def category_bar_charts():
sns.set(style="whitegrid")
sns.set_context("notebook", font_scale=1.5, rc={"lines.linewidth": 2.5})
f, (ax1, ax2, ax3) = plt.subplots(3, 1, figsize=(10, 7), sharex=False)
retirement_sums = sorted(retirement_class_sums(), reverse=True)
x = [a[1] for a in retirement_sums]
y = [a[0] for a in retirement_sums]
sns.barplot(x, y, palette="YlOrRd_d", ax=ax1)
ax1.set_ylabel("By Category")
account_type_sums = sorted(account_by_type_sums(), reverse=True)
x = [a[1] for a in account_type_sums]
y = [a[0] for a in account_type_sums]
sns.barplot(x, y, palette="BuGn_d", ax=ax2)
ax2.set_ylabel("By Category")
account_owner_sums = sorted(account_by_owner_sums(), reverse=True)
x = [a[1] for a in account_owner_sums]
y = [a[0] for a in account_owner_sums]
sns.barplot(x, y, palette="Blues_d", ax=ax3)
ax3.set_ylabel("By Owner")
sns.despine(left=True)
f.tight_layout()
canvas = FigureCanvas(plt.gcf())
png_output = io.BytesIO()
canvas.print_png(png_output)
response=make_response(png_output.getvalue())
response.headers['Content-Type'] = 'image/png'
return response
def plot_hist_algo(wave_hist_algor, pulse_hist_algor, multi_wave_hist_algor):
inch_factor = 2.54
sns.set_context("poster")
sns.axes_style('white')
# sns.set_style("ticks")
fig4= plt.figure(figsize=(35./ inch_factor, 20./ inch_factor))
ax1 = fig4.add_subplot(2, 3, (1, 4))
dafr = pd.DataFrame([wave_hist_algor, multi_wave_hist_algor, pulse_hist_algor]) #turn
dafr = dafr.transpose()
dafr.columns = ['wave', 'multi-wave', 'pulse']
sns.violinplot(data=dafr, ax=ax1, col=("blue", "green", "red"))
ax1.set_ylabel('psd_proportion')
ax1.set_xlabel('EOD-type')
ax1.set_title('Fishsorting based on PSD')
wave_psd_data = np.load('wave_psd_data.npy')
wave_hist_data = wave_psd_data[1][:len(wave_psd_data[0][wave_psd_data[0]<1500])]
ax3 = fig4.add_subplot(2, 3, (2, 5))
n, bin, patch = ax3.hist(wave_hist_data, 50, color='blue', alpha=0.7, normed=True)
# ax3.set_ylim([0, max(n)+10])
ax3.set_ylabel('counts in histogram bin')
ax3.set_xlabel('amplitude of PSD')
ax3.set_title('Histogram of pulsefish PSD')
pulse_psd_data = np.load('pulse_psd_data.npy')
pulse_hist_data = pulse_psd_data[1][:len(pulse_psd_data[0][pulse_psd_data[0]<1500])]
ax2 = fig4.add_subplot(2, 3, (3, 6))
ax2.hist(pulse_hist_data, 50, color='red', alpha=0.7, normed=True)
# ax2.set_ylim([0, max(n)+10])
ax2.set_ylabel('counts in histogram bin')
ax2.set_xlabel('amplitude of PSD')
ax2.set_title('Histogram of pulsefish PSD')
fig4.tight_layout()
def TuningResponseArea(tuningCurves, unitKey='', figPath=[]):
""" Plot the tuning response area for tuning curve data.
:param tuningCurves: pandas.DataFrame from spreadsheet with experimental data loaded from Excel file
:type tuningCurves: pandas.core.DataFrame
:param unitKey: identifying string for data, possibly unit name/number and test number
:type unitKey: str
:param figPath: Directory location for plots to be saved
:type figPath: str
"""
f = plt.figure()
colorRange = (-10,10.1)
I = np.unique(np.array(tuningCurves['intensity']))
F = np.array(tuningCurves['freq'])
R = np.array(np.zeros((len(I), len(F))))
for ci, i in enumerate(I):
for cf, f in enumerate(F):
R[ci,cf] = tuningCurves['response'].where(tuningCurves['intensity']==i).where(tuningCurves['freq']==f).dropna().values[0]
levelRange = np.arange(colorRange[0], colorRange[1], (colorRange[1]-colorRange[0])/float(25*(colorRange[1]-colorRange[0])))
sns.set_context(rc={"figure.figsize": (7, 4)})
ax = plt.contourf(F, I, R)#, vmin=colorRange[0], vmax=colorRange[1], levels=levelRange, cmap = cm.bwr )
plt.colorbar()
# plt.title(unit, fontsize=14)
plt.xlabel('Frequency (kHz)', fontsize=14)
plt.ylabel('Intensity (dB)', fontsize=14)
if len(figPath)>0:
plt.savefig(figPath + 'tuningArea_' + unitKey +'.png')
def plot_results(self):
"""
A simple script to plot the balance of the portfolio, or
"equity curve", as a function of time.
"""
sns.set_palette("deep", desat=.6)
sns.set_context(rc={"figure.figsize": (8, 4)})
# Plot two charts: Equity curve, period returns
fig = plt.figure()
fig.patch.set_facecolor('white')
df = pd.DataFrame()
df["equity"] = pd.Series(self.equity, index=self.timeseries)
df["equity_returns"] = pd.Series(self.equity_returns, index=self.timeseries)
df["drawdowns"] = pd.Series(self.drawdowns, index=self.timeseries)
# Plot the equity curve
ax1 = fig.add_subplot(311, ylabel='Equity Value')
df["equity"].plot(ax=ax1, color=sns.color_palette()[0])
# Plot the returns
ax2 = fig.add_subplot(312, ylabel='Equity Returns')
df['equity_returns'].plot(ax=ax2, color=sns.color_palette()[1])
# drawdown, max_dd, dd_duration = self.create_drawdowns(df["Equity"])
ax3 = fig.add_subplot(313, ylabel='Drawdowns')
df['drawdowns'].plot(ax=ax3, color=sns.color_palette()[2])
# Rotate dates
fig.autofmt_xdate()
# Plot the figure
plt.show()
def addRandomThemes(self):
themes = ["darkgrid", "whitegrid", "dark", "white", "ticks"]
contexts = ["paper", "notebook", "talk", "poster"]
theme = self.numFig % 5
context = theme % 4
sns.set_style(themes[theme])
sns.set_context(contexts[context])
def plot_results(self):
"""
A simple script to plot the balance of the portfolio, or
"equity curve", as a function of time.
It requires OUTPUT_RESULTS_DIR to be set in the project
settings.
"""
sns.set_palette("deep", desat=0.6)
sns.set_context(rc={"figure.figsize": (8, 4)})
equity_file = os.path.join(settings.OUTPUT_DIR, "output.csv")
equity = pd.io.parsers.read_csv(equity_file, parse_dates=True, header=0, index_col=0)
# Plot three charts: Equity curve, period returns, drawdowns
fig = plt.figure()
fig.patch.set_facecolor("white") # Set the outer colour to white
# Plot the equity curve
ax1 = fig.add_subplot(311, ylabel="Portfolio value")
equity["Equity"].plot(ax=ax1, color=sns.color_palette()[0])
# Plot the returns
ax2 = fig.add_subplot(312, ylabel="Period returns")
equity["Returns"].plot(ax=ax2, color=sns.color_palette()[1])
# Plot the returns
ax3 = fig.add_subplot(313, ylabel="Drawdowns")
equity["Drawdown"].plot(ax=ax3, color=sns.color_palette()[2])
# Plot the figure
plt.show()
def UseSeaborn(palette='deep'):
"""Call to use seaborn plotting package
"""
import seaborn as sns
#No Background fill, legend font scale, frame on legend
sns.set(style='whitegrid', font_scale=1.5, rc={'legend.frameon': True})
#Mark ticks with border on all four sides (overrides 'whitegrid')
sns.set_style('ticks')
#ticks point in
sns.set_style({"xtick.direction": "in","ytick.direction": "in"})
# sns.choose_colorbrewer_palette('q')
#Nice Blue,green,Red
# sns.set_palette('colorblind')
if palette == 'xkcd':
#Nice blue, purple, green
sns.set_palette(sns.xkcd_palette(xkcdcolors))
else:
sns.set_palette(palette)
#Nice blue, green red
# sns.set_palette('deep')
# sns.set_palette('Accent_r')
# sns.set_palette('Set2')
# sns.set_palette('Spectral_r')
# sns.set_palette('spectral')
#FIX INVISIBLE MARKER BUG
sns.set_context(rc={'lines.markeredgewidth': 0.1})
def decode_uniform_samples_from_latent_space(_):
fig, ax = plt.subplots()
nx = ny = 20
extent_x = extent_y = [-3, 3]
extent = numpy.array(extent_x + extent_y)
x_values = numpy.linspace(*(extent_x + [nx]))
y_values = numpy.linspace(*(extent_y + [nx]))
full_extent = extent * (nx + 1) / float(nx)
canvas = numpy.empty((28 * ny, 28 * nx))
for ii, yi in enumerate(x_values):
for j, xi in enumerate(y_values):
n = ii * nx + j + 1
sys.stdout.write("\rsampling p(X|z), sample %d/%d" % (n, nx*ny))
sys.stdout.flush()
np_z = numpy.array([[xi, yi]])
x_mean = sess.run(prior_model(latent=numpy.reshape(np_z, newshape=(1, LATENT_DIM)))[0])
canvas[(nx - ii - 1) * 28:(nx - ii) * 28, j * 28:(j + 1) * 28] = x_mean[0].reshape(28, 28)
with seaborn.axes_style('ticks'):
seaborn.set_context(context='notebook', font_scale=1.75)
fig, ax = plt.subplots(figsize=(12, 9))
ax.imshow(canvas, extent=full_extent)
ax.xaxis.set_ticks(numpy.linspace(*(extent_x + [nx])))
ax.yaxis.set_ticks(numpy.linspace(*(extent_y + [ny])))
ax.set_xlabel('z_1')
ax.set_ylabel('z_2')
ax.set_title('P(X|z); decoding latent space; (CONV, BNAE, IND_ERROR) = (%d,%d,%d)' % (CONV, BNAE, IND_ERROR))
plt.show()
plt.savefig(os.path.join(FLAGS.viz_dir, 'P(X|z).png'))
return fig, ax
def plot_rolling_auto_home(df_attack=None,df_defence=None, window=5, nstd=1,
detected_events_home=None,
detected_events_away=None, sky_events=None):
sns.set_context("notebook", font_scale=1.8 ,rc={"lines.linewidth": 3.5, "figure.figsize":(18,12) })
plt.subplots_adjust(bottom=0.85)
mean = pd.rolling_mean(df_attack, center=True, window=window)
std = pd.rolling_std(df_attack, center=True, window=window)
detected_plot_extrema = df_attack.ix[argrelextrema(df_attack.values, np.greater)]
df_filt_noise = df_attack[(df_attack > mean-std) & (df_attack < mean+std)]
df_filt_noise = df_filt_noise.ix[detected_plot_extrema.index].dropna()
df_filt_keep = df_attack[~((df_attack > mean-std) & (df_attack < mean+std))]
df_filt_keep = df_filt_keep.ix[detected_plot_extrema.index].dropna()
plt.plot(df_attack, color='#4CA64C', label='{} Attack'.format(all_matches[0]['home_team'].title()))
plt.fill_between(df_attack.index, (mean-nstd*std), (mean+nstd*std), interpolate=False, alpha=0.4, color='#B2B2B2', label='$\mu + {} \\times \sigma$'.format(nstd))
plt.scatter(df_filt_keep.index, df_filt_keep.values, marker='*', s=120, color='#000000', zorder=10, label='Selected maxima post-filtering')
plt.scatter(df_filt_noise.index, df_filt_noise.values, marker='x', s=120, color='#000000', zorder=10, label='Unselected maxima post-filtering')
df_defence.apply(lambda x: -1*x).plot(color='#000000', label='{} Defence'.format(all_matches[0]['home_team'].title()))
if(len(detected_events_home) > 0):
classifier_events_df_home= pd.DataFrame(detected_events_home)
classifier_events_df_home[classifier_events_df_home.category == 'GOAL']
if(len(detected_events_away) > 0):
classifier_events_df_away= pd.DataFrame(detected_events_away)
classifier_events_df_away[classifier_events_df_away.category == 'GOAL']
font0 = FontProperties(family='arial', weight='bold',style='italic', size=16)
for i, row in classifier_events_df_home.iterrows():
if row.category == 'OTHER':
continue
plt.text(row.event, df_attack.max(), "{} {} {}".format(all_matches[0]['home_team'].upper(), row.category, row.event), rotation='vertical', color='black', bbox=dict(facecolor='green', alpha=0.2))#, transform=transform)
for i, row in classifier_events_df_away.iterrows():
if row.category == 'OTHER':
continue
plt.text(row.event, (df_attack.max()), "{} {} {}".format(all_matches[0]['away_team'].upper(), row.category, row.event), rotation='vertical', color='black', bbox=dict(facecolor='red', alpha=0.2))
high_peak_position = 0;
if(df_attack.max() > df_defence.max()): high_peak_position = -(df_defence.max() * 2.0)
else: high_peak_position = -(df_defence.max() * 1.25)
# Functionality to include Sky Sports text commentary updates on plot for goal events.
# for i, row in pd.DataFrame(sky_events).iterrows():
# dedented_text = textwrap.dedent(row.text).strip()
# plt.text(row.event, high_peak_position, "@SkySports {} AT {}:\n{}:\n{}".format(row.category, row.event.time(), row.title, textwrap.fill(dedented_text, width=40)), color='black', bbox=dict(facecolor='blue', alpha=0.2))
plt.legend(loc=4)
ax = plt.gca()
label = ax.set_xlabel('time')
plt.ylabel('Tweet frequency')
plt.title('{} vs. {} (WK {}) - rolling averages window={} mins'.format(all_matches[0]['home_team'].title(), all_matches[0]['away_team'].title(), all_matches[0]['dbname'], window))
plt.savefig('{}attack_{}_plain.pdf'.format(all_matches[0]['home_team'].upper(), all_matches[0]['away_team'].upper()))
return detected_plot_extrema
def pltsns(style='ticks',context='talk'):
global figdir
sns.set_style(style)
sns.set_style({'legend.frameon':True})
sns.set_context(context)
#figdir = datadir+'samoa/WATERSHED_ANALYSIS/GoodFigures/rawfigoutput/'
return
def plot_diadem_score(neuron_distance_csv, outputDir,algorithms=None):
df_nd = pd.read_csv(neuron_distance_csv)
if not path.exists(outputDir):
os.mkdir(outputDir)
if algorithms is None:
algorithms= order_algorithms_by_size(df_nd)
### all algorithm plot
dfg = df_nd.groupby('algorithm')
sample_size_per_algorithm=[]
for alg in algorithms:
sample_size_per_algorithm.append(dfg.get_group(alg).shape[0])
#plot the average node distances
plt.figure()
sb.set_context("talk", font_scale=0.7)
a=sb.barplot(y='algorithm', x='diadem_score', data=df_nd,order=algorithms)
algorithm_name_mapping = rp.get_algorithm_name_dict()
algorithm_names = [algorithm_name_mapping[x] for x in algorithms]
a.set_yticklabels(['%s ($n$=%d )'%(algorithm_names[i], sample_size_per_algorithm[i]) for i in range(algorithms.size) ])
#sb.set_context("talk", font_scale=3.0)
#plt.xticks(rotation="90")
plt.xlabel('Diadem Scores')
plt.subplots_adjust(left=0.5,right=0.95,bottom=0.1, top=0.9)
plt.savefig(outputDir + '/Diadem_score.png', format='png')
#plt.show()
plt.close()
return
def plot_lai_comparison_thin(classification):
sns.set_context(rc={'lines.linewidth': 0.8, 'lines.markersize': 6})
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(16, 8))
palette = sns.color_palette("colorblind", 11)
lai_c, plot_c, lai_m_c, lai_s_c = ld.find_lai_lp80(classification, ld.lp80)
lai_h, plot_h, lai_m_h, lai_s_h = ld.find_lai_lp80(classification, ld.hemi)
lai_t, plot_t, lai_m_t, lai_s_t = ld.find_lai_lp80(classification, ld.trap)
lai_h_fill = np.ones(len(lai_c))*float('NaN')
lai_h_fill[plot_c.searchsorted(plot_h)] = lai_h
lai_t_fill = np.ones(len(lai_c))*float('NaN')
lai_t_fill[plot_c.searchsorted(plot_t)] = lai_t
xlist = np.arange(len(lai_c))
ax.plot(xlist, lai_c, color=palette[0], label='Ceptometer')
ax.plot(xlist, lai_h_fill, 'o', color=palette[1], label='Hemi. photos')
ax.plot(xlist, lai_t_fill, 'o', color=palette[2], label='Litter traps')
ax.axhline(lai_m_c, color=palette[0], linestyle='--')
ax.axhline(lai_m_h, color=palette[1], linestyle='--')
ax.axhline(lai_m_t, color=palette[2], linestyle='--')
ax.set_xlabel('Number of LAI observations')
ax.set_ylabel('LAI (m2/ m2)')
plt.legend(loc='upper left')
plt.ylim(0, 8)
plt.xlim(0, xlist[-1]+1)
return ax, fig
def showResults(challenger_data, model):
''' Show the original data, and the resulting logit-fit'''
# First plot the original data
plt.figure()
sns.set_context('poster')
sns.set_style('whitegrid')
np.set_printoptions(precision=3, suppress=True)
plt.scatter(challenger_data[:, 0], challenger_data[:, 1], s=75, color="k",
alpha=0.5)
plt.yticks([0, 1])
plt.ylabel("Damage Incident?")
plt.xlabel("Outside temperature (Fahrenheit)")
plt.title("Defects of the Space Shuttle O-Rings vs temperature")
plt.xlim(50, 85)
# Plot the fit
x = np.arange(50, 85)
alpha = model.params[0]
beta = model.params[1]
y = logistic(x, beta, alpha)
plt.hold(True)
plt.plot(x,y,'r')
outFile = 'ChallengerPlain.png'
C2_8_mystyle.printout_plain(outFile, outDir='..\Images')
plt.show()
def show_binomial():
"""Show an example of binomial distributions"""
bd1 = stats.binom(20, 0.5)
bd2 = stats.binom(20, 0.7)
bd3 = stats.binom(40, 0.5)
k = np.arange(40)
sns.set_context('paper')
sns.set_style('ticks')
mystyle.set(14)
markersize = 8
plt.plot(k, bd1.pmf(k), 'o-b', ms=markersize)
plt.hold(True)
plt.plot(k, bd2.pmf(k), 'd-r', ms=markersize)
plt.plot(k, bd3.pmf(k), 's-g', ms=markersize)
plt.title('Binomial distribuition')
plt.legend(['p=0.5 and n=20', 'p=0.7 and n=20', 'p=0.5 and n=40'])
plt.xlabel('X')
plt.ylabel('P(X)')
sns.despine()
mystyle.printout_plain('Binomial_distribution_pmf.png')
plt.show()
def PlotSTResponseEst(self, stResponseDF, label, duration=250, firstFreq=1):
""" Plots response rate estimate for multiple frequencies and intensities as a contour plot.
:param stResponseDF: DataFrames results of Bayesian response analysis for multiple tone stimulus intensities
:type stResponseDF: pandas DataFrame
:param label: Figure name
:type label: str
:param duration: Duration of recording window
:type duration: float
:param firstFreq: Set to skip first (spurious) entry
:type firstFreq: int
:returns: Handle to plot
"""
stResponseE = np.array(stResponseDF)
freqs = np.array(stResponseDF.index.tolist())[1:].astype(np.float)
sns.set_context(rc={"figure.figsize": (8, 4)})
maxRes = np.max(abs(stResponseE[firstFreq:,:]))
spontRate = np.average(stResponseE[firstFreq:,-1])
ax = plt.imshow(stResponseE[firstFreq:,:], vmax=maxRes+spontRate, vmin=-maxRes+spontRate, extent=[0,duration,min(freqs),max(freqs)], aspect='auto', interpolation='nearest', origin='lower', cmap = cm.bwr)
sns.despine()
plt.grid(False)
plt.title(label)
plt.xlabel('Time (ms)')
plt.ylabel('Frequency (kHz)')
plt.colorbar()
return ax
def PlotBBNResponseCurve(self, bbnResponseProb, measure, unit=[], filePath=[], attn=False):
""" Plots measure for multiple frequencies and intensities an a contour plot.
:param stResponseProb: DataFrames results of Bayesian response analysis for multiple tone stimulus intensities
:type stResponseProb: pandas DataFrame
:param measure: Bayesian response analysis measure ['resProb', 'vocalResMag', 'vocalResMag_MLE', 'effectSize', 'effectSize_MLE', 'spontRate', 'spontRateSTD', 'responseLatency', 'responseLatencySTD', 'responseDuration']
:type measure: integer [0-9]
:param unit: Unique identifier for cell
:type unit: str
:param filePath: Path to directory where results will be saved
:type filePath: str
:returns: Handle to plot
"""
measureName = ['resProb', 'vocalResMag', 'vocalResMag_MLE', 'effectSize', 'effectSize_MLE', 'spontRate', 'spontRateSTD', 'responseLatency', 'responseLatencySTD', 'responseDuration']
tuningData = bbnResponseProb
sns.set_palette(sns.color_palette("bright", 8))
sns.set_context(rc={"figure.figsize": (5, 3)})
sns.set_style("white")
sns.set_style("ticks")
if attn: ax = bbnResponseProb.loc[::-1,measure].fillna(0).plot(figsize=(6,4))
else: ax = bbnResponseProb.loc[:,measure].fillna(0).plot(figsize=(6,4))
sns.despine()
plt.grid(False)
plt.title(unit, fontsize=14)
plt.xlabel('SPL (dB)', fontsize=12)
plt.ylabel(measureName[measure], fontsize=12)
plt.ylim(0.5,1.0)
# plt.gca().invert_xaxis()
if len(filePath)>0:
plt.savefig(self.dirPath + filePath + 'bbn_'+measureName[measure]+'_'+unit+'.pdf')
plt.close()
else: plt.show()
return ax
def fishtype_barplot(data):
""" This function creates a bar plot showing the distribution of wave-fishes vs. pulse-fishes.
:param data: dictionary with fish-type as keys and array of EODfs as values.
"""
# Read the keys of the dictionary and use them to get the count of pulse- and wave-type fishes.
keys = np.array(data.keys())
bool_wave = np.array(['wave' in e for e in keys], dtype=bool)
bool_pulse = np.array(['puls' in e for e in keys], dtype=bool)
count_wave = len(data[keys[bool_wave][0]])
count_pulse = len(data[keys[bool_pulse][0]])
inch_factor = 2.54
sns.set_context("poster")
sns.axes_style('white')
sns.set_style("ticks")
fig, ax = plt.subplots(figsize=(10./inch_factor, 10./inch_factor))
width = 0.5
ax.bar(1-width/2., count_wave, width=width, facecolor='cornflowerblue', alpha=0.8)
ax.bar(2-width/2., count_pulse, width=width, facecolor='salmon', alpha=0.8)
ax.set_xticks([1, 2])
ax.set_xticklabels(['Wave-type', 'Pulse-type'])
ax.tick_params(axis='both', which='major', labelsize=14)
ax.set_ylabel('Number of Fishes', fontsize=14)
ax.set_title('Distribution of Fish-types', fontsize=16)
sns.despine(fig=fig, ax=ax, offset=10)
fig.tight_layout()
fig.savefig('figures/fishtype_barplot.pdf')
plt.close()
def plot_and_savefig(self, out_path=None):
sns.set_context('notebook')
sns.set_style('white')
plot_w = 3 + len(self.data['sample'].unique())
plot_h = 3.5
plots_per_row = 3
n_plots = len(self.data.columns) - 2
n_rows = ceil(n_plots / plots_per_row)
n_cols = ceil(n_plots / n_rows)
ax_ids = list(np.arange(n_plots) + 1)
fig = plt.figure()
fig.set_figheight(plot_h * n_rows)
fig.set_figwidth(plot_w * n_cols)
for i, category in enumerate(self.data.columns):
if category in ['CATEGORY', 'sample']:
continue
ax = fig.add_subplot(n_rows, n_cols, ax_ids.pop(0))
self.draw_ax(ax, category)
if i == 0:
ax.legend()
else:
ax.legend_.set_visible(False)
plt.tight_layout()
if out_path:
plt.savefig(out_path, dpi=300, bbox_inches='tight')
return ax
def plot_total_eui(theme):
sns.set_style("whitegrid")
sns.set_palette("Set2")
sns.set_context("talk", font_scale=1.5)
df_eui = read_eui_cnt('', theme, 'All Building')
df_eui_wecm = read_eui_cnt('_wecm', theme, 'Building with ECM')
df_eui_woutecm = read_eui_cnt('_woutecm', theme,
'Building without ECM')
df_all = reduce(lambda x, y: pd.merge(x, y, on='Fiscal Year',
how='inner'), [df_eui,
df_eui_wecm,
df_eui_woutecm])
df_all = df_all[df_all['Fiscal Year'] < 2016]
lines = []
cols = list(df_all)
cols.remove('Fiscal Year')
bx = plt.axes()
for x in cols:
line, = plt.plot(df_all['Fiscal Year'], df_all[x], ls='-',
lw=2, marker='o')
lines.append(line)
plt.legend(lines, cols, loc='center left',
bbox_to_anchor=(1, 0.5), prop={'size':13})
ylimit = 90
plt.ylim((0, ylimit))
plt.fill_between([2004.5, 2006.5], 0, ylimit, facecolor='gray',
alpha=0.2)
plt.title('GSA Portfolio (A + I) Average EUI Trend')
plt.xlabel('Fiscal Year')
plt.ylabel(lb.ylabel_dict[theme])
P.savefig(os.getcwd() + '/plot_FY_annual/ave_eui.png', dpi = 300,
bbox_inches='tight')
plt.close()
def create_histo(data):
"""
gets a list of data and creates an histogram of this data.
:param data: dictionary with fishtype as keys and np.array with EOD-Frequencies as values.
"""
print 'creating histogramm ...'
inch_factor = 2.54
sns.set_context("poster")
sns.axes_style('white')
sns.set_style("ticks")
fig, ax = plt.subplots(figsize=(15./inch_factor, 10./inch_factor))
colors = ['salmon', 'cornflowerblue']
for enu, curr_fishtype in enumerate(data.keys()):
if len(data[curr_fishtype]) >= 4:
hist, bins = np.histogram(data[curr_fishtype], bins=len(data[curr_fishtype])//4)
width = 0.7 * (bins[1] - bins[0])
center = (bins[:-1] + bins[1:]) / 2
ax.bar(center, hist, align='center', width=width, alpha=0.8, facecolor=colors[enu], label=curr_fishtype)
ax.set_ylabel('Counts', fontsize=14)
ax.set_xlabel('Frequency [Hz]', fontsize=14)
ax.set_xticks(np.arange(0, max(np.hstack(data.values()))+100, 250))
ax.tick_params(axis='both', which='major', labelsize=12)
ax.set_title('Distribution of EOD-Frequencies', fontsize=16)
ax.legend(frameon=False, loc='best', fontsize=12)
sns.despine(fig=fig, ax=ax, offset=10)
fig.tight_layout()
fig.savefig('figures/histo_of_eod_freqs.pdf')
plt.close()
def plotLcurveall(alphaarr,datadif,constdif):
"""
This will plot the L-curve for all of the lags
"""
sns.set_style('whitegrid')
sns.set_context('notebook')
Nlag=datadif.shape[-1]
nlagplot=4.
nrows=int(sp.ceil(float(Nlag)/(2*nlagplot)))
fig ,axmat= plt.subplots(nrows=nrows,ncols=2,facecolor='w',figsize=(8,4*nrows),sharey=True)
axlist=axmat.flatten()
for iaxn,iax in enumerate(axlist):
strlist=[]
handlist=[]
for ilag in range(int(nlagplot)):
curlag=int(iaxn*nlagplot+ilag)
if curlag>=Nlag:
break
handlist.append(iax.plot(datadif[:,curlag],constdif[:,curlag])[0])
strlist.append('Lag {0}'.format(curlag))
iax.set_xscale('log')
iax.set_yscale('log')
iax.set_title('L Curve',fontsize=fs)
iax.set_xlabel(r'$\|Ax-b\|_2$',fontsize=fs)
iax.set_ylabel(r'$f(x)$',fontsize=fs)
iax.legend(handlist,strlist,loc='upper right',fontsize='large')
plt.tight_layout()
return(fig,axlist)
def program_eui():
df_eng = read_energy('good_energy')
df_pro = pd.read_csv(master_dir + 'ecm_program_tidy.csv')
programs = list(set(df_pro['ECM program'].tolist()))
dfs = []
sns.set_style("whitegrid")
sns.set_palette("Set2", 8)
sns.set_context("talk", font_scale=1.5)
bx = plt.axes()
lines = []
labels = []
programs.remove('Energy Star')
for p in programs:
buildings = df_pro[df_pro['ECM program'] == p]['Building Number'].unique()
df_temp = df_eng.copy()
df_temp = df_temp[df_temp['Building Number'].isin(buildings)]
df_temp = df_temp[['Building Number', 'Fiscal Year', 'Gross Sq.Ft', 'Total Electric + Gas']]
line = plot_eui_trend(df_temp, bx)
lines.append(line)
labels.append('{0} (n={1})'.format(p, len(df_temp['Building'
' Number'].unique())))
plt.title('Energy Program EUI Trend')
plt.ylabel(lb.ylabel_dict['eui'])
plt.xlabel('Fiscal Year')
plt.gca().set_ylim(bottom=0)
ylimit = bx.get_ylim()
plt.fill_between([2004.5, 2006.5], 0, ylimit, facecolor='gray',
alpha=0.2)
plt.legend(lines, labels, loc='center left',
bbox_to_anchor=(1, 0.5), prop={'size':13})
P.savefig(os.getcwd() + '/plot_FY_annual/program_trend.png', dpi =
300, bbox_inches='tight')
plt.close()
def deviance_curve(classifier, features, labels, metaparameter_name, param_range, metric='Accuracy',
n_folds=4, njobs=-1, fig_size=(16, 9)):
training_scores, validation_scores = validation_curve(classifier,
features, labels,
metaparameter_name,
param_range,
n_jobs=njobs,
cv=n_folds, scoring=metric)
training_scores_mean = np.mean(training_scores, axis=1)
training_scores_std = np.std(training_scores, axis=1)
validation_scores_mean = np.mean(validation_scores, axis=1)
validation_scores_std = np.std(validation_scores, axis=1)
sns.set_style("darkgrid")
sns.set_context("notebook", font_scale=1.5, rc={"lines.linewidth": 2.5})
plt.figure(num=None, figsize=fig_size, dpi=600, facecolor='w', edgecolor='k')
plt.title("Validation Curve")
plt.xlabel(metaparameter_name)
plt.ylabel(metric)
plt.xlim(np.min(param_range), np.max(param_range))
plt.plot(param_range, training_scores_mean, label="Training " + metric, color="mediumblue")
plt.fill_between(param_range, training_scores_mean - training_scores_std,
training_scores_mean + training_scores_std, alpha=0.2, color="lightskyblue")
plt.plot(param_range, validation_scores_mean, label="validation " + metric,
color="coral")
plt.fill_between(param_range, validation_scores_mean - validation_scores_std,
validation_scores_mean + validation_scores_std, alpha=0.2, color="lightcoral")
plt.legend(loc="best")
plt.show()
def plot_building_temp():
sns.set_context("paper", font_scale=1.5)
b = 'AZ0000FF'
s = 'KTUS'
filelist = glob.glob(os.getcwd() + '/csv_FY/testWeather/{0}*.csv'.format(b))
dfs = [pd.read_csv(csv) for csv in filelist]
col = 'eui_gas'
dfs2 = [df[[col, 'month', 'year']] for df in dfs]
df3 = (pd.concat(dfs2))
temp = pd.read_csv(os.getcwd() + '/csv_FY/weather/weatherData_meanTemp.csv')
temp['year'] = temp['Unnamed: 0'].map(lambda x: float(x[:4]))
temp['month'] = temp['Unnamed: 0'].map(lambda x: float(x[5:7]))
temp.set_index(pd.DatetimeIndex(temp['Unnamed: 0']), inplace=True)
temp = temp[[s, 'month', 'year']]
joint2 = pd.merge(df3, temp, on = ['year', 'month'], how = 'inner')
joint2.to_csv(os.getcwd() + '/csv_FY/testWeather/test_temp.csv', index=False)
sns.lmplot(s, col, data=joint2, col='year', fit_reg=False)
plt.xlim((joint2[s].min() - 10, joint2[s].max() + 10))
plt.ylim((0, joint2[col].max() + 0.1))
P.savefig(os.getcwd() + '/csv_FY/testWeather/plot/scatter_temp_byyear.png', dpi=150)
plt.close()
joint2 = joint2[(2012 < joint2['year']) & (joint2['year'] < 2015)]
sns.regplot(s, col, data=joint2, fit_reg=False)
plt.xlim((joint2[s].min() - 10, joint2[s].max() + 10))
plt.ylim((0, joint2[col].max() + 0.1))
P.savefig(os.getcwd() + '/csv_FY/testWeather/plot/scatter_temp_1314.png', dpi=150)
plt.close()
def plot_dfs_histogram(dfs_array, binwidth='FD'):
""" Plots a histogram of the difference frequencies
:param binwidth: select the size of the binwidth. use 'FD' for Freedman-Diaconis rule
:param dfs_array: array-like. list of difference frequencies.
"""
q75, q25 = np.percentile(abs(dfs_array), [75, 25])
inch_factor = 2.54
sns.set_context("poster")
sns.axes_style('white')
sns.set_style("ticks")
fig, ax = plt.subplots(figsize=(15./inch_factor, 10./inch_factor))
if binwidth == 'FD':
ax.hist(dfs_array, bins=int(2*(q75-q25) * len(dfs_array)**(-1./3.)),
facecolor='cornflowerblue', alpha=0.8) # Freedman-Diaconis rule for binwidth
else:
ax.hist(dfs_array, bins=binwidth, color='cornflowerblue', alpha=0.8)
# Plot Cosmetics
ax.set_ylabel('Counts', fontsize=16)
ax.set_xlabel('Possible Beat-Frequencies [Hz]', fontsize=14)
ax.tick_params(axis='both', which='major', labelsize=12)
ax.set_title('Distribution of Beat-Frequencies', fontsize=16)
sns.despine(fig=fig, ax=ax, offset=10)
fig.tight_layout()
fig.savefig('figures/histo_of_dfs.pdf')
plt.close()
def quickPlot(filename, path, datalist, xlabel="x", ylabel="y", xrange=["auto", "auto"], yrange=["auto", "auto"], yscale="linear", xscale="linear", col=["r", "b"]):
"""Plots Data to .pdf File in Plots Folder Using matplotlib"""
if "plots" not in os.listdir(path):
os.mkdir(os.path.join(path, "plots"))
coltab = col*10
seaborn.set_context("notebook", rc={"lines.linewidth": 1.0})
formatter = ScalarFormatter(useMathText=True)
formatter.set_scientific(True)
formatter.set_powerlimits((-2, 3))
fig = Figure(figsize=(6, 6))
ax = fig.add_subplot(111)
for i, ydata in enumerate(datalist[1:]):
ax.plot(datalist[0], ydata, c=coltab[i])
ax.set_title(filename)
ax.set_yscale(yscale)
ax.set_xscale(xscale)
ax.set_xlabel(xlabel)
ax.set_ylabel(ylabel)
if xrange[0] != "auto":
ax.set_xlim(xmin=xrange[0])
if xrange[1] != "auto":
ax.set_xlim(xmax=xrange[1])
if yrange[0] != "auto":
ax.set_ylim(ymin=yrange[0])
if yrange[1] != "auto":
ax.set_ylim(ymax=yrange[1])
if yscale == "linear":
ax.yaxis.set_major_formatter(formatter)
ax.xaxis.set_major_formatter(formatter)
canvas = FigureCanvasPdf(fig)
canvas.print_figure(os.path.join(path, "plots", filename+".pdf"))
return
def plot_building_temp():
sns.set_context("paper", font_scale=1.5)
b = "AZ0000FF"
s = "KTUS"
filelist = glob.glob(os.getcwd() + "/csv_FY/testWeather/{0}*.csv".format(b))
dfs = [pd.read_csv(csv) for csv in filelist]
col = "eui_gas"
dfs2 = [df[[col, "month", "year"]] for df in dfs]
df3 = pd.concat(dfs2)
temp = pd.read_csv(os.getcwd() + "/csv_FY/weather/weatherData_meanTemp.csv")
temp["year"] = temp["Unnamed: 0"].map(lambda x: float(x[:4]))
temp["month"] = temp["Unnamed: 0"].map(lambda x: float(x[5:7]))
temp.set_index(pd.DatetimeIndex(temp["Unnamed: 0"]), inplace=True)
temp = temp[[s, "month", "year"]]
joint2 = pd.merge(df3, temp, on=["year", "month"], how="inner")
joint2.to_csv(os.getcwd() + "/csv_FY/testWeather/test_temp.csv", index=False)
sns.lmplot(s, col, data=joint2, col="year", fit_reg=False)
plt.xlim((joint2[s].min() - 10, joint2[s].max() + 10))
plt.ylim((0, joint2[col].max() + 0.1))
P.savefig(os.getcwd() + "/csv_FY/testWeather/plot/scatter_temp_byyear.png", dpi=150)
plt.close()
joint2 = joint2[(2012 < joint2["year"]) & (joint2["year"] < 2015)]
sns.regplot(s, col, data=joint2, fit_reg=False)
plt.xlim((joint2[s].min() - 10, joint2[s].max() + 10))
plt.ylim((0, joint2[col].max() + 0.1))
P.savefig(os.getcwd() + "/csv_FY/testWeather/plot/scatter_temp_1314.png", dpi=150)
plt.close()
def best_model_accuracy_bars(df,fig_path,metric,context):
'''
df: data frame
context: paper,talk, notebook, poster
'''
font_size = {
'paper':8,
'poster':16,
'notebook':10,
'talk':13
}
sns.set_context(context)
model_list,score_list = identify_best_of_each_model(df,metric)
#size and position of bars
bar_pos = np.arange(len(model_list))
bar_size = score_list
bar_labels = model_list
#plot
fig = plt.figure()
plt.barh(bar_pos,bar_size, align='center', alpha=0.4)
plt.yticks(bar_pos, bar_labels)
plt.xticks([],[]) #no x-axis
#Add data labels
for x,y in zip(bar_size,bar_pos):
plt.text(x+0.01, y, '%.2f' % x, ha='left', va='center',fontsize=font_size[context])
pretty_metric = {'test_accuracy':'Test','best_score':'CV'}
plt.title('Optimized %s Accuracy of Each Model' % pretty_metric[metric])
fig.savefig(fig_path, bbox_inches='tight')
def graphMetricDistn(self,metric,normType,plotType,resiType,save):
# histogram/kde plot of density metric per atom
# plotType is 'histogram' or 'kde'
# resiType is 'all' or list of residue types
# save is Boolian to save or not
if plotType not in ('hist','kde'): return 'Unknown plotting type selected.. cannot plot..'
if self.checkMetricPresent(self.atomList[0],metric,normType) is False: return # check metric valid
sns.set_palette("deep", desat=.6)
sns.set_context(rc={"figure.figsize": (10, 6)})
fig = plt.figure()
for i in range(self.getNumDatasets()):
if resiType == 'all':
datax = [atm.densMetric[metric][normType]['values'][i] for atm in self.atomList]
self.plotHist(plotType,datax,'Dataset {}'.format(i))
else:
for res in resiType:
datax = [atm.densMetric[metric][normType]['values'][i] for atm in self.atomList if atm.basetype == res]
self.plotHist(plotType,datax,'Dataset {},{}'.format(i,res))
plt.legend()
plt.xlabel('{} D{} per atom'.format(normType,metric))
plt.ylabel('Frequency')
plt.title('{} D{} per atom, residues: {}'.format(normType,metric,resiType))
if not save:
plt.show()
else:
fig.savefig('{}{}_D{}_{}.png'.format(self.outputDir,normType,metric,resiType))
def white():
"""
Set plot aesthetics for 1D plots with white backgrounds.
The plots are set up to have
* White backgrounds
* Grey minor and major gridlines
* x and y ticks on bottom and left axes
* Thin black outer border
* Minor grid lines halfway between major ticks
"""
pal = sns.color_palette('deep')
sns.set_context('talk')
sns.set_style('whitegrid', {'axes.edgecolor':'0.1',
'legend.frameon': True,
'xtick.color': '.15',
'xtick.major.size': 5,
'xtick.minor.size': 0.0,
'xtick.direction': 'out',
'ytick.color': '.15',
'ytick.major.size': 5,
'ytick.minor.size': 0.0,
'ytick.direction': 'out',
'axes.axisbelow': True,
'axes.linewidth': 0.4,
'font.family': 'sans-serif',
'font.sans-serif': ['Helvetica', 'Arial',
'Verdana', 'sans-serif']
})
# 防止pandas输出结果省略
pd.set_option('display.max_columns', 1000)
pd.set_option('display.width', 1000)
pd.set_option('display.max_colwidth', 1000)
df = pd.read_csv("./data/HR_.csv")
df = df.dropna(axis=0, how="any")
df = df[df["last_evaluation"] <= 1][df["salary"] != "nme"][
df["department"] != "sale"]
import seaborn as sns
import matplotlib.pyplot as plt
#seaborn设置样式
sns.set_style(style="whitegrid")
sns.set_context(context="poster", font_scale=0.5)
sns.set_palette("summer")
f = plt.figure()
#subplot(numRows, numCols, plotNum)
#图表的整个绘图区域被分成 numRows 行和 numCols 列
#然后按照从左到右，从上到下的顺序对每个子区域进行编号
f.add_subplot(1, 3, 1)
#画分布图
#kde=False表示没有分布曲线，hist=False表示没有直方图
sns.distplot(df["satisfaction_level"], bins=10)
f.add_subplot(1, 3, 2)
sns.distplot(df["last_evaluation"], bins=10)
f.add_subplot(1, 3, 3)
sns.distplot(df["average_monthly_hours"], bins=10)
plt.show()
import numpy as np
import matplotlib.pyplot as pyplot
import pandas as pd
import seaborn as sns
data = pd.read_csv('browsertime.csv')
result = data
result['protocol'].replace(["HTTP1.1/TLS", "HTTP2"], ["H1s", "H2"],
inplace=True)
result["pageLoadTime"] = result["pageLoadTime"] / 1000
brs = result.browser.unique()
for br in brs:
pyplot.clf()
sns.set_context('paper')
pyplot.figure(figsize=(18, 10))
sns.set(font_scale=2.2)
#sns.set_style("white")
g = sns.boxplot(x="Ops",
y="pageLoadTime",
hue="protocol",
data=result[(result.browser == br)],
order=[
"Telia (SE)", "Telenor (SE)", "Tre (SE)",
"Telenor (NO)", "Telia (NO)", "ICE (NO)", "TIM (IT)",
"Vodafone (IT)", "Wind (IT)", "Orange (ES)",
"Yoigo (ES)"
],
hue_order=["H1s", "H2"],
palette="muted",
showfliers=False)
pyplot.xticks(rotation=10)
import re
import numpy as np
import pandas as pd
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', None)
pd.set_option('display.width', 200)
import glob
from matplotlib import pyplot as plt
from matplotlib import ticker as ticker
import seaborn as sns
sns.set_style('white', {
'axes.grid': True,
'xtick.bottom': True,
'ytick.left': True
})
sns.set_context(rc={'patch.linewidth': '0.0'})
sns.set_palette(
sns.color_palette(['#ce0e2d', '#005cb9', '#f5a800', '#45c2b1', '#035c67']))
files = sorted(glob.glob('*_coverage_hist.tsv'))
names = [i.replace('_coverage_hist.tsv', '') for i in files]
names = [i.replace('_dmarked_coverage_hist.tsv', '') for i in names]
print(names)
print('')
groups = [re.sub(r'_L.*_coverage.tsv', '', i) for i in files]
print(groups)
print('')
# colnames = ['metric1', 'TOTAL_READS', 'metric3', 'metric4', 'metric5', 'metric6', 'PCT_PF_READS_ALIGNED', 'metric8', 'metric9', 'metric10', 'metric11', 'metric12', 'PF_MISMATCH_RATE', 'PF_HQ_ERROR_RATE', 'PF_INDEL_RATE', 'metric16', 'metric17', 'metric18', 'metric19', 'metric20', 'metric21', 'metric22', 'PCT_CHIMERAS', 'PCT_ADAPTER', 'metric25', 'metric26', 'metric27']
def main():
sns.set_style('white')
sns.set_context('poster')
parser = argparse.ArgumentParser(
description='%s Parameters' % __tool_name__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-m",
"--matrix",
dest="input_filename",
default=None,
help="input file name",
metavar="FILE")
parser.add_argument("-l",
"--cell_labels",
dest="cell_label_filename",
default=None,
help="filename of cell labels")
parser.add_argument("-c",
"--cell_labels_colors",
dest="cell_label_color_filename",
default=None,
help="filename of cell label colors")
parser.add_argument(
"-s",
"--select_features",
dest="s_method",
default='LOESS',
help=
"LOESS,PCA or all: Select variable genes using LOESS or principal components using PCA or all the genes are kept"
)
parser.add_argument("--TG",
"--detect_TG_genes",
dest="flag_gene_TG_detection",
action="store_true",
help="detect transition genes automatically")
parser.add_argument("--DE",
"--detect_DE_genes",
dest="flag_gene_DE_detection",
action="store_true",
help="detect DE genes automatically")
parser.add_argument("--LG",
"--detect_LG_genes",
dest="flag_gene_LG_detection",
action="store_true",
help="detect leaf genes automatically")
parser.add_argument(
"-g",
"--genes",
dest="genes",
default=None,
help=
"genes to visualize, it can either be filename which contains all the genes in one column or a set of gene names separated by comma"
)
parser.add_argument(
"-p",
"--use_precomputed",
dest="use_precomputed",
action="store_true",
help=
"use precomputed data files without re-computing structure learning part"
)
parser.add_argument("--new",
dest="new_filename",
default=None,
help="file name of data to be mapped")
parser.add_argument("--new_l",
dest="new_label_filename",
default=None,
help="filename of new cell labels")
parser.add_argument("--new_c",
dest="new_label_color_filename",
default=None,
help="filename of new cell label colors")
parser.add_argument("--log2",
dest="flag_log2",
action="store_true",
help="perform log2 transformation")
parser.add_argument("--norm",
dest="flag_norm",
action="store_true",
help="normalize data based on library size")
parser.add_argument("--atac",
dest="flag_atac",
action="store_true",
help="indicate scATAC-seq data")
parser.add_argument(
"--n_processes",
dest="n_processes",
type=int,
default=multiprocessing.cpu_count(),
help=
"Specify the number of processes to use. (default, all the available cores)"
)
parser.add_argument(
"--loess_frac",
dest="loess_frac",
type=float,
default=0.1,
help="The fraction of the data used in LOESS regression")
parser.add_argument(
"--loess_cutoff",
dest="loess_cutoff",
type=int,
default=95,
help=
"the percentile used in variable gene selection based on LOESS regression"
)
parser.add_argument("--pca_first_PC",
dest="flag_first_PC",
action="store_true",
help="keep first PC")
parser.add_argument("--pca_n_PC",
dest="pca_n_PC",
type=int,
default=15,
help="The number of selected PCs,it's 15 by default")
parser.add_argument("--lle_neighbours",
dest="lle_n_nb_percent",
type=float,
default=0.1,
help="LLE neighbour percent ")
parser.add_argument("--lle_components",
dest="lle_n_component",
type=int,
default=3,
help="number of components for LLE space ")
parser.add_argument(
"--clustering",
dest="clustering",
default='kmeans',
help=
"Clustering method used for seeding the intial structure, choose from 'ap','kmeans','sc'"
)
parser.add_argument("--damping",
dest="damping",
type=float,
default=0.75,
help="Affinity Propagation: damping factor")
parser.add_argument(
"--n_clusters",
dest="n_clusters",
type=int,
default=10,
help="Number of clusters for spectral clustering or kmeans")
parser.add_argument("--EPG_n_nodes",
dest="EPG_n_nodes",
type=int,
default=50,
help=" Number of nodes for elastic principal graph")
parser.add_argument(
"--EPG_lambda",
dest="EPG_lambda",
type=float,
default=0.02,
help="lambda parameter used to compute the elastic energy")
parser.add_argument("--EPG_mu",
dest="EPG_mu",
type=float,
default=0.1,
help="mu parameter used to compute the elastic energy")
parser.add_argument(
"--EPG_trimmingradius",
dest="EPG_trimmingradius",
type=float,
default=np.inf,
help="maximal distance of point from a node to affect its embedment")
parser.add_argument(
"--EPG_alpha",
dest="EPG_alpha",
type=float,
default=0.02,
help=
"positive numeric, the value of the alpha parameter of the penalized elastic energy"
)
parser.add_argument("--EPG_collapse",
dest="flag_EPG_collapse",
action="store_true",
help="collapsing small branches")
parser.add_argument(
"--EPG_collapse_mode",
dest="EPG_collapse_mode",
default="PointNumber",
help=
"the mode used to collapse branches. PointNumber,PointNumber_Extrema, PointNumber_Leaves,EdgesNumber or EdgesLength"
)
parser.add_argument(
"--EPG_collapse_par",
dest="EPG_collapse_par",
type=float,
default=5,
help=
"positive numeric, the cotrol paramter used for collapsing small branches"
)
parser.add_argument("--disable_EPG_optimize",
dest="flag_disable_EPG_optimize",
action="store_true",
help="disable optimizing branching")
parser.add_argument("--EPG_shift",
dest="flag_EPG_shift",
action="store_true",
help="shift branching point ")
parser.add_argument(
"--EPG_shift_mode",
dest="EPG_shift_mode",
default='NodeDensity',
help=
"the mode to use to shift the branching points NodePoints or NodeDensity"
)
parser.add_argument(
"--EPG_shift_DR",
dest="EPG_shift_DR",
type=float,
default=0.05,
help=
"positive numeric, the radius to be used when computing point density if EPG_shift_mode is NodeDensity"
)
parser.add_argument(
"--EPG_shift_maxshift",
dest="EPG_shift_maxshift",
type=int,
default=5,
help=
"positive integer, the maxium distance (as number of edges) to consider when exploring the branching point neighborhood"
)
parser.add_argument("--disable_EPG_ext",
dest="flag_disable_EPG_ext",
action="store_true",
help="disable extending leaves with additional nodes")
parser.add_argument(
"--EPG_ext_mode",
dest="EPG_ext_mode",
default='QuantDists',
help=
" the mode used to extend the graph,QuantDists, QuantCentroid or WeigthedCentroid"
)
parser.add_argument(
"--EPG_ext_par",
dest="EPG_ext_par",
type=float,
default=0.5,
help=
"the control parameter used for contribution of the different data points when extending leaves with nodes"
)
parser.add_argument("--DE_zscore_cutoff",
dest="DE_zscore_cutoff",
default=2,
help="Differentially Expressed Genes z-score cutoff")
parser.add_argument(
"--DE_logfc_cutoff",
dest="DE_logfc_cutoff",
default=0.25,
help="Differentially Expressed Genes log fold change cutoff")
parser.add_argument("--TG_spearman_cutoff",
dest="TG_spearman_cutoff",
default=0.4,
help="Transition Genes Spearman correlation cutoff")
parser.add_argument("--TG_logfc_cutoff",
dest="TG_logfc_cutoff",
default=0.25,
help="Transition Genes log fold change cutoff")
parser.add_argument("--LG_zscore_cutoff",
dest="LG_zscore_cutoff",
default=1.5,
help="Leaf Genes z-score cutoff")
parser.add_argument("--LG_pvalue_cutoff",
dest="LG_pvalue_cutoff",
default=1e-2,
help="Leaf Genes p value cutoff")
parser.add_argument(
"--umap",
dest="flag_umap",
action="store_true",
help="whether to use UMAP for visualization (default: No)")
parser.add_argument("-r",
dest="root",
default=None,
help="root node for subwaymap_plot and stream_plot")
parser.add_argument("--stream_log_view",
dest="flag_stream_log_view",
action="store_true",
help="use log2 scale for y axis of stream_plot")
parser.add_argument("-o",
"--output_folder",
dest="output_folder",
default=None,
help="Output folder")
parser.add_argument("--for_web",
dest="flag_web",
action="store_true",
help="Output files for website")
parser.add_argument(
"--n_genes",
dest="n_genes",
type=int,
default=5,
help=
"Number of top genes selected from each output marker gene file for website gene visualization"
)
args = parser.parse_args()
if (args.input_filename is None) and (args.new_filename is None):
parser.error("at least one of -m, --new required")
new_filename = args.new_filename
new_label_filename = args.new_label_filename
new_label_color_filename = args.new_label_color_filename
flag_stream_log_view = args.flag_stream_log_view
flag_gene_TG_detection = args.flag_gene_TG_detection
flag_gene_DE_detection = args.flag_gene_DE_detection
flag_gene_LG_detection = args.flag_gene_LG_detection
flag_web = args.flag_web
flag_first_PC = args.flag_first_PC
flag_umap = args.flag_umap
genes = args.genes
DE_zscore_cutoff = args.DE_zscore_cutoff
DE_logfc_cutoff = args.DE_logfc_cutoff
TG_spearman_cutoff = args.TG_spearman_cutoff
TG_logfc_cutoff = args.TG_logfc_cutoff
LG_zscore_cutoff = args.LG_zscore_cutoff
LG_pvalue_cutoff = args.LG_pvalue_cutoff
root = args.root
input_filename = args.input_filename
cell_label_filename = args.cell_label_filename
cell_label_color_filename = args.cell_label_color_filename
s_method = args.s_method
use_precomputed = args.use_precomputed
n_processes = args.n_processes
loess_frac = args.loess_frac
loess_cutoff = args.loess_cutoff
pca_n_PC = args.pca_n_PC
flag_log2 = args.flag_log2
flag_norm = args.flag_norm
flag_atac = args.flag_atac
lle_n_nb_percent = args.lle_n_nb_percent #LLE neighbour percent
lle_n_component = args.lle_n_component #LLE dimension reduction
clustering = args.clustering
damping = args.damping
n_clusters = args.n_clusters
EPG_n_nodes = args.EPG_n_nodes
EPG_lambda = args.EPG_lambda
EPG_mu = args.EPG_mu
EPG_trimmingradius = args.EPG_trimmingradius
EPG_alpha = args.EPG_alpha
flag_EPG_collapse = args.flag_EPG_collapse
EPG_collapse_mode = args.EPG_collapse_mode
EPG_collapse_par = args.EPG_collapse_par
flag_EPG_shift = args.flag_EPG_shift
EPG_shift_mode = args.EPG_shift_mode
EPG_shift_DR = args.EPG_shift_DR
EPG_shift_maxshift = args.EPG_shift_maxshift
flag_disable_EPG_optimize = args.flag_disable_EPG_optimize
flag_disable_EPG_ext = args.flag_disable_EPG_ext
EPG_ext_mode = args.EPG_ext_mode
EPG_ext_par = args.EPG_ext_par
output_folder = args.output_folder #work directory
n_genes = args.n_genes
if (flag_web):
flag_savefig = False
else:
flag_savefig = True
gene_list = []
if (genes != None):
if (os.path.exists(genes)):
gene_list = pd.read_csv(genes,
sep='\t',
header=None,
index_col=None,
compression='gzip' if genes.split('.')[-1]
== 'gz' else None).iloc[:, 0].tolist()
gene_list = list(set(gene_list))
else:
gene_list = genes.split(',')
print('Genes to visualize: ')
print(gene_list)
if (new_filename is None):
if (output_folder == None):
workdir = os.path.join(os.getcwd(), 'stream_result')
else:
workdir = output_folder
if (use_precomputed):
print('Importing the precomputed pkl file...')
adata = st.read(file_name='stream_result.pkl',
file_format='pkl',
file_path=workdir,
workdir=workdir)
else:
if (flag_atac):
print('Reading in atac zscore matrix...')
adata = st.read(file_name=input_filename,
workdir=workdir,
experiment='atac-seq')
else:
adata = st.read(file_name=input_filename, workdir=workdir)
print('Input: ' + str(adata.obs.shape[0]) + ' cells, ' +
str(adata.var.shape[0]) + ' genes')
adata.var_names_make_unique()
adata.obs_names_make_unique()
if (cell_label_filename != None):
st.add_cell_labels(adata, file_name=cell_label_filename)
else:
st.add_cell_labels(adata)
if (cell_label_color_filename != None):
st.add_cell_colors(adata, file_name=cell_label_color_filename)
else:
st.add_cell_colors(adata)
if (flag_atac):
print('Selecting top principal components...')
st.select_top_principal_components(adata,
n_pc=pca_n_PC,
first_pc=flag_first_PC,
save_fig=True)
st.dimension_reduction(adata,
n_components=lle_n_component,
nb_pct=lle_n_nb_percent,
n_jobs=n_processes,
feature='top_pcs')
else:
if (flag_norm):
st.normalize_per_cell(adata)
if (flag_log2):
st.log_transform(adata)
if (s_method != 'all'):
print('Filtering genes...')
st.filter_genes(adata, min_num_cells=5)
print('Removing mitochondrial genes...')
st.remove_mt_genes(adata)
if (s_method == 'LOESS'):
print('Selecting most variable genes...')
st.select_variable_genes(adata,
loess_frac=loess_frac,
percentile=loess_cutoff,
save_fig=True)
pd.DataFrame(adata.uns['var_genes']).to_csv(
os.path.join(workdir,
'selected_variable_genes.tsv'),
sep='\t',
index=None,
header=False)
st.dimension_reduction(adata,
n_components=lle_n_component,
nb_pct=lle_n_nb_percent,
n_jobs=n_processes,
feature='var_genes')
if (s_method == 'PCA'):
print('Selecting top principal components...')
st.select_top_principal_components(
adata,
n_pc=pca_n_PC,
first_pc=flag_first_PC,
save_fig=True)
st.dimension_reduction(adata,
n_components=lle_n_component,
nb_pct=lle_n_nb_percent,
n_jobs=n_processes,
feature='top_pcs')
else:
print('Keep all the genes...')
st.dimension_reduction(adata,
n_components=lle_n_component,
nb_pct=lle_n_nb_percent,
n_jobs=n_processes,
feature='all')
st.plot_dimension_reduction(adata, save_fig=flag_savefig)
st.seed_elastic_principal_graph(adata,
clustering=clustering,
damping=damping,
n_clusters=n_clusters)
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='seed_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='seed_elastic_principal_graph.pdf')
st.elastic_principal_graph(adata,
epg_n_nodes=EPG_n_nodes,
epg_lambda=EPG_lambda,
epg_mu=EPG_mu,
epg_trimmingradius=EPG_trimmingradius,
epg_alpha=EPG_alpha)
st.plot_branches(adata,
save_fig=flag_savefig,
fig_name='elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(adata,
save_fig=flag_savefig,
fig_name='elastic_principal_graph.pdf')
if (not flag_disable_EPG_optimize):
st.optimize_branching(adata,
epg_trimmingradius=EPG_trimmingradius)
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='optimizing_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='optimizing_elastic_principal_graph.pdf')
if (flag_EPG_shift):
st.shift_branching(adata,
epg_shift_mode=EPG_shift_mode,
epg_shift_radius=EPG_shift_DR,
epg_shift_max=EPG_shift_maxshift,
epg_trimmingradius=EPG_trimmingradius)
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='shifting_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='shifting_elastic_principal_graph.pdf')
if (flag_EPG_collapse):
st.prune_elastic_principal_graph(
adata,
epg_collapse_mode=EPG_collapse_mode,
epg_collapse_par=EPG_collapse_par,
epg_trimmingradius=EPG_trimmingradius)
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='pruning_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='pruning_elastic_principal_graph.pdf')
if (not flag_disable_EPG_ext):
st.extend_elastic_principal_graph(
adata,
epg_ext_mode=EPG_ext_mode,
epg_ext_par=EPG_ext_par,
epg_trimmingradius=EPG_trimmingradius)
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='extending_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='extending_elastic_principal_graph.pdf')
st.plot_branches(
adata,
save_fig=flag_savefig,
fig_name='finalized_elastic_principal_graph_skeleton.pdf')
st.plot_branches_with_cells(
adata,
save_fig=flag_savefig,
fig_name='finalized_elastic_principal_graph.pdf')
st.plot_flat_tree(adata, save_fig=flag_savefig)
if (flag_umap):
print('UMAP visualization based on top MLLE components...')
st.plot_visualization_2D(adata,
save_fig=flag_savefig,
fig_name='umap_cells')
st.plot_visualization_2D(adata,
color_by='branch',
save_fig=flag_savefig,
fig_name='umap_branches')
if (root is None):
print('Visualization of subwaymap and stream plots...')
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
for ns in list_node_start:
if (flag_web):
st.subwaymap_plot(adata,
percentile_dist=100,
root=ns,
save_fig=flag_savefig)
st.stream_plot(adata,
root=ns,
fig_size=(8, 8),
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_legend=False,
fig_name='stream_plot.png')
else:
st.subwaymap_plot(adata,
percentile_dist=100,
root=ns,
save_fig=flag_savefig)
st.stream_plot(adata,
root=ns,
fig_size=(8, 8),
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
else:
st.subwaymap_plot(adata,
percentile_dist=100,
root=root,
save_fig=flag_savefig)
st.stream_plot(adata,
root=root,
fig_size=(8, 8),
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
output_cell_info(adata)
if (flag_web):
output_for_website(adata)
st.write(adata)
if (flag_gene_TG_detection):
print('Identifying transition genes...')
st.detect_transistion_genes(adata,
cutoff_spearman=TG_spearman_cutoff,
cutoff_logfc=TG_logfc_cutoff,
n_jobs=n_processes)
if (flag_web):
## Plot top5 genes
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
gene_list = []
for x in adata.uns['transition_genes'].keys():
gene_list = gene_list + adata.uns['transition_genes'][
x].index[:n_genes].tolist()
gene_list = np.unique(gene_list)
for ns in list_node_start:
output_for_website_subwaymap_gene(adata, gene_list)
st.stream_plot_gene(adata,
root=ns,
fig_size=(8, 8),
genes=gene_list,
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_format='png')
else:
st.plot_transition_genes(adata, save_fig=flag_savefig)
if (flag_gene_DE_detection):
print('Identifying differentially expressed genes...')
st.detect_de_genes(adata,
cutoff_zscore=DE_logfc_cutoff,
cutoff_logfc=DE_logfc_cutoff,
n_jobs=n_processes)
if (flag_web):
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
gene_list = []
for x in adata.uns['de_genes_greater'].keys():
gene_list = gene_list + adata.uns['de_genes_greater'][
x].index[:n_genes].tolist()
for x in adata.uns['de_genes_less'].keys():
gene_list = gene_list + adata.uns['de_genes_less'][
x].index[:n_genes].tolist()
gene_list = np.unique(gene_list)
for ns in list_node_start:
output_for_website_subwaymap_gene(adata, gene_list)
st.stream_plot_gene(adata,
root=ns,
fig_size=(8, 8),
genes=gene_list,
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_format='png')
else:
st.plot_de_genes(adata, save_fig=flag_savefig)
if (flag_gene_LG_detection):
print('Identifying leaf genes...')
st.detect_leaf_genes(adata,
cutoff_zscore=LG_zscore_cutoff,
cutoff_pvalue=LG_pvalue_cutoff,
n_jobs=n_processes)
if (flag_web):
## Plot top5 genes
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
gene_list = []
for x in adata.uns['leaf_genes'].keys():
gene_list = gene_list + adata.uns['leaf_genes'][
x].index[:n_genes].tolist()
gene_list = np.unique(gene_list)
for ns in list_node_start:
output_for_website_subwaymap_gene(adata, gene_list)
st.stream_plot_gene(adata,
root=ns,
fig_size=(8, 8),
genes=gene_list,
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_format='png')
if ((genes != None) and (len(gene_list) > 0)):
print('Visualizing genes...')
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
if (root is None):
for ns in list_node_start:
if (flag_web):
output_for_website_subwaymap_gene(adata, gene_list)
st.stream_plot_gene(adata,
root=ns,
fig_size=(8, 8),
genes=gene_list,
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_format='png')
else:
st.subwaymap_plot_gene(adata,
percentile_dist=100,
root=ns,
genes=gene_list,
save_fig=flag_savefig)
st.stream_plot_gene(adata,
root=ns,
fig_size=(8, 8),
genes=gene_list,
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
else:
if (flag_web):
output_for_website_subwaymap_gene(adata, gene_list)
st.stream_plot_gene(adata,
root=root,
fig_size=(8, 8),
genes=gene_list,
save_fig=True,
flag_log_view=flag_stream_log_view,
fig_format='png')
else:
st.subwaymap_plot_gene(adata,
percentile_dist=100,
root=root,
genes=gene_list,
save_fig=flag_savefig)
st.stream_plot_gene(adata,
root=root,
fig_size=(8, 8),
genes=gene_list,
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
else:
print('Starting mapping procedure...')
if (output_folder == None):
workdir_ref = os.path.join(os.getcwd(), 'stream_result')
else:
workdir_ref = output_folder
adata = st.read(file_name='stream_result.pkl',
file_format='pkl',
file_path=workdir_ref,
workdir=workdir_ref)
workdir = os.path.join(workdir_ref, os.pardir, 'mapping_result')
adata_new = st.read(file_name=new_filename, workdir=workdir)
st.add_cell_labels(adata_new, file_name=new_label_filename)
st.add_cell_colors(adata_new, file_name=new_label_color_filename)
if (s_method == 'LOESS'):
st.map_new_data(adata, adata_new, feature='var_genes')
if (s_method == 'all'):
st.map_new_data(adata, adata_new, feature='all')
if (flag_umap):
st.plot_visualization_2D(adata,
adata_new=adata_new,
use_precomputed=False,
save_fig=flag_savefig,
fig_name='umap_new_cells')
st.plot_visualization_2D(adata,
adata_new=adata_new,
show_all_colors=True,
save_fig=flag_savefig,
fig_name='umap_all_cells')
st.plot_visualization_2D(adata,
adata_new=adata_new,
color_by='branch',
save_fig=flag_savefig,
fig_name='umap_branches')
if (root is None):
flat_tree = adata.uns['flat_tree']
list_node_start = [
value for key, value in nx.get_node_attributes(
flat_tree, 'label').items()
]
for ns in list_node_start:
st.subwaymap_plot(adata,
adata_new=adata_new,
percentile_dist=100,
show_all_cells=False,
root=ns,
save_fig=flag_savefig)
st.stream_plot(adata,
adata_new=adata_new,
show_all_colors=False,
root=ns,
fig_size=(8, 8),
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
else:
st.subwaymap_plot(adata,
adata_new=adata_new,
percentile_dist=100,
show_all_cells=False,
root=root,
save_fig=flag_savefig)
st.stream_plot(adata,
adata_new=adata_new,
show_all_colors=False,
root=root,
fig_size=(8, 8),
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
if ((genes != None) and (len(gene_list) > 0)):
if (root is None):
for ns in list_node_start:
st.subwaymap_plot_gene(adata,
adata_new=adata_new,
percentile_dist=100,
root=ns,
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
else:
st.subwaymap_plot_gene(adata,
adata_new=adata_new,
percentile_dist=100,
root=root,
save_fig=flag_savefig,
flag_log_view=flag_stream_log_view)
st.write(adata_new, file_name='stream_mapping_result.pkl')
print('Finished computation.')
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import math, copy, time
from torch.autograd import Variable
import matplotlib.pyplot as plt
import seaborn
seaborn.set_context(context="talk")
class Batch:
"Object for holding a batch of data with mask during training."
def __init__(self, src, trg=None, pad=0):
self.src = src
self.src_mask = (src != pad).unsqueeze(-2)
if trg is not None:
self.trg = trg[:, :-1]
self.trg_y = trg[:, 1:]
self.trg_mask = self.make_std_mask(self.trg, pad)
self.ntokens = (self.trg_y != pad).data.sum()
@staticmethod
def make_std_mask(tgt, pad):
"Create a mask to hide padding and future words."
tgt_mask = (tgt != pad).unsqueeze(-2)
tgt_mask = tgt_mask & Variable(
subsequent_mask(tgt.size(-1)).type_as(tgt_mask.data))
return tgt_mask
"""
Created on Fri May 8 16:30:26 2020
@author: kevin
"""
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import seaborn as sns
color_names = ["windows blue", "red", "amber", "faded green"]
colors = sns.xkcd_palette(color_names)
sns.set_style("white")
sns.set_context("talk")
# %% functions
def Threshold(u, D, mu, vv):
"""
Spiking threshold
"""
output_dim, N = D.shape
ss = np.zeros(N)
Di = np.linalg.norm(D, axis=0)**2
Ti = 0.5 * (Di + mu + vv) #threshold
ss[np.where(u > Ti)[0]] = 1
return ss
import os
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import numpy as np
from cycler import cycler
# Set seaborn to override matplotlib for plot output
sns.set()
sns.set_style("white")
# The four preset contexts, in order of relative size, are paper, notebook, talk, and poster.
# The notebook style is the default
sns.set_context("poster", font_scale=1.1)
def importfromjson(path, name):
filename = os.path.join(path, name + '.json')
importeddata = pd.read_json(filename)
return importeddata
def plotkde(df, directory, name, plotextension, grouparg, plotarg):
print 'Plotting kde of %s' % plotarg
# Create a saving name format/directory
savedir = os.path.join(directory, 'Plots')
if not os.path.exists(savedir):
os.makedirs(savedir)
# Plot and save figures
savename = os.path.join(savedir, name + plotarg + plotextension)
def visualize_perf_against_hparam(
hparam_list: List[float],
hparam_name: str,
args_or_args_list,
num_total_runs: int,
tasks=None,
plot_individual=True,
plot_ablation=False,
xlabel=None,
ylabel=None,
use_log_x=True,
):
if type(args_or_args_list) is not list:
args_list = [args_or_args_list]
else:
args_list = args_or_args_list
tasks = tasks or ["node", "link"]
# task: node or link
# dataset: cora, citeseer, pubmed, ppi
# model: go, dp
model_data_task_to_mean_list = dict()
model_data_task_to_std_list = dict()
for args in args_list:
custom_key_prefix = "perf_against_{}".format(hparam_name)
args_key = get_args_key(args)
custom_key = "{}_{}".format(custom_key_prefix, args_key)
task_to_mean_list, task_to_std_list = get_task_to_mean_and_std_per_against_hparam(
hparam_list=hparam_list,
hparam_name=hparam_name,
args=args,
num_total_runs=num_total_runs,
tasks=tasks,
)
for task_tuple, mean_list in task_to_mean_list.items():
task = task_tuple[0]
std_list = task_to_std_list[task_tuple]
model_data_task_to_mean_list[(args.m, args.dataset_name,
task)] = mean_list
model_data_task_to_std_list[(args.m, args.dataset_name,
task)] = std_list
if plot_individual and not plot_ablation:
plot_line_with_std(
tuple_to_mean_list=task_to_mean_list,
tuple_to_std_list=task_to_std_list,
x_label=xlabel or "Mixing Coefficient (Log)",
y_label=ylabel or "Test Perf. ({}., AUC)".format(
"Acc" if args_or_args_list.dataset_name != "PPI" else "F1"
),
name_label_list=["Task"],
x_list=[float(np.log10(al))
for al in hparam_list] if use_log_x else hparam_list,
hue="Task",
style="Task",
hue_order=[t.capitalize() for t in tasks],
x_lim=(None, None),
err_style="band",
custom_key=custom_key,
extension="png",
)
elif plot_individual and plot_ablation:
sns.set_context("poster")
plot_line_with_std(
tuple_to_mean_list=task_to_mean_list,
tuple_to_std_list=task_to_std_list,
x_label=xlabel + f" ({args.dataset_name})"
or "Mixing Coefficient (Log)",
y_label=ylabel or "Test Perf.",
name_label_list=["Task"],
x_list=[float(np.log10(al))
for al in hparam_list] if use_log_x else hparam_list,
hue="Task",
style="Task",
aspect=1.5,
legend=False,
err_style="band",
custom_key="ablation_against_{}_{}".format(
hparam_name, custom_key),
extension="pdf",
)
if not plot_individual and not plot_ablation:
plot_line_with_std(
tuple_to_mean_list=model_data_task_to_mean_list,
tuple_to_std_list=model_data_task_to_std_list,
x_label=xlabel or "Mixing Coefficient (Log)",
y_label=ylabel or "Test Perf.",
name_label_list=["GAT", "Dataset", "Task"],
x_list=[float(np.log10(al))
for al in hparam_list] if use_log_x else hparam_list,
hue="Dataset",
style="Dataset",
row="Task",
col="GAT",
hue_order=["Cora", "CiteSeer", "PubMed", "PPI"],
aspect=1.6,
err_style="band",
custom_key="perf_against_{}_real_world_datasets".format(
hparam_name),
extension="pdf",
)
mt_data_to_mean_list = {
(s_join(" & ", [m, t]), d): ml
for (m, d, t), ml in model_data_task_to_mean_list.items()
}
mt_data_to_std_list = {
(s_join(" & ", [m, t]), d): sl
for (m, d, t), sl in model_data_task_to_std_list.items()
}
sns.set_context("poster", font_scale=1.2)
plot_line_with_std(
tuple_to_mean_list=mt_data_to_mean_list,
tuple_to_std_list=mt_data_to_std_list,
x_label=xlabel or "Mixing Coeff. (Log)",
y_label=ylabel or "Test Perf.",
name_label_list=["GAT & Task", "Dataset"],
x_list=[float(np.log10(al))
for al in hparam_list] if use_log_x else hparam_list,
hue="GAT & Task",
palette=["darkred", "red", "dimgrey", "silver"],
style="GAT & Task",
col="Dataset",
hue_order=["GO & Link", "DP & Link", "GO & Node", "DP & Node"],
aspect=1.0,
err_style="band",
custom_key="perf_against_{}_real_world_datasets".format(
hparam_name),
extension="pdf",
)
tf.set_random_seed(20130810)
# In[8]:
import matplotlib.pyplot as plt
import seaborn as sns
# In[9]:
get_ipython().magic('matplotlib inline')
sns.set_style('ticks', {'grid_color' : '0.9'})
sns.set_context('talk', font_scale=1.2)
sns.set_palette('gray')
# In[10]:
from keras.models import Sequential, load_model
from keras.layers import Dense, Activation, Dropout
from keras.losses import binary_crossentropy
from keras.optimizers import RMSprop, Adam
from keras.metrics import binary_accuracy
colors = colors.reshape(colors.shape[0] * colors.shape[1], 3) / 255.0
# Generate a distance matrix
D = squareform(pdist(colors))
# Compute metric MDS (embedding into a 2-dimensional space)
X = pymathtoolbox.compute_classical_mds(D=D, dim=2)
# Define constants for plot
FIG_SIZE = (8, 3)
IMAGE_FORMAT = "png"
DPI = 200
# Set style
sns.set()
sns.set_context()
plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"]
# Draw plot
fig = plt.figure(figsize=FIG_SIZE, dpi=DPI)
ax = fig.add_subplot(1, 2, 1)
ax.set_title("Target Image")
ax.set_xticklabels([])
ax.set_yticklabels([])
ax.set_xticks([])
ax.set_yticks([])
ax.imshow(image)
ax = fig.add_subplot(1, 2, 2)
ax.set_title("Pixel Colors Embedded into a 2D Space")
def plot_logs(experiments: List[Summary],
smooth_factor: float = 0,
share_legend: bool = True,
ignore_metrics: Optional[Set[str]] = None,
pretty_names: bool = False,
include_metrics: Optional[Set[str]] = None) -> plt.Figure:
"""A function which will plot experiment histories for comparison viewing / analysis.
Args:
experiments: Experiment(s) to plot.
smooth_factor: A non-negative float representing the magnitude of gaussian smoothing to apply (zero for none).
share_legend: Whether to have one legend across all graphs (True) or one legend per graph (False).
pretty_names: Whether to modify the metric names in graph titles (True) or leave them alone (False).
ignore_metrics: Any keys to ignore during plotting.
include_metrics: A whitelist of keys to include during plotting. If None then all will be included.
Returns:
The handle of the pyplot figure.
"""
experiments = to_list(experiments)
n_experiments = len(experiments)
if n_experiments == 0:
return plt.subplots(111)[0]
ignore_keys = ignore_metrics or set()
ignore_keys = to_set(ignore_keys)
ignore_keys |= {'epoch'}
include_keys = to_set(include_metrics)
# TODO: epoch should be indicated on the axis (top x axis?). Problem - different epochs per experiment.
# TODO: figure out how ignore_metrics should interact with mode
metric_histories = defaultdict(_MetricGroup) # metric: MetricGroup
for idx, experiment in enumerate(experiments):
history = experiment.history
# Since python dicts remember insertion order, sort the history so that train mode is always plotted on bottom
for mode, metrics in sorted(history.items(),
key=lambda x: 0 if x[0] == 'train' else 1
if x[0] == 'eval' else 2
if x[0] == 'test' else 3
if x[0] == 'infer' else 4):
for metric, step_val in metrics.items():
if len(step_val) == 0:
continue # Ignore empty metrics
if metric in ignore_keys:
continue
if include_keys and metric not in include_keys:
continue
metric_histories[metric].add(idx, mode, step_val)
metric_list = list(sorted(metric_histories.keys()))
if len(metric_list) == 0:
return plt.subplots(111)[0]
# If sharing legend and there is more than 1 plot, then dedicate 1 subplot for the legend
share_legend = share_legend and (len(metric_list) > 1)
n_plots = len(metric_list) + share_legend
# map the metrics into an n x n grid, then remove any extra columns. Final grid will be n x m with m <= n
n_rows = math.ceil(math.sqrt(n_plots))
n_cols = math.ceil(n_plots / n_rows)
metric_grid_location = {}
nd1_metrics = []
idx = 0
for metric in metric_list:
if metric_histories[metric].ndim() == 1:
# Delay placement of the 1D plots until the end
nd1_metrics.append(metric)
else:
metric_grid_location[metric] = (idx // n_cols, idx % n_cols)
idx += 1
for metric in nd1_metrics:
metric_grid_location[metric] = (idx // n_cols, idx % n_cols)
idx += 1
sns.set_context('paper')
fig, axs = plt.subplots(n_rows,
n_cols,
sharex='all',
figsize=(4 * n_cols, 2.8 * n_rows))
# If only one row, need to re-format the axs object for consistency. Likewise for columns
if n_rows == 1:
axs = [axs]
if n_cols == 1:
axs = [axs]
for metric in metric_grid_location.keys():
axis = axs[metric_grid_location[metric][0]][
metric_grid_location[metric][1]]
if metric_histories[metric].ndim() == 1:
axis.grid(linestyle='')
else:
axis.grid(linestyle='--')
axis.ticklabel_format(axis='y', style='sci', scilimits=(-2, 3))
axis.set_title(
metric if not pretty_names else prettify_metric_name(metric),
fontweight='bold')
axis.spines['top'].set_visible(False)
axis.spines['right'].set_visible(False)
axis.spines['bottom'].set_visible(False)
axis.spines['left'].set_visible(False)
axis.tick_params(bottom=False, left=False)
for i in range(n_cols):
axs[n_rows - 1][i].set_xlabel('Steps')
# some of the columns in the last row might be unused, so disable them
last_column_idx = n_cols - (n_rows * n_cols - (n_plots - share_legend)) - 1
for i in range(last_column_idx + 1, n_cols):
axs[n_rows - 1][i].axis('off')
axs[n_rows - 2][i].set_xlabel('Steps')
axs[n_rows - 2][i].xaxis.set_tick_params(which='both',
labelbottom=True)
# the 1D metrics don't need x axis, so move them up, starting with the last in case multiple rows of them
for metric in reversed(nd1_metrics):
row = metric_grid_location[metric][0]
col = metric_grid_location[metric][1]
axs[row][col].axis('off')
if row > 0:
axs[row - 1][col].set_xlabel('Steps')
axs[row - 1][col].xaxis.set_tick_params(which='both',
labelbottom=True)
colors = sns.hls_palette(
n_colors=n_experiments,
s=0.95) if n_experiments > 10 else sns.color_palette("colorblind")
color_offset = defaultdict(lambda: 0)
# If there is only 1 experiment, we will use alternate colors based on mode
if n_experiments == 1:
color_offset['eval'] = 1
color_offset['test'] = 2
color_offset['infer'] = 3
handles = []
labels = []
has_label = defaultdict(lambda: defaultdict(lambda: defaultdict(
lambda: False))) # exp_id : {mode: {type: True}}
ax_text = defaultdict(lambda:
(0.0, 0.9)) # Where to put the text on a given axis
for exp_idx, experiment in enumerate(experiments):
for metric, group in metric_histories.items():
axis = axs[metric_grid_location[metric][0]][
metric_grid_location[metric][1]]
if group.ndim() == 1:
# Single value
for mode in group.modes(exp_idx):
ax_id = id(axis)
prefix = f"{experiment.name} ({mode})" if n_experiments > 1 else f"{mode}"
axis.text(ax_text[ax_id][0],
ax_text[ax_id][1],
f"{prefix}: {group.get_val(exp_idx, mode)}",
color=colors[exp_idx + color_offset[mode]],
transform=axis.transAxes)
ax_text[ax_id] = (ax_text[ax_id][0],
ax_text[ax_id][1] - 0.1)
if ax_text[ax_id][1] < 0:
ax_text[ax_id] = (ax_text[ax_id][0] + 0.5, 0.9)
elif group.ndim() == 2:
for mode, data in group[exp_idx].items():
title = f"{experiment.name} ({mode})" if n_experiments > 1 else f"{mode}"
if data.shape[0] < 2:
# This particular mode only has a single data point, so need to draw a shape instead of a line
xy = (data[0][0], data[0][1])
if mode == 'train':
style = MarkerStyle(marker='o', fillstyle='full')
elif mode == 'eval':
style = MarkerStyle(marker='v', fillstyle='full')
elif mode == 'test':
style = MarkerStyle(marker='*', fillstyle='full')
else:
style = MarkerStyle(marker='s', fillstyle='full')
s = axis.scatter(
xy[0],
xy[1],
s=40,
c=[colors[exp_idx + color_offset[mode]]],
marker=style,
linewidth=1.0,
edgecolors='black',
zorder=3
) # zorder to put markers on top of line segments
if not has_label[exp_idx][mode]['patch']:
labels.append(title)
handles.append(s)
has_label[exp_idx][mode]['patch'] = True
else:
# We can draw a line
y = data[:,
1] if smooth_factor == 0 else gaussian_filter1d(
data[:, 1], sigma=smooth_factor)
ln = axis.plot(
data[:, 0],
y,
color=colors[exp_idx + color_offset[mode]],
label=title,
linewidth=1.5,
linestyle='solid'
if mode == 'train' else 'dashed' if mode == 'eval'
else 'dotted' if mode == 'test' else 'dashdot')
if not has_label[exp_idx][mode]['line']:
labels.append(title)
handles.append(ln[0])
has_label[exp_idx][mode]['line'] = True
else:
# Some kind of image or matrix. Not implemented yet.
pass
plt.tight_layout()
if labels:
if share_legend:
axs[n_rows - 1][last_column_idx + 1].legend(
handles,
labels,
loc='center',
fontsize='large' if len(handles) <= 6 else
'medium' if len(handles) <= 8 else 'small')
else:
for i in range(n_rows):
for j in range(n_cols):
if i == n_rows - 1 and j > last_column_idx:
break
axs[i][j].legend(loc='best', fontsize='small')
return fig
N_iter = 1000000
lr_l = list(range(N_iter))
for i in range(N_iter):
scheduler.step()
current_lr = optimizer.param_groups[0]["lr"]
lr_l[i] = current_lr
import matplotlib as mpl # type: ignore
from matplotlib import pyplot as plt
import matplotlib.ticker as mtick # type: ignore
mpl.style.use("default")
import seaborn # type: ignore
seaborn.set(style="whitegrid")
seaborn.set_context("paper")
plt.figure(1)
plt.subplot(111)
plt.ticklabel_format(style="sci", axis="x", scilimits=(0, 0))
plt.title("Title", fontsize=16, color="k")
plt.plot(list(range(N_iter)),
lr_l,
linewidth=1.5,
label="learning rate scheme")
legend = plt.legend(loc="upper right", shadow=False)
ax = plt.gca()
labels = ax.get_xticks().tolist()
for k, v in enumerate(labels):
labels[k] = str(int(v / 1000)) + "K"
ax.set_xticklabels(labels)
#!/usr/bin/env python
import argparse
import logging
import sys
from subprocess import DEVNULL, run
import matplotlib
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import numpy as np
from matplotlib.backends.backend_pdf import PdfPages
from scipy.stats import ttest_ind
sns.set(style="whitegrid")
sns.set_context("paper", font_scale=2.0, rc={"lines.linewidth": 2.25})
# Configure logging
logging.basicConfig(
stream=sys.stdout,
format="[%(asctime)s][%(levelname)s] %(name)s:%(lineno)s - %(message)s",
level=logging.INFO,
)
logger = logging.getLogger(__name__)
FIGSIZE = (7, 6)
def ttests(a, b, c):
res = ttest_ind(a, b)
logger.info(f"A vs. B: {res}")
data = pd.DataFrame({
'Time': time,
'Direction': direction,
'NumAtoms': length
})
data.to_pickle(output_filename)
if __name__ == '__main__':
test_length(interval=(100, 100, 3000),
output_filename='Data/RMSDTime.pkl',
num_measurements=10)
data = pd.read_pickle('Data/RMSDTime.pkl')
sea.set_style("whitegrid")
sea.set_context("paper", font_scale=1.5, rc={"lines.linewidth": 1.5})
g1 = sea.relplot(x="NumAtoms",
y="Time",
hue='Direction',
kind="line",
style="Direction",
height=6,
aspect=1.3,
markers=True,
data=data)
plt.ylabel("Time, ms")
plt.xlabel("Number of atoms")
sea.despine()
# plt.show()
plt.savefig("Fig/RMSDTime.png")
#!/usr/bin/env python
# coding: utf-8
import os
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from matplotlib import cm
import matplotlib.artist as martist
from matplotlib.offsetbox import AnchoredText
import seaborn as sns
sns.set_style('whitegrid')
sns.set_context("paper")
os.chdir('/Users/pauline/Documents/Python')
df = pd.read_csv("Tab-Bathy.csv")
fig, axes = plt.subplots(6, 1, figsize=(12,14), sharex=True, sharey=False, dpi=300)
plt.suptitle('Geomorphology of the Mariana Trench: cross-section of the 25 bathymetric profiles',
x=0.54, y=.95, fontsize=12)
def add_at(axes, t, loc=2):
fp = dict(size=11)
_at = AnchoredText(t, loc=loc, prop=fp)
axes.add_artist(_at)
return _at
# subplot 1
fig = df.plot(x='observ', y=['profile1', 'profile2', 'profile3', 'profile4', 'profile5'],
linestyle='-', linewidth='.8', cmap=cm.Set1, ax=axes[0])
axes[0].legend(loc='upper right', bbox_to_anchor=(1.12, 1.1),
from __future__ import absolute_import, division, print_function
from copy import deepcopy
import json
import glob
import os
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
sns.set_style('white')
sns.set_context('poster')
COLORS = [
'#1f77b4', '#aec7e8', '#ff7f0e', '#ffbb78', '#2ca02c', '#98df8a',
'#d62728', '#ff9896', '#9467bd', '#c5b0d5', '#8c564b', '#c49c94',
'#e377c2', '#f7b6d2', '#7f7f7f', '#c7c7c7', '#bcbd22', '#dbdb8d',
'#17becf', '#9edae5'
]
def calc_iou_individual(pred_box, gt_box):
"""Calculate IoU of single predicted and ground truth box
Args:
pred_box (list of floats): location of predicted object as
[xmin, ymin, xmax, ymax]
from sklearn.manifold import TSNE
from bokeh.plotting import figure, output_file, show, save
from bokeh.models import HoverTool
import matplotlib.pyplot as plt
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.decomposition import TruncatedSVD
from mpl_toolkits.mplot3d import Axes3D
import seaborn as sns
import matplotlib.patheffects as PathEffects
import pymysql
sns.set_style('darkgrid')
sns.set_palette('muted')
sns.set_context("notebook", font_scale=1.5, rc={"lines.linewidth": 2.5})
n_features = 1000
n_samples = 2000
n_topics = 2
n_top_words = 20
def loadCsv(filename):
lines = csv.reader(open(filename, "rb"))
dataset = list(lines)
for i in range(len(dataset)):
dataset[i] = [x for x in dataset[i]]
return dataset
def plotModelOutput(df,inputs,eqTime,eqTemp,popStats,save,saveName,dimVar, exp=1):
sns.set_style('darkgrid')
sns.set_context('poster',rc={'font.size': 30.0,
'axes.labelsize': 26.0,
'axes.titlesize': 24.0,
'xtick.labelsize': 26.0,
'ytick.labelsize': 26.0,
'legend.fontsize': 22.0})
locale.setlocale(locale.LC_ALL, '')
timer = np.asarray(df['time'])
temp = np.asarray(df['temp'])
pop = np.asarray(df['pop'])
pco2=np.asarray(df['pco2'])
finalTemp = df['temp'][df.index[-1]]
timer = timer/60/60/24/365.25; #convert seconds to years
timer = timer+1820;
pop = pop/1000
dN = np.diff(pop)
pco2 = pco2*10**6
#--------------------------------------------------------------Phase Plots----------------------------------------------------------------------------------------
sns.set_context('poster',rc={'font.size': 18.0,
'axes.labelsize': 26.0,
'axes.titlesize': 24.0,
'xtick.labelsize': 25.0,
'ytick.labelsize': 25.0,
'legend.fontsize': 14.0})
fig, ax = plt.subplots(figsize=(10,5),dpi=200) #set up figure
fig.suptitle("Distance: " + str(round(inputs[0],4)) +" AU, $Carrying\ Capacity$: " + str( '{:,}'.format(round(inputs[1]/1000)) ) +" billion ppl"+", $\gamma:$ " +str(round(dimVar,3)),x=.46,fontsize=19)
ax.set_ylim(min(min(temp),eqTemp)-(5/100)*(max(temp)-min(temp)),finalTemp)
line = ax.scatter(pop,temp,c=pco2,cmap='jet')
cbar = fig.colorbar(line)
cbar.set_label(r'$pCO_{2}\ (ppm)$', size=19)
ax.set_xlabel('Population (billion)',fontsize=17)
#horozontal lines
ax.axhline(y=eqTemp,c='b',label='$T_{eq}=$'+str(round(eqTemp))+" K")
ax.axhline(y=eqTemp+inputs[3],c='springgreen',label='$T_{eq}+\Delta T=$'+str(round(eqTemp+inputs[3]))+" K")
ax.axhline(y=popStats['initPop']/1000,c='orangered',linestyle="--",label='$N_{0}=$'+str(round(popStats['initPop'],1))+" million")
#vertical lines
ax.axvline(x=popStats['maxPop'],ms=8,c='b',linestyle='--',label='$N_{peak}=$'+str(round(popStats['maxPop'],1))+" billion")
ax.axvline(x=popStats['halfPop'],ms=8,c='springgreen',linestyle='--',label='$N_{1/2}=$'+str(round(popStats['halfPop'],1))+" billion")
ax.axvline(x=popStats['finalPop'],ms=8,c='orangered',linestyle='--',label='$N_{final}=$'+str(round(popStats['finalPop'],1))+" billion")
ax.set_ylabel('Temperature (K)',fontsize=17)
ax.legend(loc='best')
plt.gcf().subplots_adjust(bottom=0.175)
# plt.tight_layout()
if save[0]:
if(exp==1): plt.savefig("../plotsPhase_exp1/"+str(saveName)+".png")
if(exp==2): plt.savefig("../plotsPhase_exp2/"+str(saveName)+".png")
if save[1]: plt.show()
plt.close('all')
#----------Normal Plots----------------------------------------------------------------------------------------
fig, (ax2, ax1) = plt.subplots(2,sharex=True,figsize=(20,10),dpi=200) #set up figure, share the x axis
fig.suptitle(" Distance: " + str(round(inputs[0],4)) +" AU, $Carrying\ Capacity$: " + str( '{:,}'.format(round(inputs[1]/1000)) ) +" billion ppl, $\gamma:$ " +str(round(dimVar,3)),x=.40, fontsize=32)
#plot time vs temp (K)
line1 = ax1.scatter(timer,temp,c=pco2,cmap='jet')
ax1.set_title('Temperature vs Time')
ax1.set(ylabel='Temperature (K)',xlabel='Time (years)')
color='black'
linestyle='--'
alpha=.5
ax1.set_xlim(min(timer),max(timer))
ax1.set_ylim(min(min(temp),eqTemp)-(5/100)*(max(temp)-min(temp)),max(temp)+(5/100)*(max(temp)-min(temp)))
ax1.set_yticks(np.linspace(min(min(temp),eqTemp)-(5/100)*(max(temp)-min(temp)),max(temp)+(5/100)*(max(temp)-min(temp)),4))
sns.set_style('darkgrid')
#plot time vs pop
line2 = ax2.scatter(timer,pop,c=pco2,cmap='jet')
ax2.set(ylabel='Population (billions)')
ax2.set_title("Population vs Time")
ax2.set_yticks(np.linspace(min(pop),popStats['maxPopPlot'],4))
sns.set_palette('colorblind')
#horizontal lines
ax2.axhline(y=popStats['maxPop'],c='b',label='$N_{peak}=$'+str(round(popStats['maxPop'],1))+" billion")
ax2.axhline(y=popStats['halfPop'],c='springgreen',label='$N_{1/2}=$'+str(round(popStats['halfPop'],1))+" billion")
ax2.axhline(y=popStats['finalPop'],c='orangered',label='$N_{final}=$'+str(round(popStats['finalPop'],1))+" billion")
ax2.axhline(y=popStats['anthroPop']/1000,c='b',linestyle="--",label='$N_{A}=$'+str(round(popStats['anthroPop']/1000,1))+" billion")
# ax2.axhline(y=popStats['initPop']/1000,c='springgreen',linestyle="--",label='$N_{0}=$'+str(round(popStats["initPop"],1))+" million")
ax1.axhline(y=eqTemp,c='b',label='$T_{eq}=$'+str(round(eqTemp))+" K")
ax1.axhline(y=eqTemp+inputs[3],c="springgreen",label='$T_{eq}+\Delta T=$'+str(round(eqTemp+inputs[3]))+" K")
# ax1.axhline(y=eqTemp+2*inputs[3],c='orangered',label='$T_{eq}+2\Delta T=$'+str(round(eqTemp+2*inputs[3]))+" K")
#vertical lines
# ax2.axvline(x=(popStats['LhalfTime']+1820),linestyle='--',c=(0,0,.7))
# ax1.axvline(x=(popStats['LhalfTime']+1820),linestyle='--',c=(0,0,.7),label="$t_{1/2}^{-}=$"+str(int((popStats['LhalfTime']+1820))))
ax2.axvline(x=(popStats['maxTime']+1820),c='b',linestyle='--')
ax1.axvline(x=(popStats['maxTime']+1820),c='b',linestyle='--',label="$t_{peak}=$"+str(int((popStats['maxTime']+1820))))
# ax2.axvline(x=(popStats['UhalfTime']+1820),linestyle='--',c="orangered")
# ax1.axvline(x=(popStats['UhalfTime']+1820),linestyle='--',c="orangered",label="$t_{1/2}=$"+str(int((popStats['UhalfTime']+1820))))
ax2.set_xlim(min(timer),max(timer))
ax2.set_ylim(min(pop)- min(pop)*(2/100),popStats['maxPopPlot'])
cbar = fig.colorbar(line2,label='pCO2 (ppm)',ax=[ax1,ax2])
cbar.set_label(r'$pCO_{2}\ (ppm)$', size=30)
ax2.legend(loc='best', prop={'size': 23})
ax1.legend(loc='lower right', prop={'size': 25})
if save[0]:
if(exp==1): plt.savefig("../plots_exp1/"+str(saveName)+".png")
if(exp==2): plt.savefig("../plots_exp2/"+str(saveName)+".png")
if save[1]: plt.show()
plt.close('all')
from pathlib import Path
import pandas as pd
import salem
import matplotlib.pyplot as plt
from matplotlib import ticker
import seaborn as sns
from _const_.default import *
sns.set_context('talk')
plt.style.use('seaborn-whitegrid')
VARS2 = ['tmean', 'precip']
RF_DATE_RANGE = slice(*BL_PERIOD)
PROJ_MID_DATE_RANGE = slice(*PROJ_PERIODS['mid'])
in_shp_dir = Path('input/shp/basins')
in_xls_dir = Path('output/xls/rcm')
out_img_dir = Path('output/img/boxplot')
out_img_dir.mkdir(parents=True, exist_ok=True)
out_stat_dir = Path('output/stat/boxplot')
out_stat_dir.mkdir(parents=True, exist_ok=True)
in_shps = list(in_shp_dir.glob('*/*.shp'))
in_shps = in_shps[1:]
stat_df = []
def draw_swarmplot(self, ax, inlier, kws):
"""Plot the data."""
s = kws.pop("s")
centers = []
swarms = []
# Set the categorical axes limits here for the swarm math
if self.orient == "v":
ax.set_xlim(-.5, len(self.plot_data) - .5)
else:
ax.set_ylim(-.5, len(self.plot_data) - .5)
# Plot each swarm
for i, group_data in enumerate(self.plot_data):
if self.plot_hues is None or not self.split:
width = self.width
if self.hue_names is None:
hue_mask = np.ones(group_data.size, np.bool)
else:
hue_mask = np.array(
[h in self.hue_names for h in self.plot_hues[i]],
np.bool)
# Broken on older numpys
# hue_mask = np.in1d(self.plot_hues[i], self.hue_names)
swarm_data = group_data[hue_mask]
# Sort the points for the beeswarm algorithm
sorter = np.argsort(swarm_data)
swarm_data = swarm_data[sorter]
point_colors = self.point_colors[i][hue_mask][sorter]
# Plot the points in centered positions
cat_pos = np.ones(swarm_data.size) * i
kws.update(c=point_colors)
if self.orient == "v":
sns.set_context(rc={'lines.markeredgewidth': 1})
ax.scatter(cat_pos[~inlier[i]],
swarm_data[~inlier[i]],
marker=r'$\mathbf{\times}$',
s=5 * s,
**kws)
sns.set_context(rc={'lines.markeredgewidth': 0})
points = ax.scatter(cat_pos[inlier[i]],
swarm_data[inlier[i]],
s=s,
**kws)
else:
points = ax.scatter(swarm_data, cat_pos, s=s, **kws)
centers.append(i)
swarms.append(points)
else:
offsets = self.hue_offsets
width = self.nested_width
for j, hue_level in enumerate(self.hue_names):
hue_mask = self.plot_hues[i] == hue_level
swarm_data = group_data[hue_mask]
# Sort the points for the beeswarm algorithm
sorter = np.argsort(swarm_data)
swarm_data = swarm_data[sorter]
point_colors = self.point_colors[i][hue_mask][sorter]
# Plot the points in centered positions
center = i + offsets[j]
cat_pos = np.ones(swarm_data.size) * center
kws.update(c=point_colors)
if self.orient == "v":
points = ax.scatter(cat_pos, swarm_data, s=s, **kws)
else:
points = ax.scatter(swarm_data, cat_pos, s=s, **kws)
centers.append(center)
swarms.append(points)
# Update the position of each point on the categorical axis
# Do this after plotting so that the numerical axis limits are correct
for center, swarm in zip(centers, swarms):
if swarm.get_offsets().size:
self.swarm_points(ax, swarm, center, width, s, **kws)
def load_and_plot_res(testName,
title,
ax,
fontscale=1.0,
folderName=None,
methods=None,
leg=False,
linewidth=2,
ylab=None,
xlab=None):
# load the right file
if type(testName) == tuple: # convert test name to string
if testName[0] == True:
testNameString = "Linear"
else:
testNameString = "Nonlinear"
testName = testNameString + testName[1].lower()
if folderName is None:
filee = "tests/" + testName + ".p"
else:
filee = "tests/" + folderName + "/" + testName + ".p"
res, parameters = loadRes(filee)
ns = parameters["ns"]
print("k = ", parameters.get('k'))
if "KCIT_AND" or "RCIT_AND" in methods: # add results for the kernel mehthods from different folder
kernel_res, kernel_par = loadRes("tests/kernel_tests/" + testName +
".p")
print("ntests (kernel) = ", len(kernel_res['RCIT_AND'][2000]['HD']))
res.update(kernel_res)
HDs = np.zeros((len(methods), len(ns)))
SDs = np.zeros((len(methods), len(ns)))
ii = 0
for method in methods:
jj = 0
for n in ns:
hds = res[method][n]["HD"]
HDs[ii, jj] = np.mean(hds)
SDs[ii, jj] = np.std(hds) / np.sqrt(
len(hds)) # standard error of the mean
jj += 1
ii += 1
print("ntests = ", len(hds))
x = range(0, len(ns))
if methods == knn_comp_methods:
linestyles = 4 * ["-"] + 4 * ["--"]
sns.set(style='ticks',
palette=sns.color_palette("Set2", 4),
font_scale=fontscale)
else:
linestyles = ['-', '--']
linestyles = (int(len(methods) / len(linestyles)) + 1) * linestyles
#palette = sns.color_palette("husl", 7)
palette = sns.color_palette("Set2", 10)
sns.set(style='ticks', palette=palette, font_scale=fontscale)
sns.set_context(font_scale=fontscale)
for i in range(0, len(methods)):
lab = methods[i]
ax.errorbar(x,
HDs[i, :],
SDs[i, :],
ls=linestyles[i],
label=lab,
marker='o',
linewidth=linewidth)
ax.set_xticks(range(0, len(ns)))
ax.set_xticklabels(ns)
ax.grid()
if xlab is not None:
ax.set_xlabel(xlab)
if ylab is not None:
ax.set_ylabel(ylab)
if title is not None:
ax.set_title(title)
if leg is True:
# Shrink current axis by 20%
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.75, box.height])
# Put a legend to the right of the current axis
ax.legend(loc='center left',
bbox_to_anchor=(1, 0.5),
prop={'size': 12})
plt.tight_layout()
def main():
sns.set_style("whitegrid")
sns.set_context("notebook")
inifile= "/Users/Bodangles/Documents/Python/RadarDataSim/Testdata/PFISRExample.pickle"
(sensdict,simparams) = readconfigfile(inifile)
simdtype = simparams['dtype']
sumrule = simparams['SUMRULE']
npts = simparams['numpoints']
amb_dict = simparams['amb_dict']
# for spectrum
ISS2 = ISRSpectrum(centerFrequency = 440.2*1e6, bMag = 0.4e-4, nspec=npts, sampfreq=sensdict['fs'],dFlag=True)
ti = 2e3
te = 2e3
Ne = 1e11
Ni = 1e11
datablock90 = sp.array([[Ni,ti],[Ne,te]])
species = simparams['species']
(omega,specorig,rcs) = ISS2.getspecsep(datablock90, species,rcsflag = True)
cur_filt = sp.sqrt(scfft.ifftshift(specorig*npts*npts*rcs/specorig.sum()))
#for data
Nrep = 10000
pulse = sp.ones(14)
lp_pnts = len(pulse)
N_samps = 100
minrg = -sumrule[0].min()
maxrg = N_samps+lp_pnts-sumrule[1].max()
Nrng2 = maxrg-minrg;
out_data = sp.zeros((Nrep,N_samps+lp_pnts),dtype=simdtype)
samp_num = sp.arange(lp_pnts)
for isamp in range(N_samps):
cur_pnts = samp_num+isamp
cur_pulse_data = MakePulseDataRep(pulse,cur_filt,rep=Nrep)
out_data[:,cur_pnts] = cur_pulse_data+out_data[:,cur_pnts]
lagsData = CenteredLagProduct(out_data,numtype=simdtype,pulse =pulse)
lagsData=lagsData/Nrep # divide out the number of pulses summed
Nlags = lagsData.shape[-1]
lagsDatasum = sp.zeros((Nrng2,Nlags),dtype=lagsData.dtype)
for irngnew,irng in enumerate(sp.arange(minrg,maxrg)):
for ilag in range(Nlags):
lagsDatasum[irngnew,ilag] = lagsData[irng+sumrule[0,ilag]:irng+sumrule[1,ilag]+1,ilag].mean(axis=0)
lagsDatasum=lagsDatasum/lp_pnts # divide out the pulse length
(tau,acf) = spect2acf(omega,specorig)
# apply ambiguity function
tauint = amb_dict['Delay']
acfinterp = sp.zeros(len(tauint),dtype=simdtype)
acfinterp.real =spinterp.interp1d(tau,acf.real,bounds_error=0)(tauint)
acfinterp.imag =spinterp.interp1d(tau,acf.imag,bounds_error=0)(tauint)
# Apply the lag ambiguity function to the data
guess_acf = sp.zeros(amb_dict['Wlag'].shape[0],dtype=sp.complex128)
for i in range(amb_dict['Wlag'].shape[0]):
guess_acf[i] = sp.sum(acfinterp*amb_dict['Wlag'][i])
# pdb.set_trace()
guess_acf = guess_acf*rcs/guess_acf[0].real
# fit to spectrums
spec_interm = scfft.fftshift(scfft.fft(guess_acf,n=npts))
spec_final = spec_interm.real
allspecs = scfft.fftshift(scfft.fft(lagsDatasum,n=len(spec_final),axis=-1),axes=-1)
# allspecs = scfft.fftshift(scfft.fft(lagsDatasum,n=npts,axis=-1),axes=-1)
fig = plt.figure()
plt.plot(omega,spec_final.real,label='In',linewidth=5)
plt.hold(True)
plt.plot(omega,allspecs[40].real,label='Out',linewidth=5)
plt.axis((omega.min(),omega.max(),0.0,2e11))
plt.show(False)
import matplotlib.pyplot as plt
import seaborn as sns
from qsforex.settings import OUTPUT_RESULTS_DIR
if __name__ == "__main__":
"""
A simple script to plot the balance of the portfolio, or
"equity curve", as a function of time.
It requires OUTPUT_RESULTS_DIR to be set in the project
settings.
"""
sns.set_palette("deep", desat=.6)
sns.set_context(rc={"figure.figsize": (8, 4)})
equity_file = os.path.join(OUTPUT_RESULTS_DIR, "equity.csv")
equity = pd.io.parsers.read_csv(equity_file,
parse_dates=True,
header=0,
index_col=0)
# Plot three charts: Equity curve, period returns, drawdowns
fig = plt.figure()
fig.patch.set_facecolor('white') # Set the outer colour to white
# Plot the equity curve
ax1 = fig.add_subplot(311, ylabel='Portfolio value')
equity["Equity"].plot(ax=ax1, color=sns.color_palette()[0])
a function of frequency.
NOTE: Also see 10_fit_alpha2.py
"""
import matplotlib as mpl
import seaborn as sns
import tables as tb
from leda_cal.leda_cal import *
from leda_cal.skymodel import *
from leda_cal.dpflgr import *
from leda_cal.useful import fit_poly, closest, trim, fourier_fit, poly_fit, rebin
from lmfit import minimize, Parameters, report_fit
sns.set_style('ticks')
sns.set_context("paper", font_scale=1.5)
def residual(params, model, x, data, errs=1.0):
model_vals = model(params, x)
return (data - model_vals) / errs
def model(params, x):
amp = params['amp'].value
alpha = params['alpha'].value
model = amp * np.power(
x, alpha) #+ off #+ a_s * np.sin(theta * x) #+ a_c * np.cos(theta * x)
#print mo
Email: [email protected] Web: www.mnguenther.com """ from __future__ import print_function, division, absolute_import #::: plotting settings import seaborn as sns sns.set(context='paper', style='ticks', palette='deep', font='sans-serif', font_scale=1.5, color_codes=True) sns.set_style({"xtick.direction": "in", "ytick.direction": "in"}) sns.set_context(rc={'lines.markeredgewidth': 1}) #::: modules import numpy as np import matplotlib.pyplot as plt import os, sys import gzip try: import cPickle as pickle except: import pickle from dynesty import utils as dyutils from tqdm import tqdm def ns_plot_bayes_factors(run_names, labels=None, return_dlogZ=False):
# python 3.5
# -*- coding: utf-8 -*-
""" Bioluminescence data from TMZ-treated mice, fitting the growth rate of the
post treatment slope in order to determine whether growth there is faster than
during the primaray. """
import numpy as np
import matplotlib.pyplot as plt
import pylab
import seaborn
from lmfit import *
plt.rc('text', usetex=True)
seaborn.set_context('talk')
seaborn.set_style('ticks')
pylab.ion()
""" starting values for fitting """
# exponential model
l0s = 0.3 # growth rate
# start value
N0s = 3 * 10000
# relative error
error_s = 0.33
""" data
structure: (animal identifier, [timepoints], [raw BLI measurement data])
"""
# Showing here only data after the lowest point has been passed as the goal is
# to fit the growth rates of the relapse
======================================================
This example shows the effect of the shrinkage factor used to generate the
smoothed bootstrap using the
:class:`~imblearn.over_sampling.RandomOverSampler`.
"""
# Authors: Guillaume Lemaitre <*****@*****.**>
# License: MIT
# %%
print(__doc__)
import seaborn as sns
sns.set_context("poster")
# %%
# First, we will generate a toy classification dataset with only few samples.
# The ratio between the classes will be imbalanced.
from collections import Counter
from sklearn.datasets import make_classification
X, y = make_classification(
n_samples=100,
n_features=2,
n_redundant=0,
weights=[0.1, 0.9],
random_state=0,
)
Counter(y)
import seaborn as sns
# favorite Seaborn settings for notebooks
rc = {
'lines.linewidth': 2,
'axes.labelsize': 16,
'axes.titlesize': 18,
'axes.facecolor': 'F4F3F6',
'axes.edgecolor': '000000',
'axes.linewidth': 1.2,
'xtick.labelsize': 13,
'ytick.labelsize': 13,
'grid.linestyle': ':',
'grid.color': 'a6a6a6'
}
sns.set_context('notebook', rc=rc)
sns.set_style('darkgrid', rc=rc)
sns.set_palette("deep", color_codes=True)
# Import the project utils
import sys
sys.path.insert(0, '../../analysis/')
import mwc_induction_utils_processing as mwc
#===============================================================================
# define variables to use over the script
date = 20170622
username = '******'
#run = 'r1'
# list the directory with the data
import matplotlib.pyplot as plt
import igraph as ig
import seaborn as sns
# import networkx as nx
from matplotlib.ticker import ScalarFormatter
import matplotlib
matplotlib.rcParams['figure.figsize'] = (6.0, 4.0)
DEL_THRESHOLD = 0
sns.set_context(
"talk",
font_scale=1,
rc={
"lines.linewidth": 2.5,
"text.usetex": False,
"font.family": 'serif',
"font.serif": ['Palatino'],
"font.size": 16
})
sns.set_style('white')
################
# MISC
################
get_full_path = lambda p: os.path.join(os.path.dirname(os.path.abspath(__file__)), p)
def ig_to_nx(ig_graph, directed=False, nodes=None):
g = nx.DiGraph() if directed else nx.Graph()
def plot_results(self, filename=None):
"""
Plot the Tearsheet
"""
rc = {
'lines.linewidth': 1.0,
'axes.facecolor': '0.995',
'figure.facecolor': '0.97',
'font.family': 'serif',
'font.serif': 'Ubuntu',
'font.monospace': 'Ubuntu Mono',
'font.size': 10,
'axes.labelsize': 10,
'axes.labelweight': 'bold',
'axes.titlesize': 10,
'xtick.labelsize': 8,
'ytick.labelsize': 8,
'legend.fontsize': 10,
'figure.titlesize': 12
}
sns.set_context(rc)
sns.set_style("whitegrid")
sns.set_palette("deep", desat=.6)
if self.rolling_sharpe:
offset_index = 1
else:
offset_index = 0
vertical_sections = 6 + offset_index
fig = plt.figure(figsize=(10, vertical_sections * 5.5))
fig.suptitle(self.title, y=0.94, weight='bold')
gs = gridspec.GridSpec(vertical_sections, 3, wspace=0.25, hspace=1)
stats = self.get_results()
ax_equity = plt.subplot(gs[:2, :])
if self.rolling_sharpe:
ax_sharpe = plt.subplot(gs[2, :])
ax_drawdown = plt.subplot(gs[2 + offset_index, :])
ax_monthly_returns = plt.subplot(gs[3 + offset_index, :2])
ax_yearly_returns = plt.subplot(gs[3 + offset_index, 2])
ax_txt_curve = plt.subplot(gs[4 + offset_index:, 0])
ax_txt_trade = plt.subplot(gs[4 + offset_index:, 1])
ax_txt_time = plt.subplot(gs[4 + offset_index:, 2])
self._plot_equity(stats, ax=ax_equity)
if self.rolling_sharpe:
self._plot_rolling_sharpe(stats, ax=ax_sharpe)
self._plot_drawdown(stats, ax=ax_drawdown)
self._plot_monthly_returns(stats, ax=ax_monthly_returns)
self._plot_yearly_returns(stats, ax=ax_yearly_returns)
self._plot_txt_curve(stats, ax=ax_txt_curve)
self._plot_txt_trade(stats, ax=ax_txt_trade)
self._plot_txt_time(stats, ax=ax_txt_time)
# Plot the figure
# plt.show(block=False)
plt.subplots_adjust(left=0.1, right=0.9, top=0.9, bottom=0.1)
plt.show()
if filename is not None:
fig.savefig(filename, dpi=150, bbox_inches='tight')
