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Merged
merged 2 commits into from
Jul 19, 2015
Merged

MEP12-on-arrow_demo.py #4660

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0fa4b94
pylab to plt and np
Jul 11, 2015
b26a521
pep8
Jul 17, 2015
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56 changes: 29 additions & 27 deletions examples/pylab_examples/arrow_demo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,12 @@


"""
from pylab import *
import matplotlib.pyplot as plt
import numpy as np

rates_to_bases = {'r1': 'AT', 'r2': 'TA', 'r3': 'GA', 'r4': 'AG', 'r5': 'CA', 'r6': 'AC',
'r7': 'GT', 'r8': 'TG', 'r9': 'CT', 'r10': 'TC', 'r11': 'GC', 'r12': 'CG'}
rates_to_bases = {'r1': 'AT', 'r2': 'TA', 'r3': 'GA', 'r4': 'AG', 'r5': 'CA',
'r6': 'AC', 'r7': 'GT', 'r8': 'TG', 'r9': 'CT', 'r10': 'TC',
'r11': 'GC', 'r12': 'CG'}
numbered_bases_to_rates = dict([(v, k) for k, v in rates_to_bases.items()])
lettered_bases_to_rates = dict([(v, 'r' + v) for k, v in rates_to_bases.items()])

Expand Down Expand Up @@ -45,17 +47,17 @@ def make_arrow_plot(data, size=4, display='length', shape='right',
linewidth and edgecolor.
"""

xlim(-0.5, 1.5)
ylim(-0.5, 1.5)
gcf().set_size_inches(size, size)
xticks([])
yticks([])
plt.xlim(-0.5, 1.5)
plt.ylim(-0.5, 1.5)
plt.gcf().set_size_inches(size, size)
plt.xticks([])
plt.yticks([])
max_text_size = size*12
min_text_size = size
label_text_size = size*2.5
text_params = {'ha': 'center', 'va': 'center', 'family': 'sans-serif',
'fontweight': 'bold'}
r2 = sqrt(2)
r2 = np.sqrt(2)

deltas = {
'AT': (1, 0),
Expand Down Expand Up @@ -103,13 +105,13 @@ def make_arrow_plot(data, size=4, display='length', shape='right',
}

def do_fontsize(k):
return float(clip(max_text_size*sqrt(data[k]),
return float(np.clip(max_text_size*np.sqrt(data[k]),
min_text_size, max_text_size))

A = text(0, 1, '$A_3$', color='r', size=do_fontsize('A'), **text_params)
T = text(1, 1, '$T_3$', color='k', size=do_fontsize('T'), **text_params)
G = text(0, 0, '$G_3$', color='g', size=do_fontsize('G'), **text_params)
C = text(1, 0, '$C_3$', color='b', size=do_fontsize('C'), **text_params)
A = plt.text(0, 1, '$A_3$', color='r', size=do_fontsize('A'), **text_params)
T = plt.text(1, 1, '$T_3$', color='k', size=do_fontsize('T'), **text_params)
G = plt.text(0, 0, '$G_3$', color='g', size=do_fontsize('G'), **text_params)
C = plt.text(1, 0, '$C_3$', color='b', size=do_fontsize('C'), **text_params)

arrow_h_offset = 0.25 # data coordinates, empirically determined
max_arrow_length = 1 - 2*arrow_h_offset
Expand All @@ -119,7 +121,7 @@ def do_fontsize(k):
max_head_length = 2*max_arrow_width
arrow_params = {'length_includes_head': True, 'shape': shape,
'head_starts_at_zero': head_starts_at_zero}
ax = gca()
ax = plt.gca()
sf = 0.6 # max arrow size represents this in data coords

d = (r2/2 + arrow_h_offset - 0.5)/r2 # distance for diags
Expand Down Expand Up @@ -179,7 +181,7 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):

x_scale, y_scale = deltas[pair]
x_pos, y_pos = positions[pair]
arrow(x_pos, y_pos, x_scale*length, y_scale*length,
plt.arrow(x_pos, y_pos, x_scale*length, y_scale*length,
fc=fc, ec=ec, alpha=alpha, width=width, head_width=head_width,
head_length=head_length, **arrow_params)

Expand All @@ -192,24 +194,24 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):

where = label_positions[pair]
if where == 'left':
orig_position = 3*array([[max_arrow_width, max_arrow_width]])
orig_position = 3*np.array([[max_arrow_width, max_arrow_width]])
elif where == 'absolute':
orig_position = array([[max_arrow_length/2.0, 3*max_arrow_width]])
orig_position = np.array([[max_arrow_length/2.0, 3*max_arrow_width]])
elif where == 'right':
orig_position = array([[length - 3*max_arrow_width,
orig_position = np.array([[length - 3*max_arrow_width,
3*max_arrow_width]])
elif where == 'center':
orig_position = array([[length/2.0, 3*max_arrow_width]])
orig_position = np.array([[length/2.0, 3*max_arrow_width]])
else:
raise ValueError("Got unknown position parameter %s" % where)

M = array([[cx, sx], [-sx, cx]])
coords = dot(orig_position, M) + [[x_pos, y_pos]]
x, y = ravel(coords)
M = np.array([[cx, sx], [-sx, cx]])
coords = np.dot(orig_position, M) + [[x_pos, y_pos]]
x, y = np.ravel(coords)
orig_label = rate_labels[pair]
label = '$%s_{_{\mathrm{%s}}}$' % (orig_label[0], orig_label[1:])

text(x, y, label, size=label_text_size, ha='center', va='center',
plt.text(x, y, label, size=label_text_size, ha='center', va='center',
color=labelcolor or fc)

for p in positions.keys():
Expand Down Expand Up @@ -302,11 +304,11 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):
display = 'length'

size = 4
figure(figsize=(size, size))
plt.figure(figsize=(size, size))

make_arrow_plot(d, display=display, linewidth=0.001, edgecolor=None,
normalize_data=scaled, head_starts_at_zero=True, size=size)

draw()
plt.draw()

show()
plt.show()