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Plotly Filled Chord Diagram
import numpy as np
import plotly.graph_objs as go
import colorlover as cl
def get_spaced_colors(n, randomized=False):
if n > 0:
max_value = 255
interval = max_value / n
hues = np.arange(0, max_value, interval)
return cl.to_rgb(["hsl(%d,80%%,40%%)" % i for i in hues])
else:
return None
PI = np.pi
def check_square(M):
d, n = M.shape
if d != n:
raise ValueError("Data array must be square.")
return n
def moduloAB(x, a, b):
if a >= b:
raise ValueError('Incorrect inverval ends')
y = (x - a) % (b - a)
return y + b if y < 0 else y + a
def test_2PI(x):
return 0 <= x < 2 * PI
def get_ideogram_ends(ideaogram_len, gap):
ideo_ends = []
left = 0
for k in range(len(ideaogram_len)):
right = left + ideaogram_len[k]
ideo_ends.append([left, right])
left = right + gap
return ideo_ends
def make_ideogram_arc(R, phi, a=50):
# R is the circle radius
# Phi is a list of the ends angle coordinates of an arc
# a is a parameter that controls the number of points to be evaluated
if not test_2PI(phi[0]) or not test_2PI(phi[1]):
phi = [moduloAB(t, 0, 2*PI) for t in phi]
length = (phi[1] - phi[0]) % 2 * PI
nr = 5 if length <= PI/4 else int(a * length / PI)
if phi[0] < phi[1]:
theta = np.linspace(phi[0], phi[1], nr)
else:
phi = [moduloAB(t, -PI, PI) for t in phi]
theta = np.linspace(phi[0], phi[1], nr)
return R * np.exp(1j*theta)
def map_data(data_matrix, row_value, ideogram_length):
n = data_matrix.shape[0] # square, so same as 1
mapped = np.zeros([n, n])
for j in range(n):
mapped[:, j] = ideogram_length * data_matrix[:, j] / row_value
return mapped
def make_ribbon_ends(mapped_data, ideo_ends, idx_sort):
n = mapped_data.shape[0]
ribbon_boundary = np.zeros((n, n+1))
for k in range(n):
start = ideo_ends[k][0]
ribbon_boundary[k][0] = start
for j in range(1, n+1):
J = idx_sort[k][j-1]
ribbon_boundary[k][j] = start + mapped_data[k][J]
start = ribbon_boundary[k][j]
return [[(ribbon_boundary[k][j], ribbon_boundary[k][j+1])
for j in range(n)] for k in range(n)]
def control_pts(angle, radius):
if len(angle) != 3:
raise ValueError('Angle must have len = 3')
b_cplx = np.array([np.exp(1j*angle[k]) for k in range(3)])
b_cplx[1] = radius * b_cplx[1]
return list(zip(b_cplx.real, b_cplx.imag))
def ctrl_rib_chords(l, r, radius):
if len(l) != 2 or len(r) != 2:
raise ValueError('The arc ends must be elements in a list of len 2')
return [control_pts([l[j], (l[j]+r[j])/2, r[j]], radius) for j in range(2)]
def make_q_bezier(b):
if len(b) != 3:
raise ValueError('Contaol polygon must have 3 points')
A, B, C = b
return 'M ' + str(A[0]) + "," + str(A[1]) + " " + "Q " + \
str(B[0]) + ", " + str(B[1]) + " " + \
str(C[0]) + ", " + str(C[1])
def make_ribbon_arc(theta0, theta1):
if test_2PI(theta0) and test_2PI(theta1):
if theta0 < theta1:
theta0 = moduloAB(theta0, -PI, PI)
theta1 = moduloAB(theta1, -PI, PI)
if theta0 * theta1 > 0:
raise ValueError('Incorrect angle coordinates for ribbon')
nr = int(40 * (theta0 - theta1) / PI)
if nr <= 2:
nr = 3
theta = np.linspace(theta0, theta1, nr)
pts = np.exp(1j * theta)
string_arc = ''
for k in range(len(theta)):
string_arc += "L " + str(pts.real[k]) + ", " + str(pts.imag[k])+' '
return string_arc
else:
raise ValueError('The angle coords for arc ribbon must be [0, 2*PI]')
def make_layout(title):
xaxis = dict(showline=False,
zeroline=False,
showgrid=False,
showticklabels=False,
title='')
yaxis = {**xaxis, 'scaleanchor': 'x'}
return dict(title=title,
xaxis=xaxis,
yaxis=yaxis,
showlegend=False,
margin=dict(t=25, b=25, l=25, r=25),
hovermode='closest',
shapes=[])
def make_ideo_shape(path, line_color, fill_color):
return dict(
line=go.Line(color=line_color, width=0.45),
path=path,
type='path',
fillcolor=fill_color,
layer='below'
)
def make_ribbon(l, r, line_color, fill_color, radius=0.2):
poligon = ctrl_rib_chords(l, r, radius)
b, c = poligon
return dict(line=go.Line(color=line_color, width=0.5),
path=make_q_bezier(b) + make_ribbon_arc(r[0], r[1]) +
make_q_bezier(c[::-1]) + make_ribbon_arc(l[1], l[0]),
type='path',
fillcolor=fill_color,
layer='below')
def make_self_rel(l, line_color, fill_color, radius):
b = control_pts([l[0], (l[0]+l[1])/2, l[1]], radius)
return dict(
line=dict(color=line_color, width=0.5),
path=make_q_bezier(b) + make_ribbon_arc(l[1], l[0]),
type='path',
fillcolor=fill_color,
layer='below'
)
def invPerm(perm):
inv = [0] * len(perm)
for i, s in enumerate(perm):
inv[s] = i
return inv
def make_filled_chord(M):
n = M.shape[0]
labels = M.columns
M = M.T
matrix = M.as_matrix()
row_sum = [np.sum(matrix[k, :]) for k in range(n)]
gap = 2 * PI * 10e-8
ideogram_length = 2*PI*np.asarray(row_sum)/sum(row_sum) - gap*np.ones(n)
ideo_colors = [x[:3] + "a" + x[3:-1] + ",.75" + x[-1] for x in
get_spaced_colors(len(labels))]
mapped_data = map_data(M.as_matrix(), row_sum, ideogram_length)
idx_sort = np.argsort(mapped_data, axis=1)
ideo_ends = get_ideogram_ends(ideogram_length, gap)
ribbon_ends = make_ribbon_ends(mapped_data, ideo_ends, idx_sort)
ribbon_color = [n * [ideo_colors[k]] for k in range(n)]
layout = make_layout(' ')
ribbon_info = []
radii_sribb = [0.2] * n
for k in range(n):
sigma = idx_sort[k]
sigma_inv = invPerm(sigma)
for j in range(k, n):
if M.iloc[k, j] == 0 and M.iloc[j, k] == 0:
continue
eta = idx_sort[j]
eta_inv = invPerm(eta)
l = ribbon_ends[k][sigma_inv[j]]
if j == k:
layout['shapes'].append(
make_self_rel(l,
'rgb(175,175,175)',
ideo_colors[k],
radius=radii_sribb[k]))
z = 0.9 * np.exp(1j * (l[0] + l[1]) / 2)
text = labels[k] + " co-occurs with " + \
"{:d}".format(M.iloc[k, k]) + " of its own appearences"
ribbon_info.append(
go.Scatter(x=[z.real],
y=[z.imag],
mode='markers',
text=text,
hoverinfo="text",
marker=dict(size=0.5,
color=ideo_colors[k])))
else:
r = ribbon_ends[j][eta_inv[k]]
zi = 0.9 * np.exp(1j * (l[0] + l[1]) / 2)
zf = 0.9 * np.exp(1j * (r[0] + r[1]) / 2)
texti = labels[k] + " co-occurs with " + \
"{:d}".format(matrix[k][j]) + " of the " + \
labels[j] + " appearences"
textf = labels[j] + " co-occurs with " + \
"{:d}".format(matrix[j][k]) + " of the " + \
labels[k] + " appearences"
ribbon_info.append(
go.Scatter(x=[zi.real],
y=[zi.imag],
mode='markers',
text=texti,
hoverinfo="text",
marker=dict(size=0.5,
color=ribbon_color[k][j])))
ribbon_info.append(
go.Scatter(x=[zf.real],
y=[zf.imag],
mode='markers',
text=textf,
hoverinfo="text",
marker=dict(size=0.5,
color=ribbon_color[j][k])))
r = (r[1], r[0])
if matrix[k][j] > matrix[j][k]:
color_of_highest = ribbon_color[k][j]
else:
color_of_highest = ribbon_color[j][k]
layout['shapes'].append(
make_ribbon(l, r, 'rgb(175, 175, 175)',
color_of_highest))
ideograms = []
for k in range(len(ideo_ends)):
z = make_ideogram_arc(1.1, ideo_ends[k])
zi = make_ideogram_arc(1.0, ideo_ends[k])
m = len(z)
n = len(zi)
ideograms.append(
go.Scatter(x=z.real,
y=z.imag,
mode='lines',
line=dict(color=ideo_colors[k],
shape='spline',
width=0.25),
text=labels[k]+'<br>'+'{:d}'.format(row_sum[k]),
hoverinfo='text'))
path = 'M '
for s in range(m):
path += str(z.real[s]) + ', ' + str(z.imag[s]) + ' L '
Zi = np.array(zi.tolist()[::-1])
for s in range(m):
path += str(Zi.real[s]) + ", " + str(Zi.imag[s]) + ' L '
path += str(z.real[0]) + ' ,' + str(z.imag[0])
layout['shapes'].append(make_ideo_shape(path,
'rgb(150,150,150)',
ideo_colors[k]))
data = ideograms + ribbon_info
fig = {
"data": data,
"layout": layout
}
return fig
@rmarren1

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@rmarren1 rmarren1 commented Mar 30, 2018

newplot

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@rmarren1 rmarren1 commented Mar 30, 2018

Input is a square pandas matrix where cell i, j is the i -> j relationship depicted in the diagram.

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@russelljjarvis russelljjarvis commented Mar 6, 2021

I hacked this code a bit more.
Fixes:

CoauthorNetVis

CoauthorNetVis
Live version of application

@LianeHughes

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@LianeHughes LianeHughes commented May 19, 2021

Hello, I am looking at using a chord plot like this one. I find that when I add a large amount of data I get a value error 'Incorrect angle coordinates for ribbon'. I am not really sure how to resolve this error. Could you provide some advice please?

@empet

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@empet empet commented Aug 1, 2021

@rmarren1 and @russelljjarvis Thank you both for picking up the code for Chord Diagram into a few functions. I edited and posted this notebook https://github.com/empet/Plotly-plots/blob/master/Chord-diagram.ipynb, as a tutorial, late in 2015 (an older version than that on github is this one: https://plotly.com/python/v3/filled-chord-diagram/). Meanwhile I updated it to work with newer Plotly versions, and replaced Python 2 string manipulation with f-strings (see the github version).

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