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combined_prior_matches['cambodia_nbow'] = combined_prior_matches.pop('cambodia_template22')
combined_prior_matches['cambodia_tfidf'] = combined_prior_matches.pop('cambodia_template23')
combined_prior_matches['mauritius_google'] = combined_prior_matches.pop('mauritius1')
combined_prior_matches['mauritius_nbow'] = combined_prior_matches.pop('mauritius2')
combined_prior_matches['mauritius_tfidf'] = combined_prior_matches.pop('mauritius3')
countries = ['liberia', 'bhutan', 'namibia', 'cambodia', 'mauritius']
num_sentences = 30
for key in combined_prior_matches.keys():
print('{0:10} {1:10.5f}%'.format(key, combined_prior_matches[key][2][num_sentences]*100))
#print('-------------------------------------------------------------------------------')
import matplotlib.pyplot as plt
import seaborn as sns
#%matplotlib inline
sns.set_context('talk')
sns.set_style("white")
plt.figure(figsize=(15,11))
i =0
for key in combined_prior_matches:
if 'tfidf' in key:
plt.plot(list(range(1, 31)), (np.asarray(sorted(combined_prior_matches[key][2]))*100)[:30], label = key.split('.')[0].split('_')[0].upper())
plt.legend(title = 'Country', bbox_to_anchor=(1.1, 0.45), loc=1, borderaxespad=10)
plt.title('Percent Matches Vs. Number of Sentences')
plt.xlabel('Number of Sentences')
plt.ylabel('Percent Matches with Policy Experts')
plt.yticks(np.arange(0, 55, 5))
#plt.savefig('matches_update_30.jpeg')
plt.show()
plt.figure(figsize=(15,11))
at 0 degrees.
**kwargs :
kwargs for the xarray.DataArray.plot.contourf function
Returns
-------
type
axes
"""
from monet.plots.mapgen import draw_map
from monet.plots import _dynamic_fig_size
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
import seaborn as sns
sns.set_context('notebook')
da = _dataset_to_monet(self._obj)
crs_p = ccrs.PlateCarree()
if 'crs' not in map_kws:
map_kws['crs'] = crs_p
if 'figsize' in kwargs:
map_kws['figsize'] = kwargs['figsize']
kwargs.pop('figsize', None)
else:
figsize = _dynamic_fig_size(da)
map_kws['figsize'] = figsize
if 'transform' not in kwargs:
transform = crs_p
else:
transform = kwargs['transform']
kwargs.pop('transform', None)
ax = draw_map(**map_kws)
reduced_df_allDays = reduced_df.reindex(index=allDates_index, fill_value=0)
# Transforming the dataframe index (DatetimeIndex object) to a regular pd.Series so "apply" can be used.
# The Pandas "apply" method is used in this case to apply an "anonymous" function
# (one we don't want to create a separate function for) to all the
# components of the DataFrame/Series
weekday_series = pd.Series(reduced_df_allDays.index, index = reduced_df_allDays.index).apply(lambda x: x.strftime('%a'))
# Adding another column with string objects representing weekdays.
reduced_df_allDays['weekday'] = weekday_series
# Setting a pre-defined style from Seaborn
sns.set_context('notebook')
# Pandas plotting
line_plot = reduced_df_allDays.plot(legend=False, title='Tasks Distribution - Next '+str(NUMBER_OF_DAYS)+' Days',
y=['tasks'], kind='line')
print("Generating Graph..")
fig = line_plot.get_figure()
fig.savefig(OUTPUT)
print("Done.")
MIT Kavli Institute for Astrophysics and Space Research,
Massachusetts Institute of Technology,
77 Massachusetts Avenue,
Cambridge, MA 02109,
USA
Email: maxgue@mit.edu
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
#::: allesfitter modules
from .. import get_mcmc_posterior_samples, get_ns_posterior_samples, get_labels
def mcmc_plot_violins(datadirs, labels, key):
'''
Inputs:
-------
import numpy as np
import seaborn as sns
import tensorflow as tf
from tensorflow.python import tf2
if not tf2.enabled():
import tensorflow.compat.v2 as tf
tf.enable_v2_behavior()
assert tf2.enabled()
import tensorflow_probability as tfp
sns.reset_defaults()
#sns.set_style('whitegrid')
#sns.set_context('talk')
sns.set_context(context='talk',font_scale=0.7)
tfd = tfp.distributions
negloglik = lambda y, rv_y: -rv_y.log_prob(y)
w0 = 0.125
b0 = 5.
x_range = [-20, 60]
def load_dataset(n=150, n_tst=150):
np.random.seed(43)
def s(x):
g = (x - x_range[0]) / (x_range[1] - x_range[0])
return 3 * (0.25 + g**2.)
def generate_informative_img():
global model
try:
allele = request.form.get('target_allele', '')
pep_seq = request.form.get('target_pepseq', '')
binder = request.form.get('target_binder', 0, type=int)
target_img_txt = request.form.get('target_img', '', type=str)
target_img = json.loads(target_img_txt)
print 'target_img:', target_img, 'allele', allele, 'pep_seq', pep_seq, 'binder:', binder
infr_img = model.find_informative_pixels(np.asarray(target_img), binder=binder)
# plot informative pixels
p_sites = range(1, 10)
h_sites = sorted(np.unique([css[1] for css in model.bdomain.contact_sites(9)]) + 1)
sns.set_context('paper', font_scale=1.1)
sns.axes_style('white')
fig, axes = plt.subplots(nrows=1, ncols=1)
fig.set_figwidth(6)
fig.set_figheight(2)
plt.tight_layout()
fig.subplots_adjust(bottom=0.22)
g = sns.heatmap(infr_img, ax=axes, annot=False, linewidths=.4, cbar=False)
# g.set(title='Informative pixels for %s-%s' % (pep_seq, allele))
g.set_xticklabels(h_sites, rotation=90)
g.set_yticklabels(p_sites[::-1])
g.set(xlabel='HLA contact site', ylabel='Peptide position')
canvas = FigureCanvas(fig)
output = StringIO.StringIO()
canvas.print_png(output)
import pandas as pd
import numpy as np
import argparse
import seaborn as sns
import matplotlib.pyplot as plt
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--csv', required=True)
parser.add_argument('--context', default='poster',
help='Modifies size of legend, axis, etc.')
args = parser.parse_args()
df = pd.read_csv(args.csv)
dff = df.replace([-np.inf, np.inf], np.nan).dropna(subset=['log10_interval_seconds'])
sns.set_context(args.context)
plt.figure(figsize=(20, 15))
sns.violinplot(y='log10_interval_seconds', x='transition', data=dff)
plt.savefig('violin_log10_interval_seconds.png', dpi=320)
print('saved figure to violin_log10_interval_seconds.png')
"dusty purple",
"orange",
"clay",
"pink",
"greyish",
"mint",
"light cyan",
"steel blue",
"forest green",
"pastel purple",
"salmon",
"dark brown"]
colors = sns.xkcd_palette(color_names)
sns.set_style("white")
sns.set_context("paper")
def gradient_cmap(gcolors, nsteps=256, bounds=None):
"""
Make a colormap that interpolates between a set of colors
"""
ncolors = len(gcolors)
if bounds is None:
bounds = np.linspace(0, 1, ncolors)
reds = []
greens = []
blues = []
alphas = []
for b, c in zip(bounds, gcolors):
reds.append((b, c[0], c[0]))
def plot_pattern_clustering_result():
import matplotlib.pyplot as plt
import seaborn as sns
sns.set()
sns.set_style("whitegrid")
sns.set_context("talk")
from advntr.models import load_unique_vntrs_data
vntrs = load_unique_vntrs_data('/home/mehrdad/workspace/adVNTR/vntr_data/hg38_selected_VNTRs_Illumina.db')
from advntr.pattern_clustering import get_pattern_clusters
patterns_dist = []
hist_data = {}
for i, vntr in enumerate(vntrs):
if vntr.annotation == 'Intron':
continue
num_of_clusters = len(get_pattern_clusters(vntr.get_repeat_segments()))
patterns_dist.append(num_of_clusters)
if vntr.annotation not in hist_data.keys():
hist_data[vntr.annotation] = []
hist_data[vntr.annotation].append(num_of_clusters)
print(i)
###############################################################
###############################################################
###############################################################
###############################################################
########### FOURTH PLOT: PHOTOMETRY BY PLANET ################
########### ALSO, SAVE PHOTOMETRY BY PLANET ################
###############################################################
# Phased transits of each planet for each instrument on different plots:
for nplanet in range(n_transit):
iplanet = numbering_transit[nplanet]
for instrument in inames_lc:
fig, axs = plt.subplots(2, 1,gridspec_kw = {'height_ratios':[3,1]}, figsize=(9,7))
sns.set_context("talk")
sns.set_style("ticks")
matplotlib.rcParams['mathtext.fontset'] = 'stix'
matplotlib.rcParams['font.family'] = 'STIXGeneral'
matplotlib.rcParams['font.size'] = '5'
matplotlib.rcParams['axes.linewidth'] = 1.2
matplotlib.rcParams['xtick.direction'] = 'out'
matplotlib.rcParams['ytick.direction'] = 'out'
matplotlib.rcParams['lines.markeredgewidth'] = 1
# First, get phases for the current planetary model. For this get median period and t0:
P,t0 = np.median(out['posterior_samples']['P_p'+str(iplanet)]),np.median(out['posterior_samples']['t0_p'+str(iplanet)])
# Get the actual phases:
phases = utils.get_phases(t_lc[instrument_indexes_lc[instrument]],P,t0)
# Now, as in the previous plot, sample models from the posterior parameters along the phases of interest.