From 0fa4b9462ee629e08ac4e46c9265d7effc98928e Mon Sep 17 00:00:00 2001 From: domspad Date: Sat, 11 Jul 2015 15:24:45 -0500 Subject: [PATCH 1/2] pylab to plt and np --- examples/pylab_examples/arrow_demo.py | 46 +++++++++++++-------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/examples/pylab_examples/arrow_demo.py b/examples/pylab_examples/arrow_demo.py index afd4d2a3e30f..23f01f1b9581 100644 --- a/examples/pylab_examples/arrow_demo.py +++ b/examples/pylab_examples/arrow_demo.py @@ -45,17 +45,17 @@ 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), @@ -103,13 +103,13 @@ 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(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 @@ -119,7 +119,7 @@ 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 @@ -179,7 +179,7 @@ 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) @@ -192,24 +192,24 @@ 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]]) + M = np.array([[cx, sx], [-sx, cx]]) coords = dot(orig_position, M) + [[x_pos, y_pos]] - x, y = ravel(coords) + 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(): @@ -302,11 +302,11 @@ 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() From b26a52194e3a94ca4d2dbf08d7dfc90796b20e70 Mon Sep 17 00:00:00 2001 From: domspad Date: Thu, 16 Jul 2015 23:23:10 -0700 Subject: [PATCH 2/2] pep8 --- examples/pylab_examples/arrow_demo.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/examples/pylab_examples/arrow_demo.py b/examples/pylab_examples/arrow_demo.py index 23f01f1b9581..a2398d8d3019 100644 --- a/examples/pylab_examples/arrow_demo.py +++ b/examples/pylab_examples/arrow_demo.py @@ -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()]) @@ -103,7 +105,7 @@ def make_arrow_plot(data, size=4, display='length', shape='right', } def do_fontsize(k): - return float(clip(max_text_size*np.sqrt(data[k]), + return float(np.clip(max_text_size*np.sqrt(data[k]), min_text_size, max_text_size)) A = plt.text(0, 1, '$A_3$', color='r', size=do_fontsize('A'), **text_params) @@ -204,7 +206,7 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor): raise ValueError("Got unknown position parameter %s" % where) M = np.array([[cx, sx], [-sx, cx]]) - coords = dot(orig_position, M) + [[x_pos, y_pos]] + 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:])