def create_colors(lr):
n_cts = lr.classes_.shape[0]
color_norm = colors.Normalize(vmin=-n_cts / 3, vmax=n_cts)
ct_arr = np.arange(n_cts)
ct_colors = cm.YlOrRd(color_norm(ct_arr))
return ct_colors
def plotFluxControlIn3D(r, upperLimit=1, lowerLimit=-1, figsize=(9, 7)):
'''
Display the flux control coefficients as a 3D plot
Args:
r : reference
roadrunner instance
upperlimit : float
optional parameter, sets the lower z axis limit
upperlimit : float
optional parameter, sets the upper z axis limit
figsize : tuble of float
optional: width and heigh of plot in inches
Example:
>>> teUtils.plotting.plotFluxControlIn3D (r)
'''
import matplotlib.cm as cm
import matplotlib.colors as colors
fig = _plt.figure(figsize=figsize)
ax = fig.add_subplot(111, projection='3d')
hist = r.getScaledFluxControlCoefficientMatrix()
xedges = _np.arange(float(hist.shape[0]) + 1)
yedges = _np.arange(float(hist.shape[1]) + 1)
# Construct arrays for the anchor positions
# Note: _np.meshgrid gives arrays in (ny, nx) so we use 'F' to flatten xpos,
# ypos in column-major order. For numpy >= 1.7, we could instead call meshgrid
# with indexing='ij'.
xpos, ypos = _np.meshgrid(xedges[:-1] + 0.25, yedges[:-1] + 0.25)
xpos = xpos.flatten('F')
ypos = ypos.flatten('F')
zpos = _np.zeros_like(xpos)
# Construct arrays with the dimensions for the 16 bars.
dx = 0.5 * _np.ones_like(zpos)
dy = dx.copy()
dz = hist.flatten()
offset = dz + _np.abs(dz.min())
fracs = offset.astype(float) / offset.max()
norm = colors.Normalize(fracs.min(), fracs.max())
colors = cm.YlOrRd(norm(fracs))
ax.set_zlim3d(lowerLimit, upperLimit)
ax.set_zlabel('Control Coefficient')
ax.set_xlabel('Fluxes')
ax.set_ylabel('Enzymes')
ax.w_xaxis.set_ticks(_np.arange(float(hist.shape[0]) + 1))
ax.w_xaxis.set_ticklabels(r.getReactionIds())
ax.w_yaxis.set_ticks(_np.arange(float(hist.shape[1]) + 1))
ax.w_yaxis.set_ticks(ypos + dy / 2.)
ax.w_yaxis.set_ticklabels(r.getReactionIds())
ax.bar3d(xpos, ypos, zpos, dx, dy, dz, color=colors, zsort='average')
def plot_by_group_simple(file_name,
coordinates,
column,
original_table,
labels,
with_legend=True,
hot_colors=False):
original_table_labels = original_table[column].loc[labels]
df = pd.DataFrame(
dict(x=coordinates[:, 0],
y=coordinates[:, 1],
label=list(original_table_labels)))
grouped_labels = sorted(list(set(original_table_labels)))
# Plot
plt.figure(figsize=(20, 12), dpi=200)
fig, ax = plt.subplots()
ax.margins(0.05) # Optional, just adds 5% padding to the autoscaling
if hot_colors == False:
colors = cm.tab20(np.linspace(0, 1, len(grouped_labels)))
else:
colors = cm.YlOrRd(np.linspace(0, 1, len(grouped_labels)))
plt.ylim((-80, 80))
plt.xlim((-80, 80))
for i, l in enumerate(grouped_labels):
subset = df.loc[df['label'] == l]
if with_legend == True:
ax.scatter(subset['x'],
subset['y'],
marker='o',
label=l,
s=0.05,
c=colors[i, :],
alpha=0.5)
else:
ax.scatter(subset['x'],
subset['y'],
marker='o',
s=0.05,
c=colors[i, :],
alpha=0.5)
if with_legend == True:
ax.legend(loc='upper right', prop={'size': 7})
path = 'results_lsa/' + file_name
plt.savefig(path, dpi=200)
def plot_tangent_one_file(bspline_course, tangent_bspline, normal_bspline,
bspline_course_tck_3, tangent_bspline_tck_3,
normal_bspline_tck_3, bspline_course_tck_5,
tangent_bspline_tck_5, normal_bspline_tck_5):
greens = cm.YlGn(np.linspace(0, 1, 10))
reds = cm.YlOrRd(np.linspace(0, 1, 10))
pyplot.figure(figsize=(8, 7))
pyplot.ylabel('x-axis component of the vector', fontsize=12)
pyplot.xlabel('x(m)', fontsize=12)
pyplot.plot(bspline_course_tck_3.x,
tangent_bspline_tck_3.x,
'-',
color=reds[9],
label='Tangent 3rd Degree B-spline')
pyplot.plot(bspline_course_tck_5.x,
tangent_bspline_tck_5.x,
'--',
color=reds[6],
label='Tangent 5th Degree B-spline')
pyplot.plot(bspline_course.x,
tangent_bspline.x,
'-',
color=reds[3],
label='Tangent Bezier curve')
pyplot.plot(bspline_course_tck_3.x,
normal_bspline_tck_3.x,
'-',
color=greens[9],
label='Normal 3rd Degree B-spline')
pyplot.plot(bspline_course_tck_5.x,
normal_bspline_tck_5.x,
'--',
color=greens[6],
label='Normal 5th Degree B-spline')
pyplot.plot(bspline_course.x,
normal_bspline.x,
'-',
color=greens[3],
label='Normal Bezier curve')
pyplot.legend(loc='upper right',
bbox_to_anchor=(2, 1.0),
shadow=False,
ncol=2,
fontsize=12)
pyplot.show()
def get_hurricane():
u = np.array([[2.444, 7.553], [0.513, 7.046], [-1.243, 5.433],
[-2.353, 2.975], [-2.578, 0.092], [-2.075, -1.795],
[-0.336, -2.870], [2.609, -2.016]])
u[:, 0] -= 0.098
codes = [1] + [2] * (len(u) - 2) + [2]
u = np.append(u, -u[::-1], axis=0)
codes += codes
return mpath.Path(3 * u, codes, closed=False)
low = cm.GnBu_r(np.linspace(0.01, 0.9, 128))
mid = np.ones((50, 4))
high = cm.YlOrRd(np.linspace(0.1, 0.95, 128))
colors = np.vstack((low, mid, high))
bwr = LinearSegmentedColormap.from_list('my_colormap', colors) #, N=24)
bwr.set_over = 'darkbrown'
bwr.set_under = 'magemta'
bwr.set_bad = 'k'
plevs = [950, 850, 500, 300, 200]
def metpy_read_wrf(tidx, froms, froms0, fwrf, lons_out, lats_out):
wrfin = Dataset(fwrf)
ds = xr.Dataset()
def plot_smoothing_tangent_normal(course):
arc_length = compute_arc_length(course)
#d_hz = arc_length / len(course.x)
d_hz = arc_length / 1000
smoothing = 0.0
b1 = bspline3Dtck(course, 3, smoothing, d_hz)
db1 = deriv_bspline3Dtck(1, course, 3, smoothing, d_hz)
tangent_b1, normal_b1, binormal_b1 = getParallelTransportVectors(db1)
b1x, error1 = compute_position_error(course, b1)
smoothing = 0.0000001
b2 = bspline3Dtck(course, 3, smoothing, d_hz)
db2 = deriv_bspline3Dtck(1, course, 3, smoothing, d_hz)
tangent_b2, normal_b2, binormal_b2 = getParallelTransportVectors(db2)
b2x, error2 = compute_position_error(course, b2)
smoothing = 0.0000003
b3 = bspline3Dtck(course, 3, smoothing, d_hz)
db3 = deriv_bspline3Dtck(1, course, 3, smoothing, d_hz)
tangent_b3, normal_b3, binormal_b3 = getParallelTransportVectors(db3)
b3x, error3 = compute_position_error(course, b3)
smoothing = 0.0000006
b4 = bspline3Dtck(course, 3, smoothing, d_hz)
db4 = deriv_bspline3Dtck(1, course, 3, smoothing, d_hz)
tangent_b4, normal_b4, binormal_b4 = getParallelTransportVectors(db4)
b4x, error4 = compute_position_error(course, b4)
smoothing = 0.0000012
b5 = bspline3Dtck(course, 3, smoothing, d_hz)
db5 = deriv_bspline3Dtck(1, course, 3, smoothing, d_hz)
tangent_b5, normal_b5, binormal_b5 = getParallelTransportVectors(db5)
b5x, error5 = compute_position_error(course, b5)
greens = cm.YlGn(np.linspace(0, 1, 10))
reds = cm.YlOrRd(np.linspace(0, 1, 10))
pyplot.figure(figsize=(8, 7))
pyplot.ylabel('Absolute position error (mm)', fontsize=12)
pyplot.xlabel('x(m)', fontsize=12)
#pyplot.plot(b1x, error1,'r-', label='s=0')
pyplot.plot(b2x, error2, 'r--', label='s=1E-7')
pyplot.plot(b3x, error3, 'y-', label='s=3E-7')
pyplot.plot(b4x, error4, 'g--', label='s=6E-7')
pyplot.plot(b5x, error5, 'b-', label='s=12E-7')
pyplot.legend(loc='upper right',
bbox_to_anchor=(1.0, 1.0),
shadow=False,
ncol=1,
fontsize=12)
pyplot.show()
pyplot.figure(figsize=(8, 7))
pyplot.ylabel('y(m)', fontsize=12)
pyplot.xlabel('x(m)', fontsize=12)
pyplot.plot(b2.x, b2.y, 'r--', label='s=1E-7')
pyplot.plot(b3.x, b3.y, 'y-', label='s=3E-7')
pyplot.plot(b4.x, b4.y, 'g--', label='s=6E-7')
pyplot.plot(b5.x, b5.y, 'b-', label='s=12E-7')
pyplot.plot(course.x,
course.y,
'k*',
markersize=8,
label='Tow Course received')
pyplot.legend(loc='lower right',
bbox_to_anchor=(1.0, 0.00),
shadow=False,
ncol=1,
fontsize=12)
pyplot.show()
pyplot.figure(figsize=(8, 7))
pyplot.ylabel('x-axis component of the vector', fontsize=12)
pyplot.xlabel('x(m)', fontsize=12)
pyplot.plot(b1.x, tangent_b1.x, '-', color=reds[9], label='Tangent s=0')
pyplot.plot(b2.x,
tangent_b2.x,
'--',
color=reds[8],
label='Tangent s=1E-7')
pyplot.plot(b3.x, tangent_b3.x, '-', color=reds[7], label='Tangent s=3E-7')
pyplot.plot(b4.x,
tangent_b4.x,
'--',
color=reds[6],
label='Tangent s=6E-7')
pyplot.plot(b5.x,
tangent_b5.x,
'-',
color=reds[3],
label='Tangent s=12E-7')
pyplot.plot(b1.x, normal_b1.x, '-', color=greens[9], label='Normal s=0')
pyplot.plot(b2.x,
normal_b2.x,
'--',
color=greens[8],
label='Normal s=1E-7')
pyplot.plot(b3.x, normal_b3.x, '-', color=greens[7], label='Normal s=3E-7')
pyplot.plot(b4.x,
normal_b4.x,
'--',
color=greens[6],
label='Normal s=6E-7')
pyplot.plot(b5.x,
normal_b5.x,
'-',
color=greens[3],
label='Normal s=12E-7')
pyplot.legend(loc='upper right',
bbox_to_anchor=(1.7, 1.0),
shadow=False,
ncol=2,
fontsize=12)
pyplot.show()
def display_closestwords_tsnescatterplot(model, word, topn, size,
approved_drugs, other_drugs,
drug_stages):
arr = np.empty((0, size), dtype='f')
word_labels = [word]
close_words = model.wv.similar_by_word(word, topn)
arr = np.append(arr, np.array([model.wv[word]]), axis=0)
for wrd_score in close_words:
wrd_vector = model.wv[wrd_score[0]]
word_labels.append(wrd_score[0])
arr = np.append(arr, np.array([wrd_vector]), axis=0)
tsne = TSNE(n_components=2, random_state=0)
np.set_printoptions(suppress=True)
Y = tsne.fit_transform(arr)
x_coords = Y[:, 0]
y_coords = Y[:, 1]
plt.figure()
# plt.scatter(x_coords, y_coords,5,'gray',alpha=0.3) # to plot a scatter dot for every word
colors = [cm.YlOrRd(x)
for x in np.linspace(0, 1, 6)] # split colormap into 6
for label, x, y in zip(word_labels, x_coords, y_coords):
# plt.annotate(label, xy=(x, y), xytext=(0, 0), textcoords='offset points') # to plot every word in text
if label in approved_drugs:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[5], alpha=0.5),
fontsize=text_size)
elif label in other_drugs:
label_stage = drug_stages[other_drugs.index(
label)] # find index of the drug to return its stage in trials
if label_stage == 0:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[int(label_stage)],
alpha=0.5),
fontsize=text_size)
elif label_stage == 1:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[int(label_stage)],
alpha=0.5),
fontsize=text_size)
elif label_stage == 2:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[int(label_stage)],
alpha=0.5),
fontsize=text_size)
elif label_stage == 3:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[int(label_stage)],
alpha=0.5),
fontsize=text_size)
elif label_stage == 4:
plt.text(x,
y,
label,
bbox=dict(facecolor=colors[int(label_stage)],
alpha=0.5),
fontsize=text_size)
plt.xlim(x_coords.min() + 0.5, x_coords.max() + 0.5)
plt.ylim(y_coords.min() + 0.5, y_coords.max() + 0.5)
plt.show()
def plot_by_group(file_name,
coordinates,
column,
original_table,
labels,
with_legend=True,
hot_colors=False):
original_table_treated = original_table[[column, 'product',
'count']].set_index('product')
# labels = [str(label) for label in list(labels)]
original_table_labels = original_table_treated[column].loc[labels]
original_table_size = original_table_treated['count'].loc[labels]
df = pd.DataFrame(
dict(x=coordinates[:, 0],
y=coordinates[:, 1],
size=(40 * np.asarray(original_table_size) /
np.max(np.asarray(original_table_size)))**2,
label=list(original_table_labels)))
grouped_labels = sorted(list(set(original_table_labels)))
# Plot
plt.figure(figsize=(20, 12), dpi=200)
fig, ax = plt.subplots()
ax.margins(0.05) # Optional, just adds 5% padding to the autoscaling
if hot_colors == False:
colors = cm.tab20(np.linspace(0, 1, len(grouped_labels)))
else:
colors = cm.YlOrRd(np.linspace(0, 1, len(grouped_labels)))
plt.ylim((-80, 80))
plt.xlim((-80, 80))
for i, l in enumerate(grouped_labels):
subset = df.loc[df['label'] == l]
if l == -1:
ax.scatter(subset['x'],
subset['y'],
marker='o',
label=l,
s=subset['size'],
c='black',
alpha=0.5)
else:
if with_legend == True:
ax.scatter(subset['x'],
subset['y'],
marker='o',
label=l,
s=subset['size'],
c=colors[i, :],
alpha=0.5)
else:
ax.scatter(subset['x'],
subset['y'],
marker='o',
s=subset['size'],
c=colors[i, :],
alpha=0.5)
if with_legend == True:
ax.legend(loc='upper right', prop={'size': 7})
path = 'results_glove3/' + file_name
plt.savefig(path, dpi=200)
def _kripp_subplot(krippendorph_summary,
axis,
what,
is_agreement,
cutoff=None):
""""""
minx = np.min(krippendorph_summary.loc[:, f'n_matches'])
maxx = np.max(krippendorph_summary.loc[:, f'n_matches'])
if is_agreement:
# annotate agreement ranges
_annotate_krippendorph_ranges(axis=axis,
minx=minx,
maxx=maxx,
shades=False)
mx = 0
for min_iou in [0.75, 0.5, 0.25]:
ksummary = krippendorph_summary.loc[
krippendorph_summary.loc[:, 'min_iou'] >= min_iou - 0.005, :]
ksummary = ksummary.loc[ksummary.loc[:,
'min_iou'] < min_iou + 0.005, :]
x = ksummary.loc[:, f'n_matches']
if is_agreement:
y = ksummary.loc[:, what]
else:
# y = 100 * ksummary.loc[:, what] / np.max(
# ksummary.loc[:, what].values)
y = ksummary.loc[:, what]
mx = np.max([np.max(y), mx])
axis.plot(
x,
y,
marker='o',
# marker='o' if min_iou == miniou else '.',
linestyle='-',
# linestyle='-' if min_iou == miniou else '--',
# linewidth=2. if min_iou == miniou else 1.,
linewidth=1.5,
c=mcmap.YlOrRd(min_iou + 0.2),
# alpha=1. if min_iou == miniou else 0.7,
label='min_iou=%.2f' % min_iou)
axis.xaxis.set_major_locator(MaxNLocator(integer=True))
if is_agreement:
ymin = -0.02 # -0.22
ymax = 1.02
else:
ymin = -mx * 0.02
ymax = mx * 1.02
# axis.set_ylim(0, 100)
axis.set_ylim(ymin=0)
minx = minx * 0.98
maxx = maxx * 1.02
if cutoff is not None:
axis.fill_betweenx(y=[ymin, ymax],
x1=minx,
x2=cutoff - 0.2,
color='gray',
alpha=0.2)
axis.set_ylim(ymin, ymax)
axis.set_xlim(minx, maxx)
axis.legend(fontsize=8)
axis.set_title(what.replace('_', ' '), fontsize=14, fontweight='bold')
axis.set_xlabel(f'At least x participants per anchor', fontsize=12)
axis.set_ylabel(
# 'Krippendorph Alpha' if is_agreement else '% anchors kept',
'Krippendorph Alpha' if is_agreement else 'No. of anchors',
fontsize=12)
#bounds = np.linspace(0,120,21)
#norm = colors.BoundaryNorm(bounds, ncolors=256)
#print norm(100)
#sys.exit()
for key, value in patches.iteritems():
print key + " " + str(color[key])
if radflux == 'diffuse':
ax.add_collection(PatchCollection(value,\
facecolor=cm.YlGnBu_r(norm(color[key])),\
cmap=cm.YlGnBu_r, edgecolor='k', linewidth=1., zorder=2))
else:
ax.add_collection(PatchCollection(value,\
facecolor=cm.YlOrRd(norm(color[key])),\
cmap=cm.YlOrRd, edgecolor='k', linewidth=1., zorder=2))
# ax.add_collection(PatchCollection(value, facecolors=color[key], cmap=cm.RdYlBu, edgecolor='k',
# linewidth=1., zorder=2, norm=norm))
### Plot colorbar
#set room for colorbar
fig.subplots_adjust(right=0.85)
axcb = fig.add_axes([0.87, 0.15, 0.03, 0.7])
cb = mpl.colorbar.ColorbarBase(axcb,
cmap=cmap,
norm=norm,
boundaries=bounds,