def test_default_dendrogram(self):
X = np.array([[1, 2, 3, 4], [1, 1, 3, 4], [1, 2, 1, 4], [1, 2, 3, 1]])
dendro = tls.FigureFactory.create_dendrogram(X=X)
expected_dendro = go.Figure(
data=go.Data([
go.Scatter(x=np.array([25., 25., 35., 35.]),
y=np.array([0., 1., 1., 0.]),
marker=go.Marker(color='rgb(61,153,112)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(x=np.array([15., 15., 30., 30.]),
y=np.array([0., 2.23606798, 2.23606798, 1.]),
marker=go.Marker(color='rgb(61,153,112)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(x=np.array([5., 5., 22.5, 22.5]),
y=np.array([0., 3.60555128, 3.60555128,
2.23606798]),
marker=go.Marker(color='rgb(0,116,217)'),
mode='lines',
xaxis='x',
yaxis='y')
]),
layout=go.Layout(autosize=False,
height='100%',
hovermode='closest',
showlegend=False,
width='100%',
xaxis=go.XAxis(mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
tickmode='array',
ticks='outside',
ticktext=np.array(
['3', '2', '0', '1']),
tickvals=[5.0, 15.0, 25.0, 35.0],
type='linear',
zeroline=False),
yaxis=go.YAxis(mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
ticks='outside',
type='linear',
zeroline=False)))
self.assertEqual(len(dendro['data']), 3)
# this is actually a bit clearer when debugging tests.
self.assert_dict_equal(dendro['data'][0], expected_dendro['data'][0])
self.assert_dict_equal(dendro['data'][1], expected_dendro['data'][1])
self.assert_dict_equal(dendro['data'][2], expected_dendro['data'][2])
self.assert_dict_equal(dendro['layout'], expected_dendro['layout'])
def make_XAxis(xaxis_title, xaxis_range):
"""
Makes the x-axis for a violin plot.
"""
xaxis = graph_objs.XAxis(title=xaxis_title,
range=xaxis_range,
showgrid=False,
zeroline=False,
showline=False,
mirror=False,
ticks='',
showticklabels=False)
return xaxis
def make_XAxis(xaxis_title, xaxis_range):
"""
Makes the x-axis for a violin plot.
"""
xaxis = graph_objs.XAxis(title='',
range=xaxis_range,
showgrid=False,
zeroline=False,
showline=False,
mirror=False,
ticks="",
tickvals=[0],
ticktext=[xaxis_title],
tickangle=35,
showticklabels=True,
titlefont=dict(size=10))
return xaxis
def get_subplots(rows=1,
columns=1,
horizontal_spacing=0.1,
vertical_spacing=0.15,
print_grid=False):
"""Return a dictionary instance with the subplots set in 'layout'.
Example 1:
# stack two subplots vertically
fig = tools.get_subplots(rows=2)
fig['data'] += [Scatter(x=[1,2,3], y=[2,1,2], xaxis='x1', yaxis='y1')]
fig['data'] += [Scatter(x=[1,2,3], y=[2,1,2], xaxis='x2', yaxis='y2')]
Example 2:
# print out string showing the subplot grid you've put in the layout
fig = tools.get_subplots(rows=3, columns=2, print_grid=True)
key (types, default=default):
description.
rows (int, default=1):
Number of rows, evenly spaced vertically on the figure.
columns (int, default=1):
Number of columns, evenly spaced horizontally on the figure.
horizontal_spacing (float in [0,1], default=0.1):
Space between subplot columns. Applied to all columns.
vertical_spacing (float in [0,1], default=0.05):
Space between subplot rows. Applied to all rows.
print_grid (True | False, default=False):
If True, prints a tab-delimited string representation of your plot grid.
"""
fig = dict(layout=graph_objs.Layout()) # will return this at the end
plot_width = (1 - horizontal_spacing * (columns - 1)) / columns
plot_height = (1 - vertical_spacing * (rows - 1)) / rows
plot_num = 0
for rrr in range(rows):
for ccc in range(columns):
xaxis_name = 'xaxis{0}'.format(plot_num + 1)
x_anchor = 'y{0}'.format(plot_num + 1)
x_start = (plot_width + horizontal_spacing) * ccc
x_end = x_start + plot_width
yaxis_name = 'yaxis{0}'.format(plot_num + 1)
y_anchor = 'x{0}'.format(plot_num + 1)
y_start = (plot_height + vertical_spacing) * rrr
y_end = y_start + plot_height
xaxis = graph_objs.XAxis(domain=[x_start, x_end], anchor=x_anchor)
fig['layout'][xaxis_name] = xaxis
yaxis = graph_objs.YAxis(domain=[y_start, y_end], anchor=y_anchor)
fig['layout'][yaxis_name] = yaxis
plot_num += 1
if print_grid:
print("This is the format of your plot grid!")
grid_string = ""
plot = 1
for rrr in range(rows):
grid_line = ""
for ccc in range(columns):
grid_line += "[{0}]\t".format(plot)
plot += 1
grid_string = grid_line + '\n' + grid_string
print(grid_string)
return graph_objs.Figure(fig) # forces us to validate what we just did...
def get_subplots(rows=1, columns=1, print_grid=False, **kwargs):
"""Return a dictionary instance with the subplots set in 'layout'.
Example 1:
# stack two subplots vertically
fig = tools.get_subplots(rows=2)
fig['data'] += [Scatter(x=[1,2,3], y=[2,1,2], xaxis='x1', yaxis='y1')]
fig['data'] += [Scatter(x=[1,2,3], y=[2,1,2], xaxis='x2', yaxis='y2')]
Example 2:
# print out string showing the subplot grid you've put in the layout
fig = tools.get_subplots(rows=3, columns=2, print_grid=True)
Keywords arguments with constant defaults:
rows (kwarg, int greater than 0, default=1):
Number of rows, evenly spaced vertically on the figure.
columns (kwarg, int greater than 0, default=1):
Number of columns, evenly spaced horizontally on the figure.
horizontal_spacing (kwarg, float in [0,1], default=0.1):
Space between subplot columns. Applied to all columns.
vertical_spacing (kwarg, float in [0,1], default=0.05):
Space between subplot rows. Applied to all rows.
print_grid (kwarg, True | False, default=False):
If True, prints a tab-delimited string representation
of your plot grid.
Keyword arguments with variable defaults:
horizontal_spacing (kwarg, float in [0,1], default=0.2 / columns):
Space between subplot columns.
vertical_spacing (kwarg, float in [0,1], default=0.3 / rows):
Space between subplot rows.
"""
warnings.warn(
"tools.get_subplots is depreciated. "
"Please use tools.make_subplots instead."
)
# Throw exception for non-integer rows and columns
if not isinstance(rows, int) or rows <= 0:
raise Exception("Keyword argument 'rows' "
"must be an int greater than 0")
if not isinstance(columns, int) or columns <= 0:
raise Exception("Keyword argument 'columns' "
"must be an int greater than 0")
# Throw exception if non-valid kwarg is sent
VALID_KWARGS = ['horizontal_spacing', 'vertical_spacing']
for key in kwargs.keys():
if key not in VALID_KWARGS:
raise Exception("Invalid keyword argument: '{0}'".format(key))
# Set 'horizontal_spacing' / 'vertical_spacing' w.r.t. rows / columns
try:
horizontal_spacing = float(kwargs['horizontal_spacing'])
except KeyError:
horizontal_spacing = 0.2 / columns
try:
vertical_spacing = float(kwargs['vertical_spacing'])
except KeyError:
vertical_spacing = 0.3 / rows
fig = dict(layout=graph_objs.Layout()) # will return this at the end
plot_width = (1 - horizontal_spacing * (columns - 1)) / columns
plot_height = (1 - vertical_spacing * (rows - 1)) / rows
plot_num = 0
for rrr in range(rows):
for ccc in range(columns):
xaxis_name = 'xaxis{0}'.format(plot_num + 1)
x_anchor = 'y{0}'.format(plot_num + 1)
x_start = (plot_width + horizontal_spacing) * ccc
x_end = x_start + plot_width
yaxis_name = 'yaxis{0}'.format(plot_num + 1)
y_anchor = 'x{0}'.format(plot_num + 1)
y_start = (plot_height + vertical_spacing) * rrr
y_end = y_start + plot_height
xaxis = graph_objs.XAxis(domain=[x_start, x_end], anchor=x_anchor)
fig['layout'][xaxis_name] = xaxis
yaxis = graph_objs.YAxis(domain=[y_start, y_end], anchor=y_anchor)
fig['layout'][yaxis_name] = yaxis
plot_num += 1
if print_grid:
print("This is the format of your plot grid!")
grid_string = ""
plot = 1
for rrr in range(rows):
grid_line = ""
for ccc in range(columns):
grid_line += "[{0}]\t".format(plot)
plot += 1
grid_string = grid_line + '\n' + grid_string
print(grid_string)
return graph_objs.Figure(fig) # forces us to validate what we just did...
def create_trisurf(x,
y,
z,
simplices,
colormap=None,
show_colorbar=True,
scale=None,
color_func=None,
title='Trisurf Plot',
plot_edges=True,
showbackground=True,
backgroundcolor='rgb(230, 230, 230)',
gridcolor='rgb(255, 255, 255)',
zerolinecolor='rgb(255, 255, 255)',
edges_color='rgb(50, 50, 50)',
height=800,
width=800,
aspectratio=None):
"""
Returns figure for a triangulated surface plot
:param (array) x: data values of x in a 1D array
:param (array) y: data values of y in a 1D array
:param (array) z: data values of z in a 1D array
:param (array) simplices: an array of shape (ntri, 3) where ntri is
the number of triangles in the triangularization. Each row of the
array contains the indicies of the verticies of each triangle
:param (str|tuple|list) colormap: either a plotly scale name, an rgb
or hex color, a color tuple or a list of colors. An rgb color is
of the form 'rgb(x, y, z)' where x, y, z belong to the interval
[0, 255] and a color tuple is a tuple of the form (a, b, c) where
a, b and c belong to [0, 1]. If colormap is a list, it must
contain the valid color types aforementioned as its members
:param (bool) show_colorbar: determines if colorbar is visible
:param (list|array) scale: sets the scale values to be used if a non-
linearly interpolated colormap is desired. If left as None, a
linear interpolation between the colors will be excecuted
:param (function|list) color_func: The parameter that determines the
coloring of the surface. Takes either a function with 3 arguments
x, y, z or a list/array of color values the same length as
simplices. If None, coloring will only depend on the z axis
:param (str) title: title of the plot
:param (bool) plot_edges: determines if the triangles on the trisurf
are visible
:param (bool) showbackground: makes background in plot visible
:param (str) backgroundcolor: color of background. Takes a string of
the form 'rgb(x,y,z)' x,y,z are between 0 and 255 inclusive
:param (str) gridcolor: color of the gridlines besides the axes. Takes
a string of the form 'rgb(x,y,z)' x,y,z are between 0 and 255
inclusive
:param (str) zerolinecolor: color of the axes. Takes a string of the
form 'rgb(x,y,z)' x,y,z are between 0 and 255 inclusive
:param (str) edges_color: color of the edges, if plot_edges is True
:param (int|float) height: the height of the plot (in pixels)
:param (int|float) width: the width of the plot (in pixels)
:param (dict) aspectratio: a dictionary of the aspect ratio values for
the x, y and z axes. 'x', 'y' and 'z' take (int|float) values
Example 1: Sphere
```
# Necessary Imports for Trisurf
import numpy as np
from scipy.spatial import Delaunay
import plotly.plotly as py
from plotly.figure_factory import create_trisurf
from plotly.graph_objs import graph_objs
# Make data for plot
u = np.linspace(0, 2*np.pi, 20)
v = np.linspace(0, np.pi, 20)
u,v = np.meshgrid(u,v)
u = u.flatten()
v = v.flatten()
x = np.sin(v)*np.cos(u)
y = np.sin(v)*np.sin(u)
z = np.cos(v)
points2D = np.vstack([u,v]).T
tri = Delaunay(points2D)
simplices = tri.simplices
# Create a figure
fig1 = create_trisurf(x=x, y=y, z=z, colormap="Rainbow",
simplices=simplices)
# Plot the data
py.iplot(fig1, filename='trisurf-plot-sphere')
```
Example 2: Torus
```
# Necessary Imports for Trisurf
import numpy as np
from scipy.spatial import Delaunay
import plotly.plotly as py
from plotly.figure_factory import create_trisurf
from plotly.graph_objs import graph_objs
# Make data for plot
u = np.linspace(0, 2*np.pi, 20)
v = np.linspace(0, 2*np.pi, 20)
u,v = np.meshgrid(u,v)
u = u.flatten()
v = v.flatten()
x = (3 + (np.cos(v)))*np.cos(u)
y = (3 + (np.cos(v)))*np.sin(u)
z = np.sin(v)
points2D = np.vstack([u,v]).T
tri = Delaunay(points2D)
simplices = tri.simplices
# Create a figure
fig1 = create_trisurf(x=x, y=y, z=z, colormap="Viridis",
simplices=simplices)
# Plot the data
py.iplot(fig1, filename='trisurf-plot-torus')
```
Example 3: Mobius Band
```
# Necessary Imports for Trisurf
import numpy as np
from scipy.spatial import Delaunay
import plotly.plotly as py
from plotly.figure_factory import create_trisurf
from plotly.graph_objs import graph_objs
# Make data for plot
u = np.linspace(0, 2*np.pi, 24)
v = np.linspace(-1, 1, 8)
u,v = np.meshgrid(u,v)
u = u.flatten()
v = v.flatten()
tp = 1 + 0.5*v*np.cos(u/2.)
x = tp*np.cos(u)
y = tp*np.sin(u)
z = 0.5*v*np.sin(u/2.)
points2D = np.vstack([u,v]).T
tri = Delaunay(points2D)
simplices = tri.simplices
# Create a figure
fig1 = create_trisurf(x=x, y=y, z=z, colormap=[(0.2, 0.4, 0.6), (1, 1, 1)],
simplices=simplices)
# Plot the data
py.iplot(fig1, filename='trisurf-plot-mobius-band')
```
Example 4: Using a Custom Colormap Function with Light Cone
```
# Necessary Imports for Trisurf
import numpy as np
from scipy.spatial import Delaunay
import plotly.plotly as py
from plotly.figure_factory import create_trisurf
from plotly.graph_objs import graph_objs
# Make data for plot
u=np.linspace(-np.pi, np.pi, 30)
v=np.linspace(-np.pi, np.pi, 30)
u,v=np.meshgrid(u,v)
u=u.flatten()
v=v.flatten()
x = u
y = u*np.cos(v)
z = u*np.sin(v)
points2D = np.vstack([u,v]).T
tri = Delaunay(points2D)
simplices = tri.simplices
# Define distance function
def dist_origin(x, y, z):
return np.sqrt((1.0 * x)**2 + (1.0 * y)**2 + (1.0 * z)**2)
# Create a figure
fig1 = create_trisurf(x=x, y=y, z=z,
colormap=['#FFFFFF', '#E4FFFE',
'#A4F6F9', '#FF99FE',
'#BA52ED'],
scale=[0, 0.6, 0.71, 0.89, 1],
simplices=simplices,
color_func=dist_origin)
# Plot the data
py.iplot(fig1, filename='trisurf-plot-custom-coloring')
```
Example 5: Enter color_func as a list of colors
```
# Necessary Imports for Trisurf
import numpy as np
from scipy.spatial import Delaunay
import random
import plotly.plotly as py
from plotly.figure_factory import create_trisurf
from plotly.graph_objs import graph_objs
# Make data for plot
u=np.linspace(-np.pi, np.pi, 30)
v=np.linspace(-np.pi, np.pi, 30)
u,v=np.meshgrid(u,v)
u=u.flatten()
v=v.flatten()
x = u
y = u*np.cos(v)
z = u*np.sin(v)
points2D = np.vstack([u,v]).T
tri = Delaunay(points2D)
simplices = tri.simplices
colors = []
color_choices = ['rgb(0, 0, 0)', '#6c4774', '#d6c7dd']
for index in range(len(simplices)):
colors.append(random.choice(color_choices))
fig = create_trisurf(
x, y, z, simplices,
color_func=colors,
show_colorbar=True,
edges_color='rgb(2, 85, 180)',
title=' Modern Art'
)
py.iplot(fig, filename="trisurf-plot-modern-art")
```
"""
if aspectratio is None:
aspectratio = {'x': 1, 'y': 1, 'z': 1}
# Validate colormap
colors.validate_colors(colormap)
colormap, scale = colors.convert_colors_to_same_type(
colormap, colortype='tuple', return_default_colors=True, scale=scale)
data1 = trisurf(x,
y,
z,
simplices,
show_colorbar=show_colorbar,
color_func=color_func,
colormap=colormap,
scale=scale,
edges_color=edges_color,
plot_edges=plot_edges)
axis = dict(
showbackground=showbackground,
backgroundcolor=backgroundcolor,
gridcolor=gridcolor,
zerolinecolor=zerolinecolor,
)
layout = graph_objs.Layout(title=title,
width=width,
height=height,
scene=graph_objs.Scene(
xaxis=graph_objs.XAxis(axis),
yaxis=graph_objs.YAxis(axis),
zaxis=graph_objs.ZAxis(axis),
aspectratio=dict(x=aspectratio['x'],
y=aspectratio['y'],
z=aspectratio['z']),
))
return graph_objs.Figure(data=data1, layout=layout)
def test_dendrogram_colorscale(self):
X = np.array([[1, 2, 3, 4], [1, 1, 3, 4], [1, 2, 1, 4], [1, 2, 3, 1]])
greyscale = [
'rgb(0,0,0)', # black
'rgb(05,105,105)', # dim grey
'rgb(128,128,128)', # grey
'rgb(169,169,169)', # dark grey
'rgb(192,192,192)', # silver
'rgb(211,211,211)', # light grey
'rgb(220,220,220)', # gainsboro
'rgb(245,245,245)'
] # white smoke
dendro = tls.FigureFactory.create_dendrogram(X, colorscale=greyscale)
expected_dendro = go.Figure(
data=go.Data([
go.Scatter(x=np.array([25., 25., 35., 35.]),
y=np.array([0., 1., 1., 0.]),
marker=go.Marker(color='rgb(128,128,128)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(x=np.array([15., 15., 30., 30.]),
y=np.array([0., 2.23606798, 2.23606798, 1.]),
marker=go.Marker(color='rgb(128,128,128)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(x=np.array([5., 5., 22.5, 22.5]),
y=np.array([0., 3.60555128, 3.60555128,
2.23606798]),
marker=go.Marker(color='rgb(0,0,0)'),
mode='lines',
xaxis='x',
yaxis='y')
]),
layout=go.Layout(autosize=False,
height='100%',
hovermode='closest',
showlegend=False,
width='100%',
xaxis=go.XAxis(mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
tickmode='array',
ticks='outside',
ticktext=np.array(
['3', '2', '0', '1']),
tickvals=[5.0, 15.0, 25.0, 35.0],
type='linear',
zeroline=False),
yaxis=go.YAxis(mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
ticks='outside',
type='linear',
zeroline=False)))
self.assertEqual(len(dendro['data']), 3)
# this is actually a bit clearer when debugging tests.
self.assert_dict_equal(dendro['data'][0], expected_dendro['data'][0])
self.assert_dict_equal(dendro['data'][1], expected_dendro['data'][1])
self.assert_dict_equal(dendro['data'][2], expected_dendro['data'][2])
def test_dendrogram_random_matrix(self):
# create a random uncorrelated matrix
X = np.random.rand(5, 5)
# variable 2 is correlated with all the other variables
X[2, :] = sum(X, 0)
names = ['Jack', 'Oxana', 'John', 'Chelsea', 'Mark']
dendro = tls.FigureFactory.create_dendrogram(X, labels=names)
expected_dendro = go.Figure(
data=go.Data([
go.Scatter(marker=go.Marker(color='rgb(61,153,112)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(marker=go.Marker(color='rgb(61,153,112)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(marker=go.Marker(color='rgb(61,153,112)'),
mode='lines',
xaxis='x',
yaxis='y'),
go.Scatter(marker=go.Marker(color='rgb(0,116,217)'),
mode='lines',
xaxis='x',
yaxis='y')
]),
layout=go.Layout(autosize=False,
height='100%',
hovermode='closest',
showlegend=False,
width='100%',
xaxis=go.XAxis(
mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
tickmode='array',
ticks='outside',
tickvals=[5.0, 15.0, 25.0, 35.0, 45.0],
type='linear',
zeroline=False),
yaxis=go.YAxis(mirror='allticks',
rangemode='tozero',
showgrid=False,
showline=True,
showticklabels=True,
ticks='outside',
type='linear',
zeroline=False)))
self.assertEqual(len(dendro['data']), 4)
# it's random, so we can only check that the values aren't equal
y_vals = [
dendro['data'][0].pop('y'), dendro['data'][1].pop('y'),
dendro['data'][2].pop('y'), dendro['data'][3].pop('y')
]
for i in range(len(y_vals)):
for j in range(len(y_vals)):
if i != j:
self.assertFalse(np.allclose(y_vals[i], y_vals[j]))
x_vals = [
dendro['data'][0].pop('x'), dendro['data'][1].pop('x'),
dendro['data'][2].pop('x'), dendro['data'][3].pop('x')
]
for i in range(len(x_vals)):
for j in range(len(x_vals)):
if i != j:
self.assertFalse(np.allclose(x_vals[i], x_vals[j]))
# we also need to check the ticktext manually
xaxis_ticktext = dendro['layout']['xaxis'].pop('ticktext')
self.assertEqual(xaxis_ticktext[0], 'John')
# this is actually a bit clearer when debugging tests.
self.assert_dict_equal(dendro['data'][0], expected_dendro['data'][0])
self.assert_dict_equal(dendro['data'][1], expected_dendro['data'][1])
self.assert_dict_equal(dendro['data'][2], expected_dendro['data'][2])
self.assert_dict_equal(dendro['data'][3], expected_dendro['data'][3])
self.assert_dict_equal(dendro['layout'], expected_dendro['layout'])