def test_valid_colorscale():
pipe = make_mapper_pipeline()
fig_2d = plot_static_mapper_graph(
pipe,
X,
layout_dim=2,
plotly_params={"node_trace": {
"marker_colorscale": "blues"
}})
fig_3d = plot_static_mapper_graph(
pipe,
X,
layout_dim=3,
plotly_params={"node_trace": {
"marker_colorscale": "blues"
}})
# Test that the custom colorscale is correctly applied both in 2d and in 3d
marker_colorscale = fig_2d.data[1]["marker"]["colorscale"]
marker_colorscale_3d = fig_3d.data[1]["marker"]["colorscale"]
assert marker_colorscale == marker_colorscale_3d
# Test that the default colorscale is "viridis" and that the custom one is
# different
fig_default = plot_static_mapper_graph(pipe, X)
marker_colorscale_default = \
fig_default.data[1]["marker"]["colorscale"]
assert marker_colorscale_default == viridis_colorscale
assert marker_colorscale != marker_colorscale_default
def test_invalid_color_features_as_array_of_indices():
pipe = make_mapper_pipeline()
with pytest.raises(ValueError):
plot_static_mapper_graph(
pipe, X_arr, color_data=X_arr,
color_features=np.arange(X_arr.shape[1])
)
def test_node_color_statistic_as_ndarray_wrong_length():
pipe = make_mapper_pipeline()
graph = pipe.fit_transform(X_arr)
node_color_statistic = np.arange(len(graph.vs) + 1)
with pytest.raises(ValueError):
plot_static_mapper_graph(pipe, X_arr,
node_color_statistic=node_color_statistic)
def test_colors_same_2d_3d(X, color_variable, node_color_statistic):
pipe = make_mapper_pipeline()
fig_2d = plot_static_mapper_graph(
pipe, X, layout_dim=2, color_variable=color_variable,
node_color_statistic=node_color_statistic
)
fig_3d = plot_static_mapper_graph(
pipe, X, layout_dim=3, color_variable=color_variable,
node_color_statistic=node_color_statistic
)
assert fig_2d.data[1].marker.color == fig_3d.data[1].marker.color
def test_colors_same_2d_3d(X, color_data, node_color_statistic):
pipe = make_mapper_pipeline()
fig_2d = plot_static_mapper_graph(
pipe, X, layout_dim=2, color_data=color_data,
node_color_statistic=node_color_statistic
)
fig_3d = plot_static_mapper_graph(
pipe, X, layout_dim=3, color_data=color_data,
node_color_statistic=node_color_statistic
)
assert np.array_equal(fig_2d.data[1].marker.color,
fig_3d.data[1].marker.color)
def test_column_dropdown(X, columns, layout_dim):
pipe = make_mapper_pipeline()
fig = plot_static_mapper_graph(pipe, X, color_data=X,
layout_dim=layout_dim)
fig_buttons = fig.layout.updatemenus[0].buttons
assert list(fig.data[1].marker.color) == \
list(fig_buttons[0].args[0]["marker.color"][1])
for i, col in enumerate(columns):
fig_col = plot_static_mapper_graph(
pipe, X, layout_dim=layout_dim, color_data=X, color_features=col
)
assert list(fig_col.data[1].marker.color) == \
list(fig_buttons[i].args[0]["marker.color"][1])
def test_valid_layout_dim(X, layout_dim):
pipe = make_mapper_pipeline()
fig = plot_static_mapper_graph(pipe, X, layout_dim=layout_dim)
edge_trace = fig.data[0]
assert hasattr(edge_trace, "x") and hasattr(edge_trace, "y")
is_z_present = hasattr(edge_trace, "z")
assert is_z_present if layout_dim == 3 else not is_z_present
def test_valid_hoverlabel_bgcolor(X, layout_dim):
pipe = make_mapper_pipeline()
fig = plot_static_mapper_graph(
pipe, X, layout_dim=layout_dim,
plotly_params={"node_trace": {"hoverlabel_bgcolor": "white"}}
)
assert fig.data[1]["hoverlabel"]["bgcolor"] == "white"
def test_unsuitable_colorscale_for_hoverlabel_3d(X):
pipe = make_mapper_pipeline()
with pytest.warns(RuntimeWarning):
_ = plot_static_mapper_graph(
pipe, X, layout_dim=3,
plotly_params={"node_trace": {"marker_colorscale": hsl_colorscale}}
)
def test_color_by_column_dropdown_2d(layout_dim):
pipe = make_mapper_pipeline()
fig = plot_static_mapper_graph(pipe,
X,
layout_dim=layout_dim,
color_by_columns_dropdown=True)
fig_buttons = fig.layout.updatemenus[0].buttons
assert list(fig.data[1].marker.color) == \
list(fig_buttons[0].args[0]["marker.color"][1])
for i in range(X.shape[1]):
fig_col_i = plot_static_mapper_graph(pipe,
X,
layout_dim=layout_dim,
color_variable=i)
assert list(fig_col_i.data[1].marker.color) == \
list(fig_buttons[i + 1].args[0]["marker.color"][1])
def test_node_color_statistic_as_ndarray():
pipe = make_mapper_pipeline()
graph = pipe.fit_transform(X_arr)
node_color_statistic = np.arange(len(graph.vs))
fig = plot_static_mapper_graph(pipe,
X_arr,
node_color_statistic=node_color_statistic)
assert np.array_equal(fig.data[1].marker.color, node_color_statistic)
def test_cluster_sizes(self):
"""Verify that the total number of calculated clusters is equal to
the number of displayed clusters."""
pipe = make_mapper_pipeline(clusterer=FirstSimpleGap())
fig = plot_static_mapper_graph(pipe, X_arr)
node_trace = fig.data[1]
node_sizes_vis = [_get_size_from_hovertext(ht) for ht in
node_trace.hovertext]
g = pipe.fit_transform(X_arr)
node_size_real = [len(node) for node in g.vs['node_elements']]
assert sum(node_sizes_vis) == sum(node_size_real)
def test_node_color_statistic_as_ndarray(is_2d):
pipe = make_mapper_pipeline()
graph = pipe.fit_transform(X_arr)
node_color_statistic_col_0 = np.arange(len(graph.vs))
if is_2d:
node_color_statistic = np.vstack([node_color_statistic_col_0,
node_color_statistic_col_0]).T
else:
node_color_statistic = node_color_statistic_col_0
fig = plot_static_mapper_graph(pipe, X_arr,
node_color_statistic=node_color_statistic)
assert np.array_equal(fig.data[1].marker.color, node_color_statistic_col_0)
def test_is_data_present(self):
"""Verify that what we see in the graph corresponds to
the number of samples in the graph."""
pipe = make_mapper_pipeline()
warnings.simplefilter("ignore")
fig = plot_static_mapper_graph(pipe,
X,
color_variable=colors,
clone_pipeline=False)
xy = np.stack([fig.get_state()['_data'][1][c]
for c in ['x', 'y']]).transpose()
assert X.shape >= xy.shape
real_colors = fig.get_state()['_data'][1]['marker']['color']
assert len(real_colors) == xy.shape[0]
def test_color_features_as_estimator_or_callable(color_features):
pipe = make_mapper_pipeline()
graph = pipe.fit_transform(X_arr)
node_elements = graph.vs["node_elements"]
pca = PCA(n_components=2)
color_data_transformed = pca.fit_transform(X_arr)
node_colors_color_features = \
np.array([np.mean(color_data_transformed[itr, 0])
for itr in node_elements])
fig = plot_static_mapper_graph(pipe, X_arr, color_data=X_arr,
color_features=color_features)
assert_almost_equal(fig.data[1].marker.color, node_colors_color_features)
def test_is_data_present(self):
"""Verify that what we see in the graph corresponds to
the number of samples in the graph."""
pipe = make_mapper_pipeline()
fig = plot_static_mapper_graph(pipe, X_arr, color_data=colors,
clone_pipeline=False)
node_trace_x = fig.data[1].x
node_trace_y = fig.data[1].y
assert node_trace_x.shape[0] == node_trace_y.shape[0]
num_nodes = node_trace_x.shape[0]
assert len(X_arr) >= num_nodes
fig_colors = fig.data[1].marker.color
assert len(fig_colors) == num_nodes
def test_interactive_plotter_attrs(X, color_data, layout_dim):
"""Simple tests on the attributes stored by MapperInteractivePlotter when
plotting."""
pipe = make_mapper_pipeline()
plotter = MapperInteractivePlotter(pipe, X)
plotter.plot(color_data=color_data, layout_dim=layout_dim)
# 1 Test graph_
graph = pipe.fit_transform(X)
assert plotter.graph_.isomorphic(graph)
# 2 Test pipeline_
assert str(plotter.pipeline_) == str(pipe)
# 3 Test color_features_
if color_data is not None:
color_data_transformed = color_data
else:
color_data_transformed = np.arange(len(X)).reshape(-1, 1)
assert np.array_equal(plotter.color_features_, color_data_transformed)
# 4 Test node_summaries_
assert len(plotter.node_summaries_) == len(graph.vs)
# 5 Test figure_
static_fig = plot_static_mapper_graph(pipe, X, color_data=color_data,
layout_dim=layout_dim)
interactive_fig = plotter.figure_
edge_trace_attrs = ["hoverinfo", "line", "name", "x", "y"]
for attr in edge_trace_attrs:
assert np.all(getattr(interactive_fig.data[0], attr) ==
getattr(static_fig.data[0], attr))
# Excluding marker, which gets treated separately below
node_trace_attrs = ["hoverinfo", "hovertext", "mode", "name", "x", "y"]
for attr in node_trace_attrs:
assert np.all(getattr(interactive_fig.data[1], attr) ==
getattr(static_fig.data[1], attr))
marker_attrs = ["color", "colorbar", "colorscale", "line", "opacity",
"reversescale", "showscale", "size", "sizemin", "sizemode",
"sizeref"]
for attr in marker_attrs:
assert np.all(getattr(interactive_fig.data[1].marker, attr) ==
getattr(static_fig.data[1].marker, attr))
def test_is_data_present(self):
"""Verify that what we see in the graph corresponds to
the number of samples in the graph."""
pipe = make_mapper_pipeline()
warnings.simplefilter("ignore")
fig = plot_static_mapper_graph(pipe, X,
color_variable=colors,
clone_pipeline=False)
node_trace_x = fig.get_state()['_data'][1]["x"]
node_trace_y = fig.get_state()['_data'][1]["y"]
assert node_trace_x["shape"][0] == node_trace_y["shape"][0]
num_nodes = node_trace_x["shape"][0]
assert len(X) >= num_nodes
fig_colors = fig.get_state()['_data'][1]['marker']['color']
assert len(fig_colors) == num_nodes
def test_invalid_layout_algorithm(X):
with pytest.raises(KeyError):
pipe = make_mapper_pipeline()
_ = plot_static_mapper_graph(pipe, X, layout="foobar")
def test_invalid_layout_dim(X, layout_dim):
with pytest.raises(ValueError):
pipe = make_mapper_pipeline()
_ = plot_static_mapper_graph(pipe, X, layout_dim=layout_dim)
def get_region_plot(pipe, data, layout, node_elements, colorscale):
'''Function to generate a figure of the mapper graph colored by identified
regions
Parameters
----------
pipe : MapperPipeline
The Mapper pipeline to compute the mapper-graph
data : ndarray (n_samples x n_dim)
Data used for mapper
layout : igraph.layout.Layout
Layout of graph
node_elements : tuple
Tuple of arrays where array at positin x contains the data points for
node x
colorscale : list
List of colors to use for each region
Returns
-------
fig : igraph object
'''
regions = utils.get_regions()
# set node color:
# 1. assign to each node of a region its color (zip())
# 2. convert zip elements to list (map())
# 3. flatten list (itertools.chain())
# 4. sort values by keys
# 5. convert to ordered dictionary
# 6. extract values and convert to list
node_color = np.array(
list(
collections.OrderedDict(
sorted(
itertools.chain(*map(list, [
zip(regions[region],
itertools.repeat(colorscale[region]))
for region in range(len(regions))
])))).values()))
# set plotly arguments:
# 1. set uniform node size
# 2. hide scale of marker color
plotly_kwargs = {
'node_trace_marker_size': [1] * len(node_elements),
'node_trace_marker_showscale': False,
'node_trace_hoverlabel': node_color,
'node_trace_marker_color': node_color
}
fig = plot_static_mapper_graph(pipe,
data,
layout,
layout_dim=2,
color_by_columns_dropdown=False,
plotly_kwargs=plotly_kwargs)
# update colors to fig
fig._data[1]['marker'][
'color'] = node_color # hack around with the new api
return fig
def test_color_features_as_columns_fails_on_series():
pipe = make_mapper_pipeline()
with pytest.raises(ValueError, match="If `color_data` is a pandas series"):
plot_static_mapper_graph(pipe, X_df, color_data=X_df["a"],
color_features="a")
def main():
directory = DOTENV_KEY2VAL["DATA_DIR"]
image_dir = directory + "/patch_92/"
diagnosis_json = "collected_diagnoses_complete.json"
(
cn_patients,
mci_patients,
ad_patients,
) = utils.get_earliest_available_diagnosis(directory + diagnosis_json)
images_all = utils.get_arrays_from_dir(
image_dir, cn_patients + mci_patients + ad_patients)
cn_patient_list = [
1 for patient in range(len(cn_patients) - 1)
] # substracting one due to unfound MRI for one CN patient
mci_patient_list = [2 for patient in range(len(mci_patients))]
ad_patient_list = [3 for patient in range(len(ad_patients))]
diags = np.array(cn_patient_list + mci_patient_list +
ad_patient_list).reshape(-1, 1)
ohe = OneHotEncoder()
labels = ohe.fit_transform(diags).toarray()
images = []
for image in images_all:
images.append(image.flatten())
images_all = np.asarray(images)
pca = PCA(n_components=440)
pca.fit(images_all)
fig, ax0 = plt.subplots(nrows=1, sharex=True, figsize=(6, 6))
ax0.plot(
np.arange(1, pca.n_components_ + 1),
pca.explained_variance_ratio_,
"+",
linewidth=2,
)
ax0.set_ylabel("PCA explained variance ratio")
ax0.legend(prop=dict(size=12))
plt.savefig(DOTENV_KEY2VAL["GEN_FIGURES_DIR"] + "elbow_plot.png")
n_components = 3
pca = PCA(n_components=n_components)
images_all_projected = pca.fit_transform(images_all)
images_all_projected = np.append(images_all_projected, labels, axis=1)
mapper_pipeline = make_mapper_pipeline(
filter_func=Projection(columns=[index for index in range(2)]),
cover=CubicalCover(n_intervals=10, overlap_frac=0.25),
clusterer=DBSCAN(eps=0.5, min_samples=5),
verbose=True,
n_jobs=4,
)
plotly_params = {"node_trace": {"marker_colorscale": "Blues"}}
fig = plot_static_mapper_graph(
mapper_pipeline,
images_all_projected,
layout_dim=3,
color_by_columns_dropdown=True,
plotly_params=plotly_params,
)
fig.write_html(DOTENV_KEY2VAL["GEN_FIGURES_DIR"] +
"mapper_2_dimensional_reduction.html")
images_all_projected = pd.DataFrame(images_all_projected)
fig = px.scatter_3d(
images_all_projected,
x=0,
y=1,
z=2,
color=3,
title="3D scatterplot of the PCA of the image data",
)
fig.write_html(DOTENV_KEY2VAL["GEN_FIGURES_DIR"] +
"scatterplot_pca_3d.html")
def test_valid_color_data_transformed(color_data, color_features):
"""Test that no errors are thrown when pandas dataframes/series are passed
as color_data and/or returned when applying color_features."""
pipe = make_mapper_pipeline()
plot_static_mapper_graph(pipe, X_arr, color_data=color_data,
color_features=color_features)
def get_graph_plot_colored_by_election_results(pipeline, year, df, data,
keep_layout):
'''Function make plot of US with counties colored by winner of election
Parameters
----------
pipe : MapperPipeline
The Mapper pipeline to compute the mapper-graph
year : np.int
Color by election results from year `year`
df : pandas data frame
Data frame containing info of winner per county, year of election and
number of electors in county
data : ndarray (n_samples x n_dim)
Data used for mapper
keep_layout : list of two dicts, with keys 'x', 'y', and such that values are 1d arrays
Positions of lines (keep_layout[0]) and markers respectively (keep_layout[1])
for the mapper graph
Returns
-------
fig: igraph object
'''
node_elements = pipeline.fit_transform(
data)['node_metadata']['node_elements']
# set node color to percentage of number of electors won by republicans
node_color = np.array([
100 * (df[df['year'] == year]['winner'].values *
df[df['year'] == year]['n_electors'].values)[x].sum() /
df[df['year'] == year]['n_electors'].values[x].sum()
for x in node_elements
])
data_cols = utils.get_cols_for_mapper()
columns_to_color = dict(zip(data_cols, range(len(data_cols))))
node_text = utils.get_node_text(
dict(zip(range(len(node_elements)), node_elements)),
utils.get_n_electors(
node_elements,
df[df['year'] == year]['n_electors'].reset_index(drop=True)),
node_color, 'Percentage of Electors Won by Republicans')
plotly_kwargs = {
'node_trace_marker_colorscale':
'RdBu',
'node_trace_marker_reversescale':
True,
'node_trace_marker_cmin':
0,
'node_trace_marker_cmax':
100,
'node_trace_text':
node_text,
'node_trace_marker_size':
utils.get_n_electors(
node_elements,
df[df['year'] == year]['n_electors'].reset_index(drop=True)),
'node_trace_marker_sizeref':
.5 / max(
utils.get_n_electors(
node_elements,
df[df['year'] == year]['n_electors'].reset_index(drop=True)))
}
fig = plot_static_mapper_graph(pipeline,
data,
'kk',
layout_dim=2,
node_color_statistic=node_color,
color_by_columns_dropdown=True,
plotly_kwargs=plotly_kwargs)
if keep_layout is not None:
fig._data[0].update(keep_layout[0])
fig._data[1].update(keep_layout[1])
return fig
def test_color_data_invalid_length():
pipe = make_mapper_pipeline()
with pytest.raises(ValueError):
plot_static_mapper_graph(pipe, X_arr, color_data=X_arr[:-1])
def test_invalid_type_node_color_statistic_static():
pipe = make_mapper_pipeline()
with pytest.raises(ValueError):
plot_static_mapper_graph(pipe, X_arr, node_color_statistic="foo")
def test_invalid_color_features_types(color_features):
pipe = make_mapper_pipeline()
with pytest.raises(ValueError):
plot_static_mapper_graph(pipe, X_arr,
color_features=color_features)
