def test_plot_violins(pca, kwargs, df_norm):
from flotilla.visualize.decomposition import DecompositionViz
kw = kwargs.copy()
kw.pop('singles')
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_,
singles=df_norm, **kw)
dv.plot(plot_violins=True)
ncols = 4
nrows = 1
top_features = pd.Index(dv.top_features)
vector_labels = list(set(dv.magnitudes[:dv.n_vectors].index.union(
top_features)))
while ncols * nrows < len(vector_labels):
nrows += 1
pdt.assert_equal(len(dv.fig_violins.axes), nrows * ncols)
# for i in np.arange(len(top_features)):
# ax = dv.fig_violins.axes[i]
# pdt.assert_equal(len(ax.collections), len(dv.grouped.groups))
plt.close('all')
def test_plot_violins(pca, kwargs, df_norm):
from flotilla.visualize.decomposition import DecompositionViz
kw = kwargs.copy()
kw.pop('singles')
dv = DecompositionViz(pca.reduced_space,
pca.components_,
pca.explained_variance_ratio_,
singles=df_norm,
**kw)
dv.plot(plot_violins=True)
ncols = 4
nrows = 1
top_features = pd.Index(dv.top_features)
vector_labels = list(
set(dv.magnitudes[:dv.n_vectors].index.union(top_features)))
while ncols * nrows < len(vector_labels):
nrows += 1
pdt.assert_equal(len(dv.fig_violins.axes), nrows * ncols)
# for i in np.arange(len(top_features)):
# ax = dv.fig_violins.axes[i]
# pdt.assert_equal(len(ax.collections), len(dv.grouped.groups))
plt.close('all')
def test_plot_loadings(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot_loadings()
ax = plt.gca()
pdt.assert_equal(len(ax.collections), 1)
plt.close('all')
def test_plot_samples(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot_samples()
ax = plt.gca()
pdt.assert_equal(len(ax.lines), kwargs['n_vectors'] + 1)
plt.close('all')
def test_plot_loadings(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot_loadings()
ax = plt.gca()
pdt.assert_equal(len(ax.collections), 1)
plt.close('all')
def test_plot_samples(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot_samples()
ax = plt.gca()
pdt.assert_equal(len(ax.lines), kwargs['n_vectors'] + 1)
plt.close('all')
def test_plot_loadings_scatter(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot(plot_loadings='scatter')
pdt.assert_equal(len(dv.fig_reduced.axes), 3)
pdt.assert_equal(len(dv.ax_loading1.collections), 1)
pdt.assert_equal(len(dv.ax_loading1.collections), 1)
plt.close('all')
def test_plot_loadings_scatter(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot(plot_loadings='scatter')
pdt.assert_equal(len(dv.fig_reduced.axes), 3)
pdt.assert_equal(len(dv.ax_loading1.collections), 1)
pdt.assert_equal(len(dv.ax_loading1.collections), 1)
plt.close('all')
def test_order(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
kw = kwargs.copy()
kw.pop('order')
kw.pop('groupby')
groups = ['group1', 'group2', 'group3']
groupby = pd.Series(
[np.random.choice(groups) for i in pca.reduced_space.index],
index=pca.reduced_space.index)
order = ['group3', 'group1', 'group2']
dv = DecompositionViz(pca.reduced_space,
pca.components_,
pca.explained_variance_ratio_,
order=order,
groupby=groupby,
**kw)
color_ordered = [dv.label_to_color[x] for x in order]
pdt.assert_series_equal(dv.groupby, groupby)
pdt.assert_array_equal(dv.order, order)
pdt.assert_array_equal(dv.color_ordered, color_ordered)
def test_large_dataframe(pca_large_dataframe, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca_large_dataframe.reduced_space,
pca_large_dataframe.components_,
pca_large_dataframe.explained_variance_ratio_,
**kwargs)
x_pc = kwargs['x_pc']
y_pc = kwargs['y_pc']
pcs = [x_pc, y_pc]
true_top_features = set([])
true_pc_loadings_labels = {}
true_pc_loadings = {}
for pc in pcs:
x = pca_large_dataframe.components_.ix[pc].copy()
x.sort(ascending=True)
half_features = int(kwargs['n_top_pc_features'] / 2)
if len(x) > kwargs['n_top_pc_features']:
a = x[:half_features]
b = x[-half_features:]
labels = np.r_[a.index, b.index]
true_pc_loadings[pc] = np.r_[a, b]
else:
labels = x.index
true_pc_loadings[pc] = x
true_pc_loadings_labels[pc] = labels
true_top_features.update(labels)
pdt.assert_array_equal(dv.top_features, true_top_features)
pdt.assert_dict_equal(dv.pc_loadings_labels, true_pc_loadings_labels)
pdt.assert_dict_equal(dv.pc_loadings, true_pc_loadings)
def test_plot(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot()
pdt.assert_equal(len(dv.fig_reduced.axes), 5)
pdt.assert_equal(len(dv.ax_components.lines), kwargs['n_vectors'] + 1)
pdt.assert_equal(len(dv.ax_explained_variance.lines), 1)
pdt.assert_equal(len(dv.ax_explained_variance.collections), 1)
pdt.assert_equal(len(dv.ax_empty.collections), 0)
pdt.assert_equal(len(dv.ax_pcs_heatmap.collections), 1)
pdt.assert_equal(len(dv.ax_pcs_colorbar.collections), 1)
assert not hasattr(dv, 'ax_loading1')
assert not hasattr(dv, 'ax_loading2')
plt.close('all')
def test_plot(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
dv.plot()
pdt.assert_equal(len(dv.fig_reduced.axes), 5)
pdt.assert_equal(len(dv.ax_components.lines),
kwargs['n_vectors']+1)
pdt.assert_equal(len(dv.ax_explained_variance.lines), 1)
pdt.assert_equal(len(dv.ax_explained_variance.collections), 1)
pdt.assert_equal(len(dv.ax_empty.collections), 0)
pdt.assert_equal(len(dv.ax_pcs_heatmap.collections), 1)
pdt.assert_equal(len(dv.ax_pcs_colorbar.collections), 1)
assert not hasattr(dv, 'ax_loading1')
assert not hasattr(dv, 'ax_loading2')
plt.close('all')
def test_init(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_,
pca.explained_variance_ratio_, **kwargs)
x_pc = kwargs['x_pc']
y_pc = kwargs['y_pc']
pcs = [x_pc, y_pc]
true_groupby = dict.fromkeys(pca.reduced_space.index, 'all')
true_grouped = pca.reduced_space.groupby(true_groupby, axis=0)
colors = iter(sns.color_palette('husl', n_colors=len(true_grouped)))
def color_factory():
return colors.next()
true_label_to_color = defaultdict(color_factory)
markers = cycle(['o', '^', 's', 'v', '*', 'D', 'h'])
def marker_factory():
return markers.next()
true_label_to_marker = defaultdict(marker_factory)
for group in true_grouped.groups:
true_label_to_marker[group]
for group in dv.grouped.groups:
dv.label_to_marker[group]
true_color_ordered = [true_label_to_color[x] for x in true_grouped.groups]
true_vars = pca.explained_variance_ratio_[[x_pc, y_pc]]
true_loadings = pca.components_.ix[[x_pc, y_pc]]
true_loadings = true_loadings.multiply(true_vars, axis=0)
reduced_space = pca.reduced_space[[x_pc, y_pc]]
farthest_sample = reduced_space.apply(np.linalg.norm, axis=0).max()
whole_space = true_loadings.apply(np.linalg.norm).max()
scale = .25 * farthest_sample / whole_space
true_loadings *= scale
ord = 2 if kwargs['distance'] == 'L2' else 1
true_magnitudes = true_loadings.apply(np.linalg.norm, ord=ord)
true_magnitudes.sort(ascending=False)
true_top_features = set([])
true_pc_loadings_labels = {}
true_pc_loadings = {}
for pc in pcs:
x = pca.components_.ix[pc].copy()
x.sort(ascending=True)
half_features = int(kwargs['n_top_pc_features'] / 2)
if len(x) > kwargs['n_top_pc_features']:
a = x[:half_features]
b = x[-half_features:]
labels = np.r_[a.index, b.index]
true_pc_loadings[pc] = np.r_[a, b]
else:
labels = x.index
true_pc_loadings[pc] = x
true_pc_loadings_labels[pc] = labels
true_top_features.update(labels)
pdt.assert_frame_equal(dv.reduced_space, pca.reduced_space)
pdt.assert_frame_equal(dv.components_, pca.components_)
pdt.assert_series_equal(dv.explained_variance_ratio_,
pca.explained_variance_ratio_)
pdt.assert_dict_equal(dv.label_to_marker, true_label_to_marker)
pdt.assert_dict_equal(dv.groupby, true_groupby)
pdt.assert_series_equal(dv.vars, true_vars)
pdt.assert_frame_equal(dv.loadings, true_loadings)
npt.assert_array_equal(dv.color_ordered, true_color_ordered)
pdt.assert_series_equal(dv.magnitudes, true_magnitudes)
npt.assert_array_equal(dv.top_features, true_top_features)
pdt.assert_dict_equal(dv.pc_loadings_labels, true_pc_loadings_labels)
pdt.assert_dict_equal(dv.pc_loadings, true_pc_loadings)
def test_explained_variance_none(pca, kwargs):
from flotilla.visualize.decomposition import DecompositionViz
dv = DecompositionViz(pca.reduced_space, pca.components_, None)
true_vars = pd.Series([1., 1.], index=[kwargs['x_pc'], kwargs['y_pc']])
pdt.assert_series_equal(dv.vars, true_vars)