def chi_2_heatmap(df,
X,
Y,
save_as_img=False,
title='Chi-2 contingency table'):
cont = contingency_table(df, X, Y)
# Chi-2
ni = cont.loc[:, ["Total"]] # ni
nj = cont.loc[["Total"], :]
n = len(df)
indep = ni.dot(nj) / n
nij = cont.fillna(0)
xi_ij = (nij - indep)**2 / indep
xi_n = xi_ij.sum().sum()
table = xi_ij / xi_n
ax = sns.heatmap(table.iloc[:-1, :-1],
annot=nij.iloc[:-1, :-1],
cmap='Blues',
fmt='g')
ax.set_xlabel(Y, labelpad=20)
ax.set_ylabel(X, labelpad=20)
ax.set_title(title, pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig('{}_{}_chi2_heatmap.jpg'.format(X, Y))
def plot_residuals(df, x, y, save_as_img=False):
ax = sns.residplot(x, y, lowess=True, data=df)
ax.set_xlabel(x, labelpad=20)
ax.set_ylabel(y, labelpad=20)
ax.set_title('Residuals dispersion', pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig('{}_{}_residplot.jpg'.format(x, y))
def plot_linear_regression(df, x, y, save_as_img=False):
ax = sns.regplot(x, y, data=df)
ax.set_xlabel(x, labelpad=20)
ax.set_ylabel(y, labelpad=20)
ax.set_title('Linear regression ({} & {})'.format(x, y), pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig('{}_{}_linear_reg.jpg'.format(x, y))
def plot_dendrogram(self, plot_size=(10, 25), title_pad=20, xlabel_pad=20, orient='left', leaf_text_size=16,
save_as_img=False, filename='cah', file_type='jpg'):
plt.figure(figsize=plot_size)
plt.title('Hierarchical Clustering Dendrogram', pad=title_pad)
plt.xlabel('distance', labelpad=xlabel_pad)
self.dendrogram_data = dendrogram(self.Z,
labels=self.categories,
orientation=orient,
leaf_font_size=leaf_text_size)
if save_as_img:
plt.tight_layout()
plt.savefig(f'{filename}.{file_type}')
plt.show()
def scree_plot(self,
threshold=None,
save_as_img=False): # (% Explained Variance)
"""
"""
scree = self.evr * 100
plt.bar(np.arange(len(scree)) + 1, scree)
if threshold is not None:
scree_freq = scree / scree.sum()
scree_cumsum = np.cumsum(scree_freq)
# Number of features needed for threshold cumulative importance
n_features = np.min(np.where(scree_cumsum > threshold)) + 1
threshold_percentage = 100 * threshold
threshold_legend = '{} features required for {:.0f}% of inertia.'.format(
n_features, threshold_percentage)
# Threshold vertical line plot
plt.vlines(n_features,
ymin=0,
ymax=threshold_percentage,
linestyles='--',
colors='red')
plt.plot(np.arange(len(scree)) + 1,
scree.cumsum(),
c="red",
marker='o',
label=threshold_legend)
plt.legend(loc='lower right', fontsize=12)
else:
plt.plot(np.arange(len(scree)) + 1,
scree.cumsum(),
c="red",
marker='o')
plt.xlabel("Inertia axis rank", labelpad=20)
plt.ylabel("Inertia (%)", labelpad=20)
plt.title("Scree plot" +
"\n(Kaiser criterion = {} : Elbow criterion = {})".format(
self.kaiser_criterion(),
elbow_criterion(total_inertia=self.evr)),
pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig('scree.jpg')
plt.show(block=False)
def scree_plot(self,
pair_comp=False,
save_as_img=False): # (% Explained Variance)
scree = self.pca.explained_variance_ratio_ * 100
plt.bar(np.arange(len(scree)) + 1, scree)
plt.plot(np.arange(len(scree)) + 1,
scree.cumsum(),
c="red",
marker='o')
plt.xlabel("rang de l'axe d'inertie", labelpad=20)
plt.ylabel("pourcentage d'inertie", labelpad=20)
plt.title("Eboulis des valeurs propres" +
"\n(Kaiser criterion = {} : Elbow criterion = {})".format(
self.kaiser_criterion(pair_comp),
self.elbow_criterion(pair_comp)),
pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig('scree.jpg')
plt.show(block=False)
def correlation_matrix(df,
as_chart=True,
precision=2,
title=None,
rotate=90,
save_as_img=False,
size=(16, 12)):
"""
"""
corr = df.corr()
if as_chart:
colormap = plt.cm.RdBu
plt.figure(figsize=size)
if title is None:
title = 'Pearson Correlation of Features'
plt.title(title, y=1.05, size=15, pad=20)
mask = np.triu(np.ones_like(corr, dtype=np.bool))
ax = sns.heatmap(corr,
linewidths=0.5,
vmax=1.0,
square=True,
cmap=colormap,
linecolor='white',
annot=True,
mask=mask,
cbar_kws={"shrink": .5},
fmt='.{}f'.format(precision))
ax.set_xlim(0, df.shape[1] - 1)
ax.set_ylim(df.shape[1], 1)
plt.xticks(rotation=rotate)
if save_as_img:
plt.tight_layout()
plt.savefig('corr_matrix.jpg')
plt.show()
else:
return corr.style.background_gradient(
cmap='coolwarm').set_precision(precision)
def plot_correlation_circle(self,
n_plan=None,
labels=None,
label_rotation=0,
lims=None,
save_as_img=False,
plot_size=(10, 8)):
"""
"""
factorial_plan_nb = self.default_factorial_plan_nb if n_plan is None else n_plan
# Build a list of tuples (example : [(0, 1), (2, 3), ... ])
axis_ranks = [(x, x + 1) for x in range(0, factorial_plan_nb, 2)]
pcs = self.pca.components_
for d1, d2 in axis_ranks:
if d2 < self.n_comp:
fig, ax = plt.subplots(figsize=plot_size)
# Fix factorial plan limits
if lims is not None:
xmin, xmax, ymin, ymax = lims
elif pcs.shape[1] < 30:
xmin, xmax, ymin, ymax = -1, 1, -1, 1
else:
xmin, xmax, ymin, ymax = min(pcs[d1, :]), max(
pcs[d1, :]), min(pcs[d2, :]), max(pcs[d2, :])
# affichage des flèches
# s'il y a plus de 30 flèches, on n'affiche pas le triangle à leur extrémité
if pcs.shape[1] < 30:
plt.quiver(np.zeros(pcs.shape[1]),
np.zeros(pcs.shape[1]),
pcs[d1, :],
pcs[d2, :],
angles='xy',
scale_units='xy',
scale=1,
color="grey")
# (doc : https://matplotlib.org/api/_as_gen/matplotlib.pyplot.quiver.html)
else:
lines = [[[0, 0], [x, y]] for x, y in pcs[[d1, d2]].T]
ax.add_collection(
LineCollection(lines, axes=ax, alpha=.1,
color='black'))
# Display variables labels
if labels is not None:
for i, (x, y) in enumerate(pcs[[d1, d2]].T):
if xmin <= x <= xmax and ymin <= y <= ymax:
plt.text(x,
y,
labels[i],
fontsize='14',
ha='center',
va='center',
rotation=label_rotation,
color="blue",
alpha=0.5) # fontsize : 14
# Plot circle
circle = plt.Circle((0, 0), 1, facecolor='none', edgecolor='b')
plt.gca().add_artist(circle)
# définition des limites du graphique
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
# affichage des lignes horizontales et verticales
plt.plot([-1, 1], [0, 0], color='grey', ls='--')
plt.plot([0, 0], [-1, 1], color='grey', ls='--')
# Axes labels with % explained variance
plt.xlabel('F{} ({}%)'.format(d1 + 1,
round(100 * self.evr[d1], 1)),
labelpad=20)
plt.ylabel('F{} ({}%)'.format(d2 + 1,
round(100 * self.evr[d2], 1)),
labelpad=20)
plt.title("Cercle des corrélations (F{} et F{})".format(
d1 + 1, d2 + 1),
pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig(
'corr_circle_{}.jpg'.format(1 if d1 == 0 else d1))
plt.show(block=False)
def plot_factorial_planes(self,
n_plan=None,
X_projected=None,
labels=None,
alpha=1,
illustrative_var=None,
illustrative_var_title=None,
save_as_img=False,
plot_size=(10, 8)):
"""
:param: axis_nb: the total number of axes to display (default is kaiser criterion divided by 2)
"""
X_projected = self.X_projected if X_projected is None else X_projected
factorial_plan_nb = self.default_factorial_plan_nb if n_plan is None else n_plan
axis_ranks = [(x, x + 1) for x in range(0, factorial_plan_nb, 2)]
for d1, d2 in axis_ranks:
if d2 < self.n_comp:
fig = plt.figure(figsize=plot_size)
# Display data points
if illustrative_var is None:
plt.scatter(X_projected[:, d1],
X_projected[:, d2],
alpha=alpha)
else:
illustrative_var = np.array(illustrative_var)
for value in np.unique(illustrative_var):
selected = np.where(illustrative_var == value)
plt.scatter(X_projected[selected, d1],
X_projected[selected, d2],
alpha=alpha,
label=value)
plt.legend(title=illustrative_var_title
if illustrative_var_title is not None else None)
# Display data points labels
if labels is not None:
for i, (x, y) in enumerate(X_projected[:, [d1, d2]]):
plt.text(x,
y,
labels[i],
fontsize='12',
ha='center',
va='bottom')
# Fix factorial plan limits
boundary = np.max(np.abs(X_projected[:, [d1, d2]])) * 1.1
plt.xlim([-boundary, boundary])
plt.ylim([-boundary, boundary])
# Display horizontal & vertical lines
plt.plot([-100, 100], [0, 0], color='grey', ls='--')
plt.plot([0, 0], [-100, 100], color='grey', ls='--')
# Axes labels with % explained variance
plt.xlabel('F{} ({}%)'.format(d1 + 1,
round(100 * self.evr[d1], 1)),
labelpad=20)
plt.ylabel('F{} ({}%)'.format(d2 + 1,
round(100 * self.evr[d2], 1)),
labelpad=20)
plt.title("Projection des individus (sur F{} et F{})".format(
d1 + 1, d2 + 1),
pad=20)
if save_as_img:
plt.tight_layout()
plt.savefig(
'factorial_plan_{}.jpg'.format(1 if d1 == 0 else d1))
plt.show(block=False)