def plot_joint_distribution_benefits_surplus(model_dict, df):
"""This function plots the joint distribution of benefits and surplus."""
coeffs_cost = model_dict['COST']['all']
B = df['Y1'] - df['Y0']
Z = df[['Z_0', 'Z_1']]
C = np.dot(coeffs_cost, Z.T) + df['UC']
S = B - C
sns.jointplot(S, B, stat_func=None).set_axis_labels('$S$', r'$B$')
def plot_pop_resids(msm, **kwargs):
"""
Plot residuals between MSM populations and raw counts.
Parameters
----------
msm : msmbuilder.msm
MSMBuilder MarkovStateModel
**kwargs : dict, optional
Extra arguments to pass to seaborn.jointplot
Returns
-------
ax : matplotlib axis
matplotlib figure axis
"""
if hasattr(msm, 'all_populations_'):
msm_pop = msm.populations_.mean(0)
elif hasattr(msm, 'populations_'):
msm_pop = msm.populations_
raw_pop = msm.countsmat_.sum(1) / msm.countsmat_.sum()
ax = sns.jointplot(np.log10(raw_pop),
np.log10(msm_pop),
kind='resid',
**kwargs)
ax.ax_joint.set_xlabel('Raw Populations', size=20)
ax.ax_joint.set_ylabel('Residuals', size=20)
return ax
def init_artists(self, ax, plot_data, plot_kwargs):
if self.joint:
if self.joint and self.subplot:
raise Exception("Joint plots can't be animated or laid out in a grid.")
return {'fig': sns.jointplot(*plot_data, **plot_kwargs).fig}
else:
return {'axis': sns.kdeplot(*plot_data, ax=ax, **plot_kwargs)}
def init_artists(self, ax, plot_data, plot_kwargs):
if self.joint:
if self.joint and self.subplot:
raise Exception("Joint plots can't be animated or laid out in a grid.")
return {'fig': sns.jointplot(*plot_data, **plot_kwargs).fig}
else:
return {'axis': sns.kdeplot(*plot_data, ax=ax, **plot_kwargs)}
def _update_plot(self, axis, view):
if self.joint:
self.style.pop('cmap', None)
self.handles['fig'] = sns.jointplot(view.data[:,0],
view.data[:,1],
**self.style).fig
else:
label = view.label if self.overlaid == 1 else ''
sns.kdeplot(view.data, ax=axis, label=label,
zorder=self.zorder, **self.style)
def _update_plot(self, axis, view):
if self.joint:
self.style.pop('cmap', None)
self.handles['fig'] = sns.jointplot(view.data[:,0],
view.data[:,1],
**self.style).fig
else:
label = view.label if self.overlaid == 1 else ''
sns.kdeplot(view.data, ax=axis, label=label,
zorder=self.zorder, **self.style)
def _update_plot(self, axis, view):
if self.joint:
self.style.pop('cmap', None)
self.handles['fig'] = sns.jointplot(view.data[:,0],
view.data[:,1],
**self.style).fig
else:
kwargs = self.style[self.cyclic_index]
label = view.label if self.overlaid >= 1 else ''
if label:
kwargs['label'] = label
sns.kdeplot(view.data, ax=axis, zorder=self.zorder, **kwargs)
def vector_cloud_kde(experiment, kinematic, i=None):
# test whether we are a simulation; if not, forbid plotting of drivers
if experiment.is_simulation is False:
if kinematic not in ['position', 'velocity', 'acceleration']:
raise TypeError("we don't know the mosquito drivers")
labels = []
for dim in ['x', 'y', 'z']:
labels.append(kinematic + '_' + dim)
ensemble = experiment.flights.get_trajectory_slice(i)
# grab labels
vecs = []
if kinematic is "velocity":
xlim, ylim = (-0.8, 0.8), (-0.8, 0.8)
else:
xlim, ylim = None, None
selection = ensemble.loc[:, labels]
sns.jointplot(x=labels[0], y=labels[1], data=selection, kind='kde', shade=True,
xlim=xlim, ylim=ylim, shade_lowest=False, space=0, stat_func=None)
sns.jointplot(x=labels[0], y=labels[2], data=selection, kind='kde', shade=True,
xlim=xlim, ylim=ylim, shade_lowest=False, space=0, stat_func=None)
sns.jointplot(x=labels[1], y=labels[2], data=selection, kind='kde', shade=True,
xlim=xlim, ylim=ylim, shade_lowest=False, space=0, stat_func=None)
def plot_distribution(df,
experiment_type,
color="C0",
title=None,
target_color="C2",
background_shade=-50,
crosshair=False,
drone_width=None):
df_ex = df[df.experiment_type == experiment_type]
df_arr = df_ex[df_ex.arrived == 1]
if title is None:
title = df_ex.experiment.iloc[0]
g = sns.jointplot(df_arr.xn, df_arr.yn, kind="kde", space=0, color=color)
g.plot_marginals(sns.rugplot, height=0.1, color=color)
g.ax_joint.get_children()[0].set_zorder(-1)
for child in g.ax_joint.get_children()[1:]:
if isinstance(child, mpl.collections.PathCollection):
child.set_alpha(0.8)
plt.sca(g.ax_joint)
plot_targets(show_start=False,
show_final=False,
target_coords=[TARGET],
target_color=target_color,
zorder=0,
crosshair=crosshair,
drone_width=drone_width)
g.set_axis_labels("$x$", "$y$")
plt.axis("equal")
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
xsize = xmax - xmin
ysize = ymax - ymin
if xsize > ysize:
ymin -= (xsize - ysize) / 2
ymax += (xsize - ysize) / 2
ysize = xsize
else:
xmin -= (ysize - xsize) / 2
xmax += (ysize - xsize) / 2
xsize = ysize
plt.gca().add_patch(
mpl.patches.Rectangle((min(xmin, ymin) - abs(min(xmin, ymin)),
min(xmin, ymin) - abs(min(xmin, ymin))),
max(xsize, ysize) * 5,
max(xsize, ysize) * 5,
color=change_color(color,
saturation=background_shade),
zorder=-1))
g.fig.suptitle(title)
def plot_pop_resids(msm, **kwargs):
if hasattr(msm, 'all_populations_'):
msm_pop = msm.populations_.mean(0)
elif hasattr(msm, 'populations_'):
msm_pop = msm.populations_
raw_pop = msm.countsmat_.sum(1) / msm.countsmat_.sum()
ax = sns.jointplot(np.log10(raw_pop), np.log10(msm_pop), kind='resid',
**kwargs)
ax.ax_joint.set_xlabel('Raw Populations', size=20)
ax.ax_joint.set_ylabel('Residuals', size=20)
return ax
def jointplot(x=None, y=None, data=None, xlabel=None, ylabel=None,
color=None, zeromin=True, one2one=True):
""" Plots the joint distribution of two variables via seaborn
Parameters
----------
x, y : array-like or string
Sequences of values or column names found within ``data``.
data : pandas DataFrame or None, optional
An optional DataFrame containing the data.
xlabel, ylabel : string, optional
Overrides the default x- and y-axis labels.
color : matplotlib color, optional
Color used for the plot elements.
zeromin : bool, optional
When True (default), force lower axes limits to 0.
one2one : bool, optional
When True (default), plots the 1:1 line on the axis and sets
the x- and y-axis limits to be equal.
Returns
-------
jg : seaborn.JointGrid
"""
jg = seaborn.jointplot(x=x, y=y, color=color, data=data,
marginal_kws=dict(rug=True, kde=True))
if xlabel is None:
xlabel = jg.ax_joint.get_xlabel()
if ylabel is None:
ylabel = jg.ax_joint.get_ylabel()
jg.set_axis_labels(xlabel=xlabel, ylabel=ylabel)
if zeromin:
jg.ax_joint.set_xlim(left=0)
jg.ax_joint.set_ylim(bottom=0)
if one2one:
ax_limit_max = np.max([jg.ax_joint.get_xlim(), jg.ax_joint.get_ylim()])
jg.ax_joint.set_xlim(left=0, right=ax_limit_max)
jg.ax_joint.set_ylim(bottom=0, top=ax_limit_max)
jg.ax_joint.plot([0, ax_limit_max], [0, ax_limit_max], marker='None',
linestyle='-', linewidth=1.75, color=color or 'k',
alpha=0.45, label='1:1 line')
jg.ax_joint.legend(frameon=False, loc='upper left')
return jg
def graph_regression_numerical(dataset_id, df, col, target):
"""
display a reg scatter plot graph of col in x axis and target in y axis
:param dataset_id: id of the dataset
:param df: dataframe, with col and target values
:param col: name of column
:param target: name of target column
:return:
"""
try:
for dark, theme in [(True, 'dark_background'),
(False, 'seaborn-whitegrid')]:
with plt.style.context(theme, after_reset=True):
g = sns.jointplot(x=col, y=target, data=df, kind="kde", size=7)
g.plot_joint(plt.scatter, s=5, alpha=0.7)
g.ax_joint.collections[0].set_alpha(0)
plt.xlim(__standard_range(df[col].values, 1, 99))
plt.ylim(__standard_range(df[target].values, 1, 99))
__save_fig(dataset_id, '_col_' + col, dark)
except:
log.error('error in graph_regression_numerical with dataset_id %s' %
dataset_id)
def graph_predict_regression(dataset, round_id, y, y_pred, part='eval'):
"""
generate a graph prediction versus actuals
:param dataset: dataset object
:param round_id: id of the round
:param y: actual values
:param y_pred: predicted values
:param part: part of the dataset
:return: None
"""
try:
for dark, theme in [(True, 'dark_background'),
(False, 'seaborn-whitegrid')]:
with plt.style.context(theme, after_reset=True):
plt.figure(figsize=(6, 6))
# plot a graph prediction versus actuals
df = pd.DataFrame([y, y_pred]).transpose()
df.columns = ['actuals', 'predict']
g = sns.jointplot(x='actuals',
y='predict',
data=df,
kind="kde",
size=6)
g.plot_joint(plt.scatter, s=5, alpha=0.8)
g.ax_joint.collections[0].set_alpha(0)
mn, mx = __standard_range(y, 1, 99)
plt.plot((mn, mx), (mn, mx), color='r', lw=0.7)
plt.xlim(mn, mx)
plt.ylim(mn, mx)
plt.title('%s' % part)
__save_fig(dataset.dataset_id,
'predict_%s_%s' % (part, round_id), dark)
except:
log.error('error in graph_predict_regression with dataset_id %s' %
dataset.dataset_id)
def plottingData():
df = pd.read_csv(os.getcwd() + "/" + args.data,
delimiter='\t',
header=0,
sep='\t')
if ',' in args.option and not args.pdf:
# Spliting variable
numVar = args.option.split(',')
# Deleting quotes
numVar[0].strip('"')
numVar[1].strip('"')
fig, (ax1) = plt.subplots(nrows=1)
# Color by the Probability Density Function.
# Kernel density estimation is a way to estimate
# the probability density function (PDF) of a random
# variable in a non-parametric way
# Setting data
x = df[numVar[0]]
y = df[numVar[1]]
# Calculate the point density
xy = np.vstack([x, y])
z = gaussian_kde(xy)(xy)
# Sort the points by density, so that the densest points are plotted last
idx = z.argsort()
x, y, z = x[idx], y[idx], z[idx]
# Setting plot type
pdf = ax1.scatter(x, y, c=z, s=50, edgecolor='')
# Plot title
ax1.set_title(numVar[0] + ' by ' + numVar[1])
# Hide right and top spines
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
ax1.yaxis.set_ticks_position('left')
ax1.xaxis.set_ticks_position('bottom')
# Set x and y limits
xmin = df["" + numVar[0] + ""].min() - 1
xmax = df["" + numVar[0] + ""].max() + 1
ymin = df["" + numVar[1] + ""].min() - 1
ymax = df["" + numVar[1] + ""].max() + 1
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
# Set x and y labels
plt.xlabel(numVar[0])
plt.ylabel(numVar[1])
# Adding the color bar
colbar = plt.colorbar(pdf)
colbar.set_label('Probability Density Function')
plt.show()
elif not ',' in args.option:
fig, (ax1) = plt.subplots(nrows=1)
ax1.plot(df['#Frame'], df[args.option])
ax1.set_title(args.option + ' by Time')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
ax1.yaxis.set_ticks_position('left')
ax1.xaxis.set_ticks_position('bottom')
plt.xlabel('Time (ps)')
xmin1 = df['#Frame'].min() - 1
xmax1 = df['#Frame'].max() + 1
plt.xlim(xmin1, xmax1)
plt.ylabel(args.option)
plt.show()
elif ',' in args.option and args.pdf == 'kde':
import seaborn.apionly as sns
sns.set(style='white')
numVar = args.option.split(',')
numVar[0].strip('"')
numVar[1].strip('"')
# Distribution plot of two variables using KDE method with seaborn
sns.jointplot(x=numVar[0],
y=numVar[1],
data=df,
kind="kde",
space=0,
color="b")
plt.show()
def jointplot(self, x=None, y=None, data=None, *args, **kwargs):
"""
Fit and plot a univariate or bivariate kernel density estimate
Parameters
----------
x : a list of names of variable in data that need to visualize \
their distribution
y : a list of names of variable in data that need to visualize \
its joint distribution against every x above
data : pandas dataframe
**kwargs : other arguments in seaborn.jointplot
kind : { 'scatter' | 'reg' | 'resid' | 'kde' | 'hex' }, optional
stat_func : callable or None, optional
color : matplotlib color, optional
size : numeric, optional
ratio : numeric, optional
space : numeric, optional
dropna : bool, optional
{x, y}lim : two-tuples, optional
{joint, marginal, annot}_kws : dicts, optional
Returns
-------
JointGrid object with the plot on it
References
----------
Seaborn jointplot further documentation
https://seaborn.pydata.org/generated/seaborn.jointplot.html
"""
# check data
if not isinstance(data, (pd.DataFrame)):
raise ValueError('data must be pandas dataframe')
# check x and y
if x is None:
raise ValueError('x can NOT be None')
else: # x is NOT None
if not isinstance(x, (list, tuple, np.ndarray, pd.Index)):
x = [x]
if y is None:
raise ValueError('y can NOT be None')
else: # y is NOT None
if not isinstance(y, (list, tuple, np.ndarray, pd.Index)):
y = [y]
# no figure configuration needed
plt.close()
# iterate thru x
for i, col_y in enumerate(y):
if col_y not in data.columns.values:
raise ValueError('{} is NOT in data'.format(col_y))
b = data[col_y]
b_not_nan = np.ones(b.shape[0], dtype=np.bool)
if np.logical_not(np.isfinite(b)).any():
logger.warning('RUNTIME WARNING: {} column has inf or nan '
''.format(col_y))
b = b.replace([-np.inf, np.inf], np.nan)
# filter
b_not_nan = np.logical_not(b.isnull())
for j, col_x in enumerate(x):
# check if col in data
if col_x not in data.columns.values:
raise ValueError('{} is NOT in data'.format(col_x))
a = data[col_x]
a_not_nan = np.ones(a.shape[0], dtype=np.bool)
if np.logical_not(np.isfinite(a)).any():
logger.warning('RUNTIME WARNING: {} column has inf or '
'nan'.format(col_x))
a = a.replace([-np.inf, np.inf], np.nan)
# filter
a_not_nan = np.logical_not(a.isnull())
# joint filter
not_nan = b_not_nan & a_not_nan
joint_grid = sns.jointplot(x=a[not_nan],
y=b[not_nan],
size=self.size[0],
*args,
**kwargs)
joint_grid.fig.axes[1].set_title(
label='Joint Distribution of {} and {} '
''.format(col_y, col_x),
fontsize=self.title_fontsize)
joint_grid.fig.axes[0].set_xlabel(xlabel=col_x,
fontsize=self.label_fontsize)
joint_grid.fig.axes[0].set_ylabel(ylabel=col_y,
fontsize=self.label_fontsize)
joint_grid.fig.axes[0].tick_params(
axis='both', which='maj', labelsize=self.tick_fontsize)
joint_grid.fig.axes[0].legend(loc='upper right')
joint_grid.fig.subplots_adjust(wspace=0.5,
hspace=0.3,
left=0.125,
right=0.9,
top=0.9,
bottom=0.1)
joint_grid.fig.tight_layout()
plt.show()
def plot_joint_distribution_unobservables(df):
"""This function plots the joint distribution of the relevant unobservables."""
sns.jointplot(df['V'], df['U1'],
stat_func=None).set_axis_labels('$V$', '$U_1$')
def plot_joint_distribution_potential(df):
"""This function plots the joint distribution of potential outcomes."""
sns.jointplot(df['Y1'], df['Y0'],
stat_func=None).set_axis_labels('$Y_1$', r'$Y_0$')
plt.pie(med_age, labels=med_age.index, autopct='%1.1f%%')
plt.show()
counts_peace = peace_df['Sex'].value_counts()
pie(counts, labels=counts_peace.index, autopct='%1.1f%%')
show()
peace_age = peace_df['Age Category'].value_counts()
print(peace_age)
plt.pie(peace_age, labels=peace_age.index, autopct='%1.1f%%')
plt.show()
sns.jointplot(x="Year",
y="Age",
kind='reg',
data=data)
plt.show()
sns.boxplot(data=data,
x='Category',
y='Age')
plt.show()
sns.lmplot('Year','Age',data=data,lowess=True, aspect=2, line_kws={'color' : 'black'})
plt.show()
# Question 2: What words are most frequently written in the prize motivation?
top_N = 10
stopwords = nltk.corpus.stopwords.words('english')
# plt.legend(loc = 'best')
# plt.grid()
# f.savefig('BPT.png')
# plt.close(f)
#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
#ax.autoscale(False)
H, xedges, yedges = np.histogram2d(xm.compressed(), ym.compressed(), bins = (40,40))
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]
#f = plt.figure()
#f.set_dpi(100)
#f.set_size_inches(10, 8)
#ax = f.gca()
#with sns.axes_style("white"):
sns.jointplot(xm.compressed(), ym.compressed(), kind="hex")
f = plt.gcf()
f.set_dpi(100)
f.set_size_inches(10, 8)
ax = f.axes[0]
#print f.axes
#ax = f.axes
im = ax.imshow(H, cmap=plt.cm.Blues, aspect = 'auto', interpolation='none', origin='low', extent = extent)
#ax.scatter(xm, ym, marker = 'o', c = 'g', s = 5, edgecolor = 'none', alpha = 0.1, label = '')
#ax.contour(H,extent=extent,linewidths=1, interpolation='nearest', origin = 'lower', levels=[16, 50, 84], cmap = plt.cm.YlGn)
#ax.hist2d(xm.compressed(), ym.compressed(), bins = (10,10))
nBox = 1000
#nBox = len(xm.compressed()) / 50.
#slope, intercept, sigma_slope, sigma_intercep = OLS_bisector(logOH_M13, Zneb_mpa)