
ax1.plot(time, signal, 'ro', label='Data')
ax1.plot(time, fit_solution, label='Regression', path_effects=[path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()])
ax1.legend(loc=0)
util.plot_style(ax1, 'Fitted Model')
ax2.plot(residuals, path_effects=[path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()])
util.plot_style(ax2, 'Residuals')
ax3.plot(noise, path_effects=[path_effects.SimpleLineShadow(alpha=0.2, rho=0.2),
path_effects.Normal()])
util.plot_style(ax3, 'Noise')
plt.tight_layout()
def plotValues(dates, vals, col_name, ticker):
plt.figure(1)
plt.plot(dates,
vals,
linewidth=2,
color='red',
path_effects=[
path_effects.SimpleLineShadow(),
path_effects.Normal(offset=(0.0, 5.0))
])
plt.xlabel("Date (Month)")
plt.ylabel("Value ($)")
title = str("Daily " + col_name.capitalize() + " Values (" + ticker + ")")
plt.title(title)
plt.show()
def draw(series, name, active):
plt.rcParams['figure.figsize'] = (4, 2.5) # 设置figure_size尺寸
plt.rcParams['axes.facecolor'] = 'FFAE00' if active else '282C35'
plt.xticks([])
plt.yticks([])
plt.axis('off')
pd.Series(series).plot(
linewidth='3',
color=('#ffffff' if active else '#FFAE00'),
path_effects=[path_effects.SimpleLineShadow(),
path_effects.Normal()])
plt.savefig(path + name + ".png",
bbox_inches='tight',
facecolor=('#FFAE00' if active else '#282C35'))
plt.clf()
def __init__(self, ax, orbit_collection, calval=True):
# Prepare Input
orbit_ensemble = orbit_collection.orbit_ensemble
orbit_ensemble_mean = orbit_ensemble.get_ensemble_mean()
calval_ensemble = orbit_collection.calval_ensemble
# Plot all datasets
for dataset_id in orbit_ensemble.dataset_ids:
color = DATASET_COLOR[dataset_id]
marker = DATASET_MARKER[dataset_id]
# Get statistics for each dataset
dataset_mean = orbit_ensemble.get_member_mean(dataset_id)
ax.scatter(orbit_ensemble.time,
dataset_mean - orbit_ensemble_mean,
color=color,
marker=marker,
**self.datasets_props)
# Plot the calval ensembles
if calval:
calval_props = dict(aem=self.calval_props_aem,
oib=self.calval_props_oib)
shadow = [
path_effects.SimpleLineShadow(offset=(1, -1)),
path_effects.Normal()
]
for calval_id in calval_ensemble.dataset_ids:
source_id = calval_id[-3:]
dataset_mean = calval_ensemble.get_member_mean(calval_id)
ax.scatter(calval_ensemble.time,
dataset_mean - orbit_ensemble_mean,
path_effects=shadow,
**calval_props[source_id])
ax.axhline(0, **self.zero_line_props)
ax.set_ylim(-2, 2)
ax.set_xlim(orbit_collection.time_range)
def single_plot(robot, p, fig, link_plot, joint_plot, eff_plot, cfg_path_plots=None, path_history=None, save_dir=None, ax=None):
from copy import copy
from matplotlib.lines import Line2D
points_traj = robot.fkine(p)
points_traj = torch.cat([torch.zeros(len(p), 1, 2, dtype=points_traj.dtype), points_traj], dim=1)
traj_alpha = 0.3
ends_alpha = 0.5
lw = link_plot.get_lw()
link_traj = [ax.plot(points[:, 0], points[:, 1], color='gray', alpha=traj_alpha, lw=lw, solid_capstyle='round')[0] for points in points_traj]
joint_traj = [ax.plot(points[:-1, 0], points[:-1, 1], 'o', color='tab:red', alpha=traj_alpha, markersize=lw)[0] for points in points_traj]
eff_traj = [ax.plot(points[-1:, 0], points[-1:, 1], 'o', color='black', alpha=traj_alpha, markersize=lw)[0] for points in points_traj]
# for link_plot, joint_plot, eff_plot, points in zip(link_traj, joint_traj, eff_traj, points_traj):
# link_plot.set_data(points[:, 0], points[:, 1])
# joint_plot.set_data(points[:-1, 0], points[:-1, 1])
# eff_plot.set_data(points[-1:, 0], points[-1:, 1])
for i in [0, -1]:
link_traj[i].set_alpha(ends_alpha)
link_traj[i].set_path_effects([path_effects.SimpleLineShadow(), path_effects.Normal()])
joint_traj[i].set_alpha(ends_alpha)
eff_traj[i].set_alpha(ends_alpha)
link_traj[0].set_color('green')
link_traj[-1].set_color('orange')
# ax.add_artist(link_traj[2])
# def divide(p): # divide the path into several segments that obeys the wrapping around rule [TODO]
# diff = torch.abs(p[:-1]-p[1:])
# div_idx = torch.where(diff.max(1) > np.pi)
# div_idx = torch.cat([-1, div_idx])
# segments = []
# for i in range(len(div_idx)-1):
# segments.append(p[div_idx[i]+1:div_idx[i+1]+1])
# segments.append(p[div_idx[-1]+1:])
# for i in range(len(segments)-1):
# if torch.sum(torch.abs(segments[i]) > np.pi) == 2:
for cfg_path in cfg_path_plots:
cfg_path.set_data(p[:, 0], p[:, 1])
def make_chart(data, filename):
#this function creates a chart from a dataframe
df = data
print("generating matplotlib chart")
plt.style.use('bmh')
plt.figure(figsize=(20,15))
x = ['1 month', '2 month', '3 month', '6 month', '1 year', '2 year', '3 year', '5 year', '7 year', '10 year', '20 year', '30 year']
y1 = list(df.iloc[-1][2:])
y2 = list(df.iloc[-2][2:])
y3 = list(df.iloc[-3][2:])
plt.plot(x, y1, 'gs-', label = df.iloc[-1][1],markersize=8, linewidth=3.0, path_effects=[path_effects.SimpleLineShadow(shadow_color="green", linewidth=5),path_effects.Normal()])
plt.plot(x, y2, '^-' ,color='red', label = df.iloc[-2][1], markersize=6, path_effects=[path_effects.SimpleLineShadow(shadow_color="red", linewidth=5),path_effects.Normal()])
plt.plot(x, y3, 'bo-' , label = df.iloc[-3][1], markersize=4, path_effects=[path_effects.SimpleLineShadow(shadow_color="blue", linewidth=5),path_effects.Normal()])
plt.title('Treasury Yield Curve')
plt.xlabel('Maturity')
plt.ylabel('Interest Rates')
plt.title('Daily US Treasury Yield Curve')
plt.legend(loc='upper left')
plt.grid(False)
#saving chart in a file with the date when it was created
plt.savefig(f'charts/{filename}.png')
print("completed")
plt.show()
cID=Identifier
cDir=UniprotDir+'\\'+cID+'.txt'
cLines=GetFileLines(cDir) #Load the data
nLines=len(cLines)
SeqLoc=[j for j in range(nLines) if re.match('(.*)'+'SEQUENCE'+'(.*)',cLines[j])] #Find the location of the SEQUENCE pattern
SeqLine=cLines[SeqLoc[-1]].split()
return int(SeqLine[2])
#
ProteinSizes=[GetSize(val) for val in TargetList]
plt.figure(1,figsize=(7,7))
plt.plot(ProteinSizes,path_effects=[path_effects.SimpleLineShadow(alpha=0.2,rho=0.2),
path_effects.Normal()])
ax=plt.gca()
PlotStyle(ax,'Protein Sequence Lenght')
###############################################################################
# Pattern mathching functions
###############################################################################
#Iterates through an uniprot file and a term list
def FileIterator(File,TermList):
cF=GetFileLines(File)
nLines=len(cF)
import matplotlib.pyplot as plt
import matplotlib.patheffects as path_effects
fig = plt.figure(figsize=(5, 1.5))
text = fig.text(0.5,
0.5, 'Hello path effects world!\nThis is the normal '
'path effect.\nPretty dull, huh?',
ha='center',
va='center',
size=20)
text.set_path_effects([path_effects.Normal()])
plt.show()
text = plt.text(0.5,
0.5,
'Hello path effects world!',
path_effects=[path_effects.withSimplePatchShadow()])
plt.plot([0, 3, 2, 5],
linewidth=5,
color='blue',
path_effects=[path_effects.SimpleLineShadow(),
path_effects.Normal()])
plt.show()
def plot_spectrum_heatmap(self,
plot_spec1=True,
frange=[],
title="Audio Comparison",
cmap="plasma",
background_color="white",
background_alpha=0.5):
"""
Plots a heatmap and spectrogram showing the relative hot and cool spots of thw two compared AudioAnalyzer class instances.
A number of options are available to customize the appearance of the generated plot.
"""
# DATAFRAME SETUP
if plot_spec1:
df = self.original_df
else:
df = self.modified_df
df['ratio_amplitude'] = self.ratio_df.scaled_amplitude
df['attenuated_scaled'] = df.scaled_amplitude
df['boosted_scaled'] = df.scaled_amplitude
if len(frange):
plot_df = df.loc[(df.bins >= frange[0] / 1000)
& (df.bins <= frange[1] / 1000)]
ratio_df = self.ratio_df.loc[
(self.ratio_df.bins >= frange[0] / 1000)
& (self.ratio_df.bins <= frange[1] / 1000)]
else:
plot_df = df
ratio_df = self.ratio_df
# FIGURE SETUP
fig = plt.figure(figsize=(20, 10))
ax1 = fig.add_subplot(211, facecolor="white")
# ax1 = plt.subplot2grid((8,1), (0,0), rowspan=5, facecolor="white", fig=fig)
ax2 = fig.add_subplot(211, facecolor="#00000000")
# ax2 = plt.subplot2grid((8,1), (0,0), rowspan=2, facecolor="#00000000", fig=fig)
# fig2 = plt.figure(figsize=(32, 8))
# cbaxes = fig2.add_subplot(32,1,1)
cbaxes = plt.subplot2grid((16, 1), (10, 0))
cbaxes.set_title("Scaled Amplitude Ratio", size=14)
# HEATMAP PLOT
sns.heatmap(data=ratio_df.set_index('bins').transpose(),
cbar=True,
cbar_ax=cbaxes,
cbar_kws={"orientation": "horizontal"},
cmap=cmap,
alpha=0.95,
zorder=1,
ax=ax1,
vmin=0.0,
vmax=1.0)
ax1.set_xlabel("")
ax1.set_xticks([])
ax1.set_ylabel("")
ax1.set_yticks([])
# FREQUENCY PLOT
sns.lineplot(data=plot_df,
x="bins",
y="scaled_amplitude",
color='black',
zorder=10,
ax=ax2,
path_effects=[
path_effects.SimpleLineShadow(),
path_effects.Normal()
])
ax2.fill_between(x=plot_df.bins,
y1=plot_df.scaled_amplitude,
color='white',
alpha=0.0)
ax2.fill_between(x=plot_df.bins,
y1=plot_df.scaled_amplitude,
y2=1.0,
color=background_color,
alpha=background_alpha)
ax2.set_xlabel("Frequency (kHz)", size=28)
ax2.set_ylabel("Scaled Amplitude", size=28)
ax2.margins(0)
fig.suptitle(title, size=36, y=0.95)
fig.savefig(title)
def create_plots(robot, obstacles, cfg=None):
from matplotlib.cm import get_cmap
cmaps = [get_cmap('Reds'), get_cmap('Blues')]
plt.rcParams.update({
"text.usetex": True,
"font.family": "sans-serif",
"font.sans-serif": ["Helvetica"]
})
fig = plt.figure(figsize=(3, 3))
ax = fig.add_subplot(111) #, projection='3d'
# Plot ostacles
# ax.axis('tight')
ax.set_xlim(-8, 8)
ax.set_ylim(-8, 8)
ax.set_aspect('equal', adjustable='box')
ax.set_xticks([-4, 0, 4])
ax.set_yticks([-4, 0, 4])
for obs in obstacles:
cat = obs[3] if len(obs) >= 4 else 1
# print('{}, cat {}, {}'.format(obs[0], cat, obs))
if obs[0] == 'circle':
ax.add_patch(Circle(obs[1], obs[2], color=cmaps[cat](
0.5))) #path_effects=[path_effects.withSimplePatchShadow()],
elif obs[0] == 'rect':
ax.add_patch(
Rectangle((obs[1][0] - float(obs[2][0]) / 2,
obs[1][1] - float(obs[2][1]) / 2),
obs[2][0],
obs[2][1],
color=cmaps[cat](0.5))
) #, path_effects=[path_effects.withSimplePatchShadow()]
# Plot robot
if cfg is None:
cfg = torch.rand(1, robot.dof, dtype=torch.float32)
cfg = cfg * (robot.limits[:, 1] - robot.limits[:, 0]) + robot.limits[:,
0]
points = robot.fkine(cfg)[0]
points = torch.cat([torch.zeros(1, points.shape[1]), points], dim=0)
trans = ax.transData.transform
lw = ((trans((1, robot.link_width)) - trans(
(0, 0))) * 72 / ax.figure.dpi)[1]
link_plot, = ax.plot(
points[:, 0],
points[:, 1],
color='silver',
lw=lw,
solid_capstyle='round',
path_effects=[path_effects.SimpleLineShadow(),
path_effects.Normal()])
joint_plot, = ax.plot(points[:-1, 0],
points[:-1, 1],
'o',
color='tab:red',
markersize=lw)
eff_plot, = ax.plot(points[-1:, 0],
points[-1:, 1],
'o',
color='black',
markersize=lw)
def drawFunicular(x, y, CapLam=0.1, M=2, drawArrows=False):
pSize = 2.009
goldRat = 1.618
lineWidth = 1
pathEffects = [path_effects.SimpleLineShadow(), path_effects.Normal()]
fig = plt.figure(figsize=(pSize * goldRat, pSize))
ax = fig.gca()
fig.subplots_adjust(left=0.1, right=1.0 - 0.1, bottom=0.24, top=0.99)
rx = 0.05
ry = rx
shifty = 0.75 / goldRat
cvb_bot = np.zeros((90, 2))
cvb_bot[:, 0] = np.linspace(calc_lam(CapLam, 1, numsys=2), 1.0 - rx, 90)
cvb_bot[:, 1] = np.ones(90) * shifty
cvb_top = np.zeros((90, 2))
cvb_top[:, 0] = np.linspace(calc_lam(CapLam, 0, numsys=2), 1.0 - rx, 90)
cvb_top[:, 1] = np.ones(90) * (shifty + 2.0 * ry)
lamVals = x - x.min()
lamVals /= lamVals.max()
gVals = y - y.min()
gVals /= (2.0 * gVals.max() * goldRat)
ax.plot(lamVals[2:], gVals[2:], 'k', lw=lineWidth)
l = CapLam
numsys = M
rotation = []
y = []
for i in range(M):
if calc_lam(CapLam, i, numsys=M) > rx and calc_lam(
CapLam, i, numsys=M) < (1.0 - rx):
rotation.append(45)
y.append(1.0)
elif calc_lam(CapLam, i, numsys=M) < rx:
alpha = np.arcsin((rx - calc_lam(CapLam, i, numsys=M)) / rx)
rotation.append(45 - alpha / np.pi * 180.0)
y.append(np.cos(alpha))
else:
alpha = np.arcsin((rx - (1 - calc_lam(CapLam, i, numsys=M))) / rx)
rotation.append(45 - alpha / np.pi * 180.0)
y.append(np.cos(alpha))
shiftMarker = 0.02 * np.sqrt(2)
ax.plot(cvb_bot[:, 0], cvb_bot[:, 1], 'k', lw=lineWidth, zorder=1)
ax.plot(cvb_top[:, 0], cvb_top[:, 1], 'k', lw=lineWidth, zorder=1)
# ax.add_artist(patches.Arc((rx,shifty+ry), 2*rx, 2*ry, theta1=90, theta2=270, lw=lineWidth))
ax.add_artist(
patches.Arc((1.0 - rx, shifty + ry),
2 * rx,
2 * ry,
theta1=270,
theta2=90,
lw=lineWidth))
# ax.add_artist(patches.Arc((rx,shifty+ry), 1.4*rx, 1.4*ry, lw=lineWidth))
ax.add_artist(
patches.Arc((1.0 - rx, shifty + ry), 1.4 * rx, 1.4 * ry, lw=lineWidth))
# ax.annotate(r'$\Lambda=0$', xy=(-0.01, shifty+ry), xytext=(-0.05, shifty+ry), va='center', ha='right', arrowprops=dict(arrowstyle='-'))
# ax.annotate(r'$\Lambda=\frac{\pi}{2}$', xy=(0.5, shifty+2*ry+0.01), xytext=(0.5, shifty+2*ry+0.05), va='bottom', ha='center', arrowprops=dict(arrowstyle='-'))
# ax.annotate(r'$\Lambda=\frac{3\pi}{2}$', xy=(0.5, shifty-0.01), xytext=(0.5, shifty-0.05), va='top', ha='center', arrowprops=dict(arrowstyle='-'))
# ax.annotate(r'$\Lambda=\pi$', xy=(1.01, shifty+ry), xytext=(1.05, shifty+ry), va='center', ha='left', arrowprops=dict(arrowstyle='-'))
# if np.fabs(rotation[0]-45)>0.0001:
# print(alpha)
# ax.annotate('Current state:\n$\Lambda={:.1f}$'.format(CapLam), xy=(calc_lam(CapLam, 0, numsys=M), shifty+ry+np.cos(alpha)*ry),
# xytext=(calc_lam(CapLam, 0, numsys=M)-np.sin(alpha)*1.5*rx, shifty+(1+np.cos(alpha)*2.5)*ry),
# arrowprops=dict(arrowstyle='<-', linewidth=3), va='center', ha='center', zorder=0)
# else:
# ax.annotate('Current state:\n$\Lambda={:.1f}$'.format(CapLam), xy=(calc_lam(CapLam, 0, numsys=M), shifty+2.0*ry+shiftMarker),
# xytext=(calc_lam(CapLam, 0, numsys=M), shifty+3.5*ry),
# arrowprops=dict(arrowstyle='<-', linewidth=3), va='center', ha='center', zorder=0)
#arrows in the conveyor belt
# drawCirc(ax,rx*0.8,rx,shifty+ry,45,270, color_='red')
drawCirc(ax,
rx * 0.8,
1.0 - rx,
shifty + ry,
225,
270,
lineWidth=lineWidth,
color_='red')
for i in range(int(M / 2)):
x = calc_lam(CapLam, i, numsys=M) - np.sqrt(1 - y[i]**2) * shiftMarker
ax.add_patch( #Create triangle as arrow head
patches.RegularPolygon(
(x, shifty + ry + y[i] * ry), # (x,y)
4, # number of vertices
0.02, # radius
rotation[i] / 180.0 * np.pi, # orientation
color='red',
zorder=10))
ax.scatter(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker,
s=30,
marker='o',
edgecolors='face',
color='r',
zorder=10)
if drawArrows:
ax.annotate('',
xy=(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker),
xytext=(x + 0.1,
gVals[np.abs(lamVals - x - 0.1).argmin()] +
shiftMarker),
arrowprops=dict(arrowstyle='<-', linewidth=lineWidth))
ax.plot([x, x],
[gVals[np.abs(lamVals - x).argmin()], shifty + ry + y[i] * ry],
color='0.8',
lw=lineWidth,
zorder=0)
for i in range(int(M / 2)):
x = calc_lam(CapLam, i + int(M / 2),
numsys=M) - np.sqrt(1 - y[i]**2) * shiftMarker
ax.add_patch( #Create triangle as arrow head
patches.RegularPolygon(
(x, shifty), # (x,y)
4, # number of vertices
0.02, # radius
rotation[i] / 180.0 * np.pi, # orientation
color='red',
zorder=10))
ax.plot(
[x, x],
[gVals[np.abs(lamVals - x).argmin()], shifty + (1.0 - y[i]) * ry],
color='0.8',
lw=lineWidth,
zorder=0)
ax.scatter(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker,
s=30,
marker='o',
edgecolors='face',
color='r',
zorder=10)
if drawArrows:
ax.annotate('',
xy=(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker),
xytext=(x - 0.1,
gVals[np.abs(lamVals - x + 0.1).argmin()] +
shiftMarker),
arrowprops=dict(arrowstyle='<-', linewidth=lineWidth))
ax.set_xlim(-0.1, 1.1)
ax.set_ylim(0, 1.2 / goldRat)
ax.set_xticks([0.0, 0.5, 1.0])
ax.set_xticklabels(['0\n(A)', r'$\sfrac{1}{2}$', '1\n(B)'])
# ax.text(lamVals[-1], gVals[-1]-0.05, 'Free energy profile', ha='right', va='top')
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.set_yticks([])
ax.spines['left'].set_color('None')
ax.spines['bottom'].set_smart_bounds(True)
ax.spines['right'].set_color('None')
ax.spines['top'].set_color('None')
yarrow = ax.annotate('',
xy=(0, 0),
xytext=(0, 0.5 / goldRat),
ha='center',
va='bottom',
arrowprops=dict(arrowstyle='<|-',
facecolor='k',
linewidth=1.5))
ax.text(-0.025,
0.25 / goldRat,
'$G(\lambda)$',
ha='right',
va='center',
fontsize=14)
ax.text(1.025, 0.0, '$\lambda$', ha='left', va='center', fontsize=14)
return fig
def updateEnsembler(x, y, ax, CapLam=0.1, M=8, drawArrows=False):
pSize = 6.027
goldRat = 1.70
lineWidth = 1
pathEffects = [path_effects.SimpleLineShadow(), path_effects.Normal()]
rx = 0.05
ry = rx
shifty = 0.75 / goldRat
cvb_bot = np.zeros((90, 2))
cvb_bot[:, 0] = np.linspace(rx, 1.0 - rx, 90)
cvb_bot[:, 1] = np.ones(90) * shifty
cvb_top = np.zeros((90, 2))
cvb_top[:, 0] = np.linspace(rx, 1.0 - rx, 90)
cvb_top[:, 1] = np.ones(90) * (shifty + 2.0 * ry)
lamVals = x - x.min()
lamVals /= lamVals.max()
gVals = y - y.min()
gVals /= (2.0 * gVals.max() * goldRat)
ax.plot(lamVals[2:], gVals[2:], 'k', lw=lineWidth)
l = CapLam
numsys = M
rotation = []
y = []
#buildBox
for i in range(M):
if calc_lam(CapLam, i, numsys=M) > rx and calc_lam(
CapLam, i, numsys=M) < (1.0 - rx):
rotation.append(45)
y.append(1.0)
elif calc_lam(CapLam, i, numsys=M) < rx:
alpha = np.arcsin((rx - calc_lam(CapLam, i, numsys=M)) / rx)
if (CapLam + i * 2 * np.pi / float(M)) % (2. * np.pi) < np.pi:
rotation.append(45 + alpha / np.pi * 180.0)
else:
rotation.append(45 - alpha / np.pi * 180.0)
y.append(np.cos(alpha))
else:
alpha = np.arcsin((rx - (1 - calc_lam(CapLam, i, numsys=M))) / rx)
if (CapLam + i * 2 * np.pi / float(M)) % (2. * np.pi) < np.pi:
rotation.append(45 - alpha / np.pi * 180.0)
else:
rotation.append(45 + alpha / np.pi * 180.0)
y.append(np.cos(alpha))
shiftMarker = 0.02 * np.sqrt(2)
#arrow
if drawArrows:
if np.fabs(rotation[0] - 45) > 0.0001:
ax.annotate(
'Current state:\n$\Lambda={:.1f}$'.format(CapLam),
xy=(calc_lam(CapLam, 0, numsys=M),
shifty + ry + np.cos(alpha) * (ry + shiftMarker)),
xytext=(calc_lam(CapLam, 0, numsys=M) - np.sin(alpha) * 2 * rx,
shifty + (1 + np.cos(alpha) * 5) * ry),
fontsize='small',
arrowprops=dict(arrowstyle='<-', linewidth=1.0, shrinkA=0.0),
va='top',
ha='center',
zorder=0,
bbox=dict(pad=-.1, lw=0.0, color='None'))
else:
ax.annotate('Current state:\n$\Lambda={:.1f}$'.format(CapLam),
xy=(calc_lam(CapLam, 0, numsys=M),
shifty + 2.0 * ry + shiftMarker),
xytext=(calc_lam(CapLam, 0,
numsys=M), shifty + 6 * ry),
arrowprops=dict(arrowstyle='<-',
linewidth=1.0,
shrinkA=0.0),
fontsize='small',
va='top',
ha='center',
zorder=0,
bbox=dict(pad=-.1, lw=0.0, color='None'))
#arrows in the conveyor belt
drawCirc(ax,
rx * 0.8,
rx,
shifty + ry,
45,
270,
lineWidth=1.0,
color_='red')
drawCirc(ax,
rx * 0.8,
1.0 - rx,
shifty + ry,
225,
270,
lineWidth=1.0,
color_='red')
#box arrow?
for i in range(M):
x = calc_lam(CapLam, i, numsys=M)
if x < rx:
rx -= np.sqrt(1 - y[i]**2) * shiftMarker
elif x > 1 - rx:
rx += np.sqrt(1 - y[i]**2) * shiftMarker
if (CapLam + i * 2 * np.pi / float(M)) % (2. * np.pi) < np.pi:
ax.add_patch( #Create triangle as arrow head
patches.RegularPolygon(
(x, shifty + ry + y[i] * ry + y[i] * shiftMarker), # (x,y)
4, # number of vertices
0.02, # radius
rotation[i] / 180.0 * np.pi, # orientation
color='red',
zorder=10))
ax.scatter(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker,
s=30,
marker='o',
edgecolors='face',
color='r',
zorder=10)
if drawArrows:
ax.annotate('',
xy=(x, gVals[np.abs(lamVals - x).argmin()] +
shiftMarker),
xytext=(x + 0.1,
gVals[np.abs(lamVals - x - 0.1).argmin()] +
shiftMarker),
arrowprops=dict(arrowstyle='<-',
linewidth=lineWidth))
ax.plot([x, x], [
gVals[np.abs(lamVals - x).argmin()],
shifty + ry + y[i] * ry + y[i] * shiftMarker
],
color='0.8',
lw=lineWidth,
zorder=0)
else:
ax.add_patch( #Create triangle as arrow head
patches.RegularPolygon(
(x, shifty - y[i] * shiftMarker), # (x,y)
4, # number of vertices
0.02, # radius
rotation[i] / 180.0 * np.pi, # orientation
color='red',
zorder=10))
ax.plot([x, x], [
gVals[np.abs(lamVals - x).argmin()], shifty +
(1.0 - y[i]) * ry - y[i] * shiftMarker
],
color='0.8',
lw=lineWidth,
zorder=0)
ax.scatter(x,
gVals[np.abs(lamVals - x).argmin()] + shiftMarker,
s=30,
marker='o',
edgecolors='face',
color='r',
zorder=10)
if drawArrows:
ax.annotate('',
xy=(x, gVals[np.abs(lamVals - x).argmin()] +
shiftMarker),
xytext=(x - 0.1,
gVals[np.abs(lamVals - x + 0.1).argmin()] +
shiftMarker),
arrowprops=dict(arrowstyle='<-',
linewidth=lineWidth))
color='k',
lw=2,
path_effects=[pe.Stroke(linewidth=5, foreground='g'),
pe.Normal()])
# custom plot settings
plt.grid(True)
plt.ylim((-2, 2))
plt.legend(['sine'])
plt.savefig(
r'D:\GoogleChromeDownloads\MyWebSites\100vragenKNS\toetskns.nl//sin1.png')
plt.show()
# In[32]:
# create line plot including an simple line shadow using path_effects
plt.plot(x,
y,
color='k',
lw=2,
path_effects=[pe.SimpleLineShadow(shadow_color='g'),
pe.Normal()])
# custom plot settings
plt.grid(True)
plt.ylim((-2, 2))
plt.legend(['sine'])
plt.savefig(
r'D:\GoogleChromeDownloads\MyWebSites\100vragenKNS\toetskns.nl//sin2.png')
plt.show()
# In[ ]: