def plot_xy(self,
df_to_plot,
x_index,
y_index,
x_label,
y_label,
title,
dest_path,
median_filter=0):
time = df_to_plot[x_index]
temperature = df_to_plot[y_index]
if median_filter > 1:
#temperature = pd.rolling_median(temperature, median_filter)
temperature = temperature.rolling(window=median_filter,
center=False).median()
time = time.rolling(window=median_filter, center=False).median()
#filtered_data = self.median_filter(temperature, median_filter, time)
#temperature = filtered_data[0]
#time = filtered_data[1]
plt.xlabel(x_label)
plt.ylabel(y_label)
fig = plt.figure(figsize=(10, 7))
#fig.suptitle('Titel', fontsize=25)
ax = fig.gca()
ax.plot(self.timeListToFloatList(time), temperature)
ax.set_title(title, fontsize=25)
ax.set_xlabel(x_label, fontsize=18)
ax.set_ylabel(y_label, fontsize=18)
#mpld3.show(fig)
mpld3.save_html(fig, dest_path)
print('DONE')
def graphme(self, pngfilename="my_sample_png.png"):
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import mpld3
import datetime
""" creating background info"""
# create a plot with as may subplots as you choose
fig, ax = plt.subplots()
# add a grid to the background
ax.grid(True, alpha = 0.2)
# the x axis contains date
fig.autofmt_xdate()
# the dates are year, month
ax.fmt_xdata = mdates.DateFormatter('%Y-%m')
if self.table not in ['MS04314', 'MS00114', 'MS04334','MS04315','MS00115']:
final_glitch = self.decide()
dates = sorted(final_glitch.keys())
dates2 = [x for x in dates if final_glitch[x]['mean'] != None and final_glitch[x]['mean'] != "None"]
vals = [final_glitch[x]['mean'] for x in dates2]
glitched_values = ax.plot(dates2, vals, 'b-')
ax.legend(loc=4)
ax.set_xlabel("dates")
ax.set_ylabel("values")
mpld3.show()
mpld3.save_html(fig, 'my_output_html.html')
import pylab
pylab.savefig(pngfilename)
def graph():
data1 = pandas.read_csv(lambdaOutModeName, header=None)
data2 = pandas.read_csv(dockerOutModeName, header=None)
# print(data1)
x = data1[data1.columns[0]].replace(',', '.', regex=True).astype(float)
y = data1[data1.columns[1]].replace(',', '.', regex=True).astype(float)
x2 = data2[data2.columns[0]].replace(',', '.', regex=True).astype(float)
y2 = data2[data2.columns[1]].replace(',', '.', regex=True).astype(float)
fig, axes = plt.subplots(1, 2, figsize=(20, 8))
axes[0].set_xlabel('memory')
axes[0].set_ylabel('pcpu')
axes[0].set_title('Lambda')
axes[0].plot(list(x), list(y), '-bo')
axes[0].axis([0, 3050, 0, 210])
axes[1].set_xlabel('cpu')
axes[1].set_ylabel('pcpu')
axes[1].set_title('Docker')
axes[1].plot(list(x2), list(y2), '-ro')
axes[1].axis([0, 2.5, 0, 210])
mpld3.save_html(fig, 'figure1.html')
print('figure1.html created!')
def plot_multi_axis(time, axes, labels=None, fname=None):
"""Plots a 3-axis set of data, with the three axes and an envelope.
Args:
time (array): time series to plot data against in seconds
axes (list): the three axes to plot, pre-scaled to desired units
labels (list): title, xlabel, ylabel, legend labels
fname (str): name of the file to store the mpld3 html in
"""
fig = plt.figure(figsize=(10, 6))
if labels:
for i in range(len(axes)):
plt.plot(time, axes[i], label=labels[3][i])
plt.plot(time, vecnorm(*axes), 'k', label=labels[3][len(axes)])
plt.title(labels[0])
plt.xlabel(labels[1])
plt.ylabel(labels[2])
plt.legend(loc='upper left')
else:
for i in range(len(axes)):
plt.plot(time, axes[i])
plt.plot(time, vecnorm(axes), 'k')
if fname:
with open(fname, 'w') as f:
mpld3.save_html(fig, f)
def drawMultiplePlot(data, dataSumNE, xlab='Jahr', filename='figboth', recolor=False):
objects = data.loc['Elektrisch',]
y_pos = np.arange(len(objects))
fig = plt.figure(figsize=[16, 9], dpi=250)
p1 = plt.bar(y_pos, height=objects)
p2 = plt.bar(y_pos, height=dataSumNE, bottom=objects)
if recolor:
p1[(len(p1) - 1)].set_color('C3')
p2[(len(p2) - 1)].set_color('#FFC080')
plt.xticks(y_pos, data)
plt.ylabel('Zulassungen')
plt.xlabel(xlab)
plt.legend(['Elektroautos', 'Andere Antriebe'])
plt.savefig('outputs/png/' + genDate() + '_' + filename + '_legend.png')
plt.close(fig)
fig2 = plt.figure()
p1 = plt.bar(y_pos, height=objects)
p2 = plt.bar(y_pos, height=dataSumNE, bottom=objects)
if recolor:
p1[(len(p1) - 1)].set_color('C3')
p2[(len(p2) - 1)].set_color('#FFC080')
plt.xticks(y_pos, data)
plt.ylabel('Zulassungen')
plt.xlabel(xlab)
plt.legend(['Elektroautos', 'Andere Antriebe'])
mpld3.save_html(fig, 'outputs/mpld3/' + genDate() + '_' + filename + '_code.html')
def graph():
total_tomatoes = []
total_tomatoes_count = 0
db = SQL("sqlite:///pomodoro.db")
user_daily_history = db.execute(
"SELECT * FROM daily_history WHERE table_id=:table_id",
table_id=int(decrypt_message(request.cookies.get("table_id"))),
)
for row in user_daily_history:
total_tomatoes_count += row["tomato_count"]
total_tomatoes.append(total_tomatoes_count)
fig = figure()
ax = fig.gca()
ax.plot(total_tomatoes)
# if os.path.exists("./templates/myfig.html"):
# os.remove("./templates/myfig.html")
mpld3.save_html(
fig,
"./templates/myfig{}.html".format(
decrypt_message(request.cookies.get("table_id"))
),
)
return render_template(
"myfig{}.html".format(decrypt_message(request.cookies.get("table_id")))
)
def drawRelativePlot(data, dataSumNE, xlab='Jahr', filename='figboth', recolor=False):
objects = data
y_pos = np.arange(len(objects))
fig = plt.figure(figsize=[16, 9], dpi=72)
p1 = plt.bar(y_pos, height=objects)
p2 = plt.bar(y_pos, height=dataSumNE, bottom=objects)
if recolor:
p1[(len(p1) - 1)].set_color('C3')
p2[(len(p2) - 1)].set_color('#FFC080')
plt.xticks(ticks=y_pos, labels=dataSumNE.index)
plt.ylabel('Anteile Gesamte Inverkehrssetzungen')
plt.xlabel(xlab)
plt.legend(['Elektroautos', 'Andere Antriebe'])
plt.savefig('outputs/png/' + genDate() + '_' + filename + '_legend.png')
plt.close(fig)
fig2 = plt.figure()
p1 = plt.bar(y_pos, height=objects)
p2 = plt.bar(y_pos, height=dataSumNE, bottom=objects)
if recolor:
p1[(len(p1) - 1)].set_color('C3')
p2[(len(p2) - 1)].set_color('#FFC080')
plt.xticks(ticks=y_pos, labels=dataSumNE.index)
plt.ylabel('Anteile Gesamte Inverkehrssetzungen')
plt.xlabel(xlab)
plt.legend(['Elektroautos', 'Andere Antriebe'])
mpld3.save_html(fig2, 'outputs/mpld3/' + genDate() + '_' + filename + '_code.html')
def save_fig(fig, title, plot_dict, pic_path):
output_file = plot_dict.get('output_file', '')
if output_file is not '':
# We do not want to have to remember whether the ending has to be supplied
if output_file.endswith('.pdf'):
out_file = output_file
else:
out_file = output_file + '.pdf'
else:
out_file = title + '.pdf'
print 'Writing to output:', out_file.replace('.pdf', '')
out_path = os.path.join(pic_path, out_file).replace(' ', '_')
strip_chars = ['(', ')', ',', ';']
for sc in strip_chars:
out_path = out_path.replace(sc, '')
fig.savefig(out_path, dpi=fig.dpi)
out_path = out_path.replace('.pdf', '.svg')
fig.savefig(out_path, dpi=fig.dpi)
if mpld3 is not None:
out_path = out_path.replace('.svg', '.html')
with open(out_path, 'w') as fileobj:
mpld3.save_html(fig,
fileobj,
template_type='simple',
mpld3_url='../mpld3.v0.2.js',
d3_url='../d3.v3.min.js')
plt.close(fig)
def main():
G = nx.Graph()
N = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
E = [(1, 2), (1, 8), (2, 3), (2, 4), (4, 5), (6, 7), (6, 8), (8, 9),
(8, 10), (4, 9), (2, 5), (3, 7)]
G.add_nodes_from(N)
G.add_edges_from(E)
plt.title("Title")
plt.axis('equal') #両軸を同じスケールに
plt.gcf().set_facecolor('w')
pos = nx.spring_layout(G) #描画位置はここで確定,全ノードの重みを1にするので重みがかかるのは引力計算のみ
nx.draw_networkx(G, pos=pos, node_color='w')
#ax=plt.gca()
#zoom_factory(ax,base_scale=2.)
#plt.show()
fig = plt.gcf()
print mpld3.plugins.get_plugins(fig)
mpld3.plugins.clear(fig)
zoom_plugin = mpld3.plugins.Zoom(button=False, enabled=True)
print mpld3.plugins.get_plugins(fig)
mpld3.plugins.connect(fig, zoom_plugin)
mpld3.save_html(fig, "test.html")
mpld3.show(template_type="general", no_extras=True) # showする！
def plot_html(coordinates, labels=None, ids=None, title="plot",
discrete=False, output="output", pointsize=1.0, alpha=0.3,
cname="Spectral_r"):
if labels is None:
colvec = "black"
elif discrete:
uniqClasses, label_numeric = np.unique(labels, return_inverse=True)
colvec = np.squeeze(label_numeric)
elif not discrete:
label_numeric = labels
colvec = np.squeeze(label_numeric)
fig, ax = plt.subplots(subplot_kw=dict(facecolor='#EEEEEE'))
ax.grid(color='white', linestyle='solid')
ax.set_title(title, size=30)
pointsidx = ['point {0}'.format(i + 1)
for i in range(coordinates.shape[0])]
scatter = ax.scatter(coordinates[:, 0].tolist(),
coordinates[:, 1].tolist(),
c=colvec, s=20*pointsize, alpha=alpha,
cmap=plt.get_cmap(cname),
edgecolor='black')
if ids is not None and labels is not None:
tooltipstr = ["%s: label=%s" % t for t in zip(ids, labels)]
elif ids is not None:
tooltipstr = ["%s: id=%s" % t for t in zip(pointsidx, ids)]
elif labels is not None:
tooltipstr = ["%s: label=%s" % t for t in zip(pointsidx, labels)]
else:
tooltipstr = list(pointsidx)
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=tooltipstr)
mpld3.plugins.connect(fig, tooltip)
mpld3.save_html(fig, output+".html")
plt.close(fig)
print("\nWrote html plot to disk: %s\n" % (output+".html"))
def visualize(X, contexts, file):
import matplotlib.pyplot
import mpld3
fig, ax = matplotlib.pyplot.subplots()
ax.grid(True, alpha=0.3)
points = ax.plot(X[:, 0], X[:, 1], 'o', color='b',
mec='k', ms=5, mew=1, alpha=.6)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_title('Hover mouse to reveal context', size=20)
tooltip = mpld3.plugins.PointHTMLTooltip(
points[0],
contexts,
voffset=10,
hoffset=10
)
mpld3.plugins.connect(fig, tooltip)
mpld3.save_html(fig, file)
def plot(self, data, notebook=False, show=True, savename=None):
fig = pyplot.figure()
ncenters = len(self.centers)
colorizer = Colorize()
colorizer.get = lambda x: self.colors[int(self.predict(x)[0])]
# plot time series of each center
# TODO move into a time series plotting function in viz.plots
for i, center in enumerate(self.centers):
ax = pyplot.subplot2grid((ncenters, 3), (i, 0))
ax.plot(center, color=self.colors[i], linewidth=5)
fig.add_axes(ax)
# make a scatter plot of the data
ax2 = pyplot.subplot2grid((ncenters, 3), (0, 1),
rowspan=ncenters,
colspan=2)
ax2, h2 = scatter(data, colormap=colorizer, ax=ax2)
fig.add_axes(ax2)
plugins.connect(fig, HiddenAxes())
if show and notebook is False:
mpld3.show()
if savename is not None:
mpld3.save_html(fig, savename)
elif show is False:
return mpld3.fig_to_html(fig)
def main(args):
# Import data
logger.info(u'Importing data with following parameters: \n\tWide: {0}\n\tDesign: {1}\n\tUnique ID: {2}\n\tGroup Column: {3}'.format(args.fname, args.dname, args.uniqID, args.group))
dat = wideToDesign(args.fname, args.dname, args.uniqID, args.group)
dat.wide.convert_objects(convert_numeric=True)
fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(20, 20))
plt.subplots_adjust(hspace=0.3)
# If there is group information, color by group.
if hasattr(dat, 'group'):
logger.info('Plotting sample distributions by group')
legend1 = pltByTrt(dat, ax1)
else:
logger.info('Plotting sample distributions')
pltBySample(dat, ax1)
# Create Legend
handles, labels = ax1.get_legend_handles_labels()
ax1.legend(handles, labels, ncol=5, loc='upper right', fontsize=10)
# Create second legend if there is group information
if hasattr(dat, 'group'):
ax1.add_artist(legend1)
# Plot boxplot of samples
pltBoxplot(dat, ax2)
plt.savefig(args.ofig, format='pdf')
mpld3.save_html(fig, args.ofig2, template_type='simple')
def save(fig, filename, kw):
"""
Save the figure
Args:
fig (mpl.Figure): current figure
filename (str): output filename
kw (dict): kwargs dict
"""
# is this deprecated??
st()
try:
if kw['save_ext'] == 'html':
import mpld3
mpld3.save_html(fig, filename)
else:
fig.savefig(filename)
if kw['show']:
os.startfile(filename)
except:
if kwargs.get('show_filename', False):
print(filename)
raise NameError('%s is not a valid filename!' % filename)
def export_fmt(self, filename, size, sizeofsizes, format):
if sizeofsizes == 1:
size = 'none'
if format is 'png':
add = '.png'
elif format is 'pgf':
add = '.pgf'
elif format is 'pdf':
add = '.pdf'
elif format is 'html':
add = '.html'
elif format is 'svg':
# save as pdf, then pdf2svg
self.fig.savefig(filename + self.sizestring[size] + '.pdf',
bbox_extra_artists=self.artists, bbox_inches='tight',
transparent=True)
os.system('pdf2svg ' + filename + self.sizestring[size] + '.pdf ' +
filename + self.sizestring[size] + '.svg')
os.remove(filename + self.sizestring[size] + '.pdf')
elif format is 'websvg':
add = 'web.svg'
if (format is not 'svg') and (format is not 'html'):
self.fig.savefig(filename + self.sizestring[size] + add,
bbox_extra_artists=self.artists, bbox_inches='tight',
transparent=True)
if format is 'html':
add = '.html'
mpld3.save_html(self.fig, filename + add)
self.add_math_jax(filename + add)
if format is 'pgf':
self.remove_font_sizes(filename + self.sizestring[size] + add)
def plot(self, notebook=False, colormap='polar', scale=1, maptype='points', show=True, savename=None):
# make a spatial map based on the scores
fig = pyplot.figure(figsize=(12, 5))
ax1 = pyplot.subplot2grid((2, 3), (0, 1), colspan=2, rowspan=2)
if maptype is 'points':
ax1, h1 = pointmap(self.scores, colormap=colormap, scale=scale, ax=ax1)
elif maptype is 'image':
ax1, h1 = imagemap(self.scores, colormap=colormap, scale=scale, ax=ax1)
fig.add_axes(ax1)
# make a scatter plot of sampled scores
ax2 = pyplot.subplot2grid((2, 3), (1, 0))
ax2, h2, samples = scatter(self.scores, colormap=colormap, scale=scale, thresh=0.01, nsamples=1000, ax=ax2, store=True)
fig.add_axes(ax2)
# make the line plot of reconstructions from principal components for the same samples
ax3 = pyplot.subplot2grid((2, 3), (0, 0))
ax3, h3, linedata = tsrecon(self.comps, samples, ax=ax3)
plugins.connect(fig, LinkedView(h2, h3[0], linedata))
plugins.connect(fig, HiddenAxes())
if show and notebook is False:
mpld3.show()
if savename is not None:
mpld3.save_html(fig, savename)
elif show is False:
return mpld3.fig_to_html(fig)
def save_abstractness_x_instability_scatter(x_values, x_label, y_values, y_label, ball_values, ball_label, color_values, color_label, annotations, filename_prefix, scope_name, show_diagonal=True):
#plt.figure() # new one, or they will be mixed
fig, ax = plt.subplots()
ax.set_xticks([0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]) # http://stackoverflow.com/questions/8209568/how-do-i-draw-a-grid-onto-a-plot-in-python
ax.set_yticks([0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0])
plt.grid()
if show_diagonal:
plt.plot([0.0, 1.0], [1.0, 0.0], 'k-', ls="--", lw=2, alpha=0.5, color='green') # http://matplotlib.org/api/lines_api.html
plt.plot([0.0, 0.7], [0.7, 0.0], 'k-', ls="--", lw=1, alpha=0.7, color='orange') # http://matplotlib.org/api/lines_api.html
plt.plot([0.3, 1.0], [1.0, 0.3], 'k-', ls="--", lw=1, alpha=0.7, color='orange') # http://matplotlib.org/api/lines_api.html
plt.plot([0.0, 0.4], [0.4, 0.0], 'k-', ls="--", lw=1, alpha=0.9, color='red') # http://matplotlib.org/api/lines_api.html
plt.plot([0.6, 1.0], [1.0, 0.6], 'k-', ls="--", lw=1, alpha=0.9, color='red') # http://matplotlib.org/api/lines_api.html
scatter = ax.scatter(x_values, y_values, ball_values, alpha=0.5, c=color_values)
plt.xlabel(x_label)
plt.ylabel(y_label)
plt.title("%i %s items. Circles: %s & %s" % (len(x_values), scope_name, ball_label, color_label))
tooltip = mpld3.plugins.PointHTMLTooltip(scatter, labels=annotations, hoffset=10, voffset=-25)
mpld3.plugins.connect(fig, tooltip)
mpld3.plugins.connect(fig, mpld3.plugins.MousePosition(fmt=".2f"))
mpld3.plugins.connect(fig, ClickSendToBack(scatter))
filename = "%s-scatter-%s-%s_%s_%s.html" % (filename_prefix, scope_name, x_label, y_label, ball_label)
mpld3.save_html(fig, filename)
return filename
def italy_graph():
#get total cases
affected = [dic.get('totale_casi') for dic in italy_list]
#creating x and y coordinates
x = [i for i in range(0, len(italy_list))]
y = [int(num) for num in affected]
#creating the figure with matplotlib
fig = Figure(figsize=(10, 4))
#divinding into subplots
ax = fig.subplots()
#setting x label
ax.set_xticks(x)
ax.set_xticklabels(ticks, rotation=45)
#plotting diagram
ax.plot(x, y, color='magenta')
#setting labels
ax.set_ylabel('affected people', size=20)
ax.set_title('People discovered to have virus', size=40)
#save html with library function
mpld3.save_html(fig, 'dynamic_html_files/graph.html')
def turn_scatter_into_interactive(fig,
scatter_plot,
df,
file_name,
figsize=False):
from jinja2 import Template, Environment, FileSystemLoader
from mpld3 import plugins
# file_path = './assets/interactive_plots/'+file_name
file_path = './' + file_name
env = Environment(loader=FileSystemLoader('./views'))
movie_template = env.get_template('movie.jinjia')
movies = df.to_dict(orient='records')
movie_cards = [
movie_template.render(movie=movie, show_ratings_num=True)
for movie in movies
]
if figsize:
fig.set_size_inches(figsize)
else:
fig.set_size_inches(8.5, 8.5)
plugins.connect(
fig,
plugins.PointHTMLTooltip(scatter_plot,
movie_cards,
css=load_css(raw=True)))
mpld3.save_html(fig, file_path)
button = '''<a class='btn btn-default' style="text-decoration: none;;"
href="{0}" target='_blank'>
Interactive Scatter Plot</a>
'''.format(file_path)
return HTML(button)
def save_residuals_plot(obs, save_path, data_name):
import matplotlib.pyplot as plt
import mpld3 # pylint: disable=import-error
fig = plt.figure(figsize=(10, 20))
fig.suptitle('Residuals of ' + data_name, fontsize=24)
n = len(list(obs.keys()))
start_times = [obs[kind]['t'][0] for kind in obs]
start_time = min(start_times)
xlims = [start_time + 3, start_time + 60]
for i, kind in enumerate(obs):
ax = fig.add_subplot(n, 1, i + 1)
ax.set_xlim(xlims)
t = obs[kind]['t']
res = obs[kind]['residual']
start_idx = bisect(t, xlims[0])
if len(res) == start_idx:
continue
ylim = max(np.linalg.norm(res[start_idx:], axis=1))
ax.set_ylim([-ylim, ylim])
if int(kind) in SAT_OBS:
svIds = obs[kind]['svIds']
for svId in set(svIds):
svId_idx = (svIds == svId)
t = obs[kind]['t'][svId_idx]
res = obs[kind]['residual'][svId_idx]
ax.plot(t, res, label='SV ' + str(int(svId)))
ax.legend(loc='right')
else:
ax.plot(t, res)
plt.title('Residual of kind ' + ObservationKind.to_string(int(kind)),
fontsize=20)
plt.tight_layout()
os.makedirs(save_path)
mpld3.save_html(fig, save_path + 'residuals_plot.html')
def as_html(pd_data: pd.DataFrame, output_file_dir: str) -> None:
""" Create HTML page with graphics. """
fig = plt.figure()
ax = fig.subplots()
ax.plot(pd_data)
file_obj = os.path.join(output_file_dir, "plots.html")
mpld3.save_html(fig, file_obj)
def plot_by_mpld3(dataframe,figsize=(12,6),marker='o',grid=True,
alpha_ax=0.3,alpha_plot=0.4,alpha_unsel=0.3,alpha_over=1.5,
title=None,xlabel=None,ylabel=None,mode="display",file=None):
## DataFrame 데이터를 이용하여 웹용 D3 chart 스크립트 생성
# plot line + confidence interval
fig, ax = plt.subplots(figsize=figsize)
ax.grid(grid, alpha=alpha_ax)
for key, val in dataframe.iteritems():
l, = ax.plot(val.index, val.values, label=key, marker=marker)
ax.plot(val.index,val.values, color=l.get_color(), alpha=alpha_plot)
# define interactive legend
handles, labels = ax.get_legend_handles_labels() # return lines and labels
interactive_legend = plugins.InteractiveLegendPlugin(handles,labels,
alpha_unsel=alpha_unsel,
alpha_over=alpha_over,
start_visible=True)
plugins.connect(fig, interactive_legend)
if xlabel:
ax.set_xlabel(xlabel)
if ylabel:
ax.set_ylabel(ylabel)
if title:
ax.set_title(title, size=len(title)+5)
## mode
if mode == 'html': # return html script
return mpld3.fig_to_html(fig)
elif mode == 'save' and file: # save file
mpld3.save_html(fig,file)
else: # display chart
#mpld3.enable_notebook()
return mpld3.display()
def test_interactive_linearPP(save_to_html=False):
## Define left and right state
ql = np.array([-2.0, 2.0])
qr = np.array([0.0, -3.0])
# Define two eigenvectors and eigenvalues (acoustics)
zz = 2.0
rho0 = 1.0
r1 = np.array([zz, 1.0])
r2 = np.array([-zz, 1.0])
lam1 = zz / rho0
lam2 = -zz / rho0
plotopts = {
'q1min': -5,
'q1max': 5,
'q2min': -5,
'q2max': 5,
'domain': 5,
'time': 1,
'title1': "Pressure",
'title2': "Velocity"
}
pt = linear_phase_plane(ql, qr, r1, r2, lam1, lam2, **plotopts)
if save_to_html:
mpld3.save_html(pt, "test_linearPP.html")
mpld3.show()
def to_html(self, filename, node_formatter=_node_to_label_IC, **kwargs):
"""Draw an interactive lattice using :class:`clustering.Node`'s drawing function and mpld3.
Arguments:
filename (str): filename of the exported html page.
node_formatter (func): custom function to format nodes
"""
css = _load_external_text("table.css")
fig, lines, ordered_nodes = self._draw_one(
self.nodes,
figsize=(20, 9),
n=4,
scale=False,
point={"s": 50}, # TODO: Something wrong here
interactive=True,
**kwargs)
paths = list(
filter(
lambda obj: type(obj) is matplotlib.collections.PathCollection,
fig.axes[0].get_children(),
))
lines = list(
filter(
lambda obj: type(obj) is matplotlib.lines.Line2D and len(
obj.get_xdata(orig=True)) > 1, fig.axes[0].get_children()))
points_ids = []
corrd_to_points = {}
for p, v in zip(paths, ordered_nodes):
x, y = v.attributes["_x"], v.attributes["_y"]
p_id = mpld3.utils.get_id(p) # ,"pts")
corrd_to_points[(x, y)] = p_id
label = node_formatter(v, comp=self.comp)
points_ids.append(p_id)
tooltip = mpld3.plugins.PointHTMLTooltip(p, [label], css=css)
mpld3.plugins.connect(fig, tooltip)
point_to_artists = defaultdict(set)
lines = sorted(lines, key=lambda l: min(l.get_ydata()))
for l in lines:
parent, child = zip(*l.get_data(orig=True))
childp = corrd_to_points[tuple(child)]
parentp = corrd_to_points[tuple(parent)]
if 0 in child:
point_to_artists[childp] = set()
point_to_artists[parentp].add(childp)
point_to_artists[parentp].add(mpld3.utils.get_id(l))
point_to_artists[parentp].update(point_to_artists[childp])
point_to_artists = {
p: list(point_to_artists[p])
for p in point_to_artists
}
# root = corrd_to_points[(node.attributes["_x"],node.attributes["_y"])]
mpld3.plugins.connect(
fig, _HighlightSubTrees(points_ids, dict(point_to_artists)))
mpld3.save_html(fig, filename, template_type="simple")
def term_sheet_to_html(self,
window=30,
windows=[30, 60, 90, 120],
quantiles=[0.25, 0.75],
bins=100,
normed=True,
bench='SPY',
open=False):
ext = '.html'
cones_fig, cones_plt = self.cones(windows=windows, quantiles=quantiles)
rolling_quantiles_fig, rolling_quantiles_plt = self.rolling_quantiles(
window=window, quantiles=quantiles)
rolling_extremes_fig, rolling_extremes_plt = self.rolling_extremes(
window=window)
rolling_descriptives_fig, rolling_descriptives_plt = self.rolling_descriptives(
window=window)
histogram_fig, histogram_plt = self.histogram(window=window,
bins=bins,
normed=normed)
mpld3.save_html(cones_fig, self.define_fig("cones", ext))
mpld3.save_html(rolling_quantiles_fig,
self.define_fig("rolling_quantiles", ext))
mpld3.save_html(rolling_extremes_fig,
self.define_fig("rolling_extremes", ext))
mpld3.save_html(rolling_descriptives_fig,
self.define_fig("rolling_desc", ext))
mpld3.save_html(histogram_fig, self.define_fig("histogram", ext))
pyplt.close(cones_fig)
pyplt.close(rolling_quantiles_fig)
pyplt.close(rolling_extremes_fig)
pyplt.close(rolling_descriptives_fig)
pyplt.close(histogram_fig)
def generate_embedding(param_file, model_file, mnist_file, output_file=None,
param_key=None):
predictor = optimus.load(model_file)
params = biggie.Stash(param_file)
param_key = sorted(params.keys())[-1] if param_key is None else param_key
predictor.param_values = params.get(param_key)
train, valid, test = datatools.load_mnist_npz(mnist_file)
idx = np.random.permutation(len(valid[0]))[:2000]
x_in = valid[0][idx]
y_true = valid[1][idx]
z_out = predictor(x_in=x_in)['z_out']
imgfiles = [datatools.generate_imagename(i, y)
for i, y in enumerate(idx, y_true)]
labels = ['<img src="{}{}" width=100 height=100>'.format(URL_BASE, img)
for img in imgfiles]
palette = seaborn.color_palette("Set3", 10)
colors = np.asarray([palette[y] for y in y_true])
fig = plt.figure(figsize=(10, 10))
ax = fig.gca()
handle = ax.scatter(z_out.T[0], z_out.T[1],
c=colors, s=75, alpha=0.66)
tooltip = plugins.PointHTMLTooltip(
handle, labels,
voffset=10, hoffset=10)
plugins.connect(fig, tooltip)
plt.show()
if output_file:
with open(output_file, 'w') as fp:
mpld3.save_html(fig, fp)
def test_american_cities(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if sys.version_info[:2] <= (3, 4):
warnings.warn(
"Issue with Python 3.4, bug probably related to wrong pointers")
return
fix_tkinter_issues_virtualenv()
import matplotlib.pyplot as plt
import mpld3
filter = {"NewYork": "NY", "Chicago": "CH",
"SanFrancisco": "SF", "Seattle": "Sea"}
temp = get_temp_folder(__file__, "temp_american_cities")
data = os.path.join(temp, "..", "data", "american_cities.txt")
df = pandas.read_csv(data)
df["Longitude"] = -df["Longitude"]
df["City"] = df["City"].apply(lambda v: filter.get(v, ""))
fig, ax = plt.subplots(figsize=(32, 32))
df = df[df.Latitude < 52]
df = df[df.Longitude > -130].copy()
ax = graph_cities(df, ax=ax, markersize=3, fontcolor=(0, 1.0, 0), fontsize='40',
fontname="Courrier", fontweight="bold")
assert ax is not None
img = os.path.join(temp, "img.png")
fig.savefig(img)
assert os.path.exists(img)
name2 = os.path.join(temp, "picture.html")
mpld3.save_html(fig, name2)
assert os.path.exists(name2)
if __name__ == "__main__":
fig.show()
plt.close('all')
fLOG("end")
def draw_scatter(input_file_name,
output_file_name,
axis1_col="axis1",
axis2_col="axis2",
group_col="group",
title_text="Scatter plot",
title_size=20,
point_size=100,
point_alpha=0.3,
grid_color="white",
grid_style="solid",
backgroud_color="#EEEEEE",
sep="\t"):
"""
Draw scatter plot from mothur's axes file and save figure to file.
Parameters
-------
input_file_name: str
Input file name.
output_file_name: str
Output file name.
axis1_col: str, default <axis1>
Axis 1 column name in axis file.
axis2_col: str, default <axis2>
Axis 2 column name in axis file.
group_col: str, default <group>
Group column name in axis file.
title_text: str, default <Scatter plot>
Text displayed as plot title.
title_size: int, default <20>
Plot title size.
point_size: int, default <100>
Point size.
point_alpha: float, default <0.3>
Point transparency.
grid_color: str, default <white>
Color of the plot grid.
grid_style: str, default <solid>
Style of the plot grid.
backgroud_color: str, default <#EEEEEE>
Color of the plot backgroud.
sep: str, default <\t>
Delimiter to use for reading-in axes file.
"""
df = read_csv(input_file_name,
sep=sep)
fig, ax = plt.subplots()
scatter = ax.scatter(np.array(df[axis1_col]),
np.array(df[axis2_col]),
c=np.random.random(size=len(df)),
s=100,
alpha=0.3,
cmap=plt.cm.jet)
ax.grid(color=grid_color, linestyle=grid_style)
ax.set_title(title_text, size=title_size)
labels = list(df[group_col])
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig, tooltip)
mpld3.save_html(fig, output_file_name)
def scatter_interactive(fig, scatter_plot, df, file_name, figsize=False):
from jinja2 import Environment, FileSystemLoader
from mpld3 import plugins
from helpers.application_helper import PointClickableHTMLTooltip2
# file_path = './assets/interactive_plots/'+file_name
file_path = file_name
env = Environment(loader=FileSystemLoader('./views'))
restaurants = df.to_dict(orient='records')
restaurant_template = env.get_template('restaurant.jinja')
cards = [
restaurant_template.render(restaurant=restaurant)
for restaurant in restaurants
]
if figsize:
fig.set_size_inches(figsize)
else:
fig.set_size_inches(8.5, 8.5)
plugins.connect(
fig,
PointClickableHTMLTooltip2(scatter_plot,
labels=cards,
targets=df['url'].tolist(),
css=load_css(raw=True)))
mpld3.save_html(fig, file_path)
button = '''<a class='btn btn-default' style="text-decoration: none;;"
href="{0}" target='_blank'>
Interactive Scatter Plot</a>
'''.format(file_path)
return HTML(button)
def plot(self, data, notebook=False, show=True, savename=None):
fig = pyplot.figure()
ncenters = len(self.centers)
colorizer = Colorize()
colorizer.get = lambda x: self.colors[int(self.predict(x)[0])]
# plot time series of each center
# TODO move into a time series plotting function in viz.plots
for i, center in enumerate(self.centers):
ax = pyplot.subplot2grid((ncenters, 3), (i, 0))
ax.plot(center, color=self.colors[i], linewidth=5)
fig.add_axes(ax)
# make a scatter plot of the data
ax2 = pyplot.subplot2grid((ncenters, 3), (0, 1), rowspan=ncenters, colspan=2)
ax2, h2 = scatter(data, colormap=colorizer, ax=ax2)
fig.add_axes(ax2)
plugins.connect(fig, HiddenAxes())
if show and notebook is False:
mpld3.show()
if savename is not None:
mpld3.save_html(fig, savename)
elif show is False:
return mpld3.fig_to_html(fig)
def update_sentiment_plot(self):
fig, ax = plt.subplots(figsize=(9, 4))
#plt.xticks(range(len(self.df["Positivity"])),ticks,rotation=45)
#plt.xticks(range(len(ticks)),ticks,rotation=45)
plt.setp(ax.get_xticklabels(), visible=False)
plt.plot(self.df['Negativity'], color="red", label='Negativity')
plt.plot(self.df['Positivity'], color="green", label='Positivity')
plt.legend(loc='upper center')
plt.locator_params(nbins=10)
plt.title('Sentiment analysis of the articles')
plt.ylabel('Strength of the feeling')
# fig.canvas.draw()
# ax.set_xlim([0, len(self.df['Negativity'])])
#
# ax.set_xticks(range(len(self.df['Negativity'])))
# ax.set_xticklabels(self.labels, rotation=45)
# plt.plot(self.df['Negativity'], color="red")
# plt.plot(self.df['Positivity'], color="green")
#
# plt.legend(loc='upper center')
# plt.locator_params(nbins=10)
# plt.title('Sentiment analysis of the articles')
# plt.ylabel('Strength of the feeling')
mpld3.save_html(fig, 'templates/' + self.prefix + 'sentiment.html')
def html_scatter(fig, ax, h, x_col, y_col, title, labels='dflt', outpath='dflt'):
outpath = gt.check_dfltarg(outpath, gt.dflt_outpath('foo'))
labels = gt.check_dfltarg(labels, h.label)
scatter = ax.scatter(h[x_col].tolist(), h[y_col].tolist(), alpha=0.001)
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig, tooltip)
myoutpath = os.path.join(outpath, title + '.html')
mpld3.save_html(fig, myoutpath)
def render_mpl(self, fig, path, **kwargs):
import mpld3
kwargs.pop('dpi')
mpld3.save_html(
fig,
fileobj=path,
**kwargs)
def allTrend(self):
self.loadAlldata()
fig = plt.figure(figsize=(17, 13)) # 8 inches wide by 6 inches tall
ax = fig.add_subplot(2, 2, 1)
ax.set_ylabel('hours')
ax.set_xlabel('days in a month')
ax.set_ylim(0, 12)
ax.set_title('time trend for different activity')
labels = [
"light activity", "fairly activity", "very activity",
'very not productive', 'not productive', 'neutural', 'productive',
'very productive', 'awake', 'REM', 'light sleep', 'deep sleep'
]
colors = [
'lime', 'green', 'darkgreen', 'gray', 'brown', 'blue', 'darkblue',
'navy', 'coral', 'violet', 'plum', 'purple'
]
line_collections = []
activityvalue = np.array(list(self.activity.values()))
for i in range(3):
y1 = activityvalue[:, i] / 60
x1 = np.array(range(
len(y1))) # light activity, fairly activity, very activity
l1 = ax.plot(x1, y1, lw=3, alpha=0.4, c=colors[i], label=labels[i])
line_collections.append(l1)
provalues = np.array(list(self.desk.values()))
for i in range(5):
y1 = provalues[:, i]
x1 = np.array(range(len(y1))) #
l1 = ax.plot(x1,
y1,
lw=3,
alpha=0.4,
c=colors[3 + i],
label=labels[3 + i])
line_collections.append(l1)
sleepvalues = np.array(list(self.sleep.values()))
for i in range(4):
y1 = sleepvalues[:, i] / 60
x1 = np.array(range(len(y1))) #
l1 = ax.plot(x1,
y1,
lw=4,
alpha=0.4,
c=colors[8 + i],
label=labels[8 + i])
line_collections.append(l1)
plugins.connect(
fig, plugins.InteractiveLegendPlugin(line_collections, labels))
# mpld3.show()
mpld3.save_html(fig, 'trend.html')
def pcoa_plot_interactive(profile, output_dir, dist_type):
"""Generate interactive PCoA plot.
Args:
profile (metagenomic_profile): Profile instance containing data.
output_dir (str): path to directory to save output
dist_type (str): distance metric to use in PCoA.
Returns:
Path to output file.
"""
try:
import mpld3 # Provides interactive graphs
import plugins # Custom mpld3 plugins
except ImportError:
print(
"Could not import mpld3. Please install mpld3 or set 'interactive_plots' option to 'false.'"
)
return
__check_input(output_dir)
df = __partition_abundance_data(profile)
eig_pairs = __get_eig_pairs(df, dist_type)
eig_pairs.sort()
eig_pairs.reverse()
PCo1 = eig_pairs[0][1]
PCo2 = eig_pairs[1][1]
# Begin plotting
# Clear any current figures from the plot
plt.clf()
lgd_labels = __plot_markers_interactive(profile, PCo1, PCo2,
a=0.7) # Main plotting
# Padding for x and y labels
ax = plt.gca()
ax.tick_params(axis='both', which='major', pad=15)
plt.xlabel("PCo1", fontsize=16)
plt.ylabel("PCo2", fontsize=16)
fname = output_dir + "/" + "pcoa_" + dist_type + ".html"
fig = plt.gcf()
mpld3.plugins.connect(fig, plugins.TweakToolbar())
mpld3.save_html(fig, fname)
# Create legend
lgd_fname = __create_legend(lgd_labels, output_dir)
return fname, lgd_fname
def plotdataPop(data, vals):
"""
simple data popup, take in data and values, plots it as a mpld3 plot allowing for interaction,
add it to an Iframe what then can be used in a folium map popup
returns a popup
Last edit: 25/05/2019
-added exceptions with line number
"""
try:
df = data[vals]
# print(df)
width = 300
height = 320
#If more than one varable add fadding
alpha = 1
if len(vals) > 1:
alpha = 0.8
#define figure
fig, ax = plt.subplots(figsize=(4, 4))
#plot data
for val in vals:
ax.plot(df[val], alpha=alpha, label=val)
ax.legend()
#Plot information
ax.set_ylabel('Mass concentration (ug/m^3)')
ax.set_xlabel('') #solving issue with x labes being cut in 1/2
#set tile based of time interval
ax.set_title(df.index[0].strftime("%Y/%m/%d") + "-(" +
df.index[0].strftime("%H:%M") + " to " +
df.index[len(df) - 1].strftime("%H:%M"))
ax.grid() #grid
#setppop up in mld3
now = datetime.datetime.now()
date = df.index[0].strftime("%Y%m%d") #get the date
#save=datetime.datetime.strptime(now,"%HH%MM%SS")
figname = 'popup_plot' + date + str(now.microsecond) + '.html'
mpld3.save_html(fig, 'Mapoutput//' + figname)
time.sleep(0.1)
a = mpld3.fig_to_html(fig)
#put pop up in iframe format ready to be put into the popup
iframe = IFrame(a, width=(width), height=(height))
popup = folium.Popup(iframe, max_width=600)
return popup
except Exception as e:
print("Error in GPS Data cirlce generation")
print('Error on line {}'.format(sys.exc_info()[-1].tb_lineno))
print(type(e))
print(e.args)
pass
def html_node(self, node, fileobj):
''' plots node and saves to html using mpld3 '''
import mpld3
n = node.getnumdata()
self.subplts = [
plot_single_data(node, i, n, self.log) for i in range(n)
]
mpld3.save_html(pylab.gcf(), fileobj)
def plot_param(df, path, param, units):
fig, ax = plt.subplots(figsize=(8,6))
df[param].plot(marker='o', ax=ax, legend=None)
try:
plt.ylabel(units[df.columns.get_loc(param)], labelpad=10)
except:
pass
plt.xlabel('')
plt.title(param + ' (time in UTC)')
mpld3.save_html(fig, '{o}{p}.html'.format(o=path, p=param))
plt.close(fig)
def pcoa_plot_interactive(profile, output_dir, dist_type):
"""Generate interactive PCoA plot.
Args:
profile (metagenomic_profile): Profile instance containing data.
output_dir (str): path to directory to save output
dist_type (str): distance metric to use in PCoA.
Returns:
Path to output file.
"""
try:
import mpld3 # Provides interactive graphs
import plugins # Custom mpld3 plugins
except ImportError:
print("Could not import mpld3. Please install mpld3 or set 'interactive_plots' option to 'false.'")
return
__check_input(output_dir)
df = __partition_abundance_data(profile)
eig_pairs = __get_eig_pairs(df, dist_type)
eig_pairs.sort()
eig_pairs.reverse()
PCo1 = eig_pairs[0][1]
PCo2 = eig_pairs[1][1]
# Begin plotting
# Clear any current figures from the plot
plt.clf()
lgd_labels = __plot_markers_interactive(profile, PCo1, PCo2, a=0.7) # Main plotting
# Padding for x and y labels
ax = plt.gca()
ax.tick_params(axis='both', which='major', pad=15)
plt.xlabel("PCo1", fontsize=16)
plt.ylabel("PCo2", fontsize=16)
fname = output_dir + "/" + "pcoa_" + dist_type + ".html"
fig = plt.gcf()
mpld3.plugins.connect(fig, plugins.TweakToolbar())
mpld3.save_html(fig, fname)
# Create legend
lgd_fname = __create_legend(lgd_labels, output_dir)
return fname, lgd_fname
def test_interactive_shallowPP(save_to_html=False):
# Define left and right state (h,hu)
ql = np.array([3.0, 5.0])
qr = np.array([3.0, -5.0])
# Define optional parameters (otherwise chooses default values)
plotopts = {'g':1.0, 'time':2.0, 'tmax':5, 'hmax':10, 'humin':-15, 'humax':15}
# Call interactive function (can be called without any argument)
pt = shallow_water(ql,qr,**plotopts)
if save_to_html:
mpld3.save_html(pt, "test_shallow.html")
mpld3.show()
def plot_observed_aimpoints(obs_aimpoints):
"""
Make png and html (mpld3) plot of data in the ``obs_aimpoints`` table.
"""
plt.close(1)
fig = plt.figure(1, figsize=(8, 4))
dates = DateTime(obs_aimpoints['mean_date'])
years = dates.frac_year
times = dates.secs
ok = years > np.max(years) - float(opt.lookback) / 365.25
obs_aimpoints = obs_aimpoints[ok]
times = times[ok]
lolims = {}
uplims = {}
for axis in ('dx', 'dy'):
lolims[axis] = obs_aimpoints[axis] > 10
uplims[axis] = obs_aimpoints[axis] < -10
obs_aimpoints[axis] = obs_aimpoints[axis].clip(-10, 10)
ok = ((np.abs(obs_aimpoints['target_offset_y']) < 100) &
(np.abs(obs_aimpoints['target_offset_z']) < 100))
plot_cxctime(times[ok], obs_aimpoints['dx'][ok], 'ob', label='CHIPX')
plot_cxctime(times[ok], obs_aimpoints['dy'][ok], 'or', label='CHIPY')
plot_cxctime(times[~ok], obs_aimpoints['dx'][~ok], '*b', label='CHIPX (offset > 100")')
plot_cxctime(times[~ok], obs_aimpoints['dy'][~ok], '*r', label='CHIPY (offset > 100")')
for axis in ('dx', 'dy'):
if np.any(lolims[axis]):
plt.errorbar(DateTime(times[lolims[axis]]).plotdate,
obs_aimpoints[axis][lolims[axis]], marker='.', yerr=1.5, lolims=True)
if np.any(uplims[axis]):
plt.errorbar(DateTime(times[uplims[axis]]).plotdate,
obs_aimpoints[axis][uplims[axis]], marker='.', yerr=1.5, uplims=True)
plt.grid()
ymax = max(12, np.max(np.abs(obs_aimpoints['dx'])), np.max(np.abs(obs_aimpoints['dy'])))
plt.ylim(-ymax, ymax)
plt.ylabel('Offset (arcsec)')
plt.title('Observed aimpoint offsets')
plt.legend(loc='upper left', fontsize='small', title='', framealpha=0.5)
outroot = os.path.join(opt.data_root, 'observed_aimpoints')
logger.info('Writing plot files {}.png,html'.format(outroot))
mpld3.plugins.connect(fig, mpld3.plugins.MousePosition(fmt='.1f'))
mpld3.save_html(fig, outroot + '.html')
fig.patch.set_visible(False)
plt.savefig(outroot + '.png', frameon=False)
def plot_housing_temperature():
dat = fetch.Msid('aach1t', '2000:001', stat='daily')
plt.close(1)
fig = plt.figure(figsize=(8, 4))
year = Time(dat.times, format='cxcsec').decimalyear
plt.plot(year, dat.vals)
plt.grid()
plt.xlabel('Year')
plt.ylabel('Temperature (degF)')
plt.title('Aspect Camera housing temperature trend')
outroot = os.path.join(opt.data_root, 'aca_housing_temperature')
logger.info('Writing plot files {}.png,html'.format(outroot))
mpld3.plugins.connect(fig, mpld3.plugins.MousePosition(fmt='.1f'))
mpld3.save_html(fig, outroot + '.html')
fig.patch.set_visible(False)
plt.savefig(outroot + '.png', frameon=False)
def test_interactive_linearPP(save_to_html=False):
## Define left and right state
ql = np.array([-2.0, 2.0])
qr = np.array([0.0, -3.0])
# Define two eigenvectors and eigenvalues (acoustics)
zz = 2.0
rho0 = 1.0
r1 = np.array([zz,1.0])
r2 = np.array([-zz,1.0])
lam1 = zz/rho0
lam2 = -zz/rho0
plotopts={'q1min':-5, 'q1max':5, 'q2min':-5, 'q2max':5, 'domain':5, 'time':1,
'title1':"Pressure", 'title2':"Velocity"}
pt = linear_phase_plane(ql,qr,r1,r2,lam1,lam2,**plotopts)
if save_to_html:
mpld3.save_html(pt, "test_linearPP.html")
mpld3.show()
def show_mpld3(self,fig,ax,points,xl_list,xl_labels):
import mpld3
from mpld3 import plugins
import pandas as pd
# Define some CSS to control our custom labels
css = """
table
{
border-collapse: collapse;
}
th
{
color: #000000;
background-color: #ffffff;
}
td
{
background-color: #cccccc;
}
table, th, td
{
font-family:Arial, Helvetica, sans-serif;
border: 1px solid black;
text-align: right;
font-size: 10px;
}
"""
df = pd.DataFrame(index=xl_labels)
sorted_keys=sorted(xl_list[0].keys())
for k in sorted_keys:
df[k] = np.array([xl[k] for xl in xl_list])
labels = []
for i in range(len(xl_labels)):
label = df.ix[[i], :].T
# .to_html() is unicode; so make leading 'u' go away with str()
labels.append(str(label.to_html()))
tooltip = plugins.PointHTMLTooltip(points, labels,
voffset=10, hoffset=10, css=css)
plugins.connect(fig, tooltip)
mpld3.save_html(fig,"output.html")
def downloadVideoAndEntropy(f, frame):
fhandle = open(f, 'ab')
ftp.retrbinary('RETR ' + f, fhandle.write)
cap = cv2.VideoCapture(f)
if cap.isOpened():
cap.set(1, frame)
ret, newframe = cap.read()
if ret:
newname = f.split(".")[0]
finalname = newname + '_frame_' + str(frame) + '.png'
cv2.imwrite(finalname, newframe)
colorIm = Image.open(finalname)
greyIm = colorIm.convert('L')
colorIm = np.array(colorIm)
greyIm = np.array(greyIm)
N = 5
S = greyIm.shape
E = np.array(greyIm)
for row in range(S[0]):
for col in range(S[1]):
Lx = np.max([0, col - N])
Ux = np.min([S[1], col + N])
Ly = np.max([0, row - N])
Uy = np.min([S[0], row + N])
region = greyIm[Ly:Uy, Lx:Ux].flatten()
E[row, col] = entropy(region)
grayImage = cv2.applyColorMap(greyIm, cv2.COLOR_BGR2GRAY)
entropyImage = cv2.applyColorMap(greyIm, cv2.COLORMAP_JET)
cv2.imwrite('gray_' + finalname, greyIm)
# cv2.imwrite('color_' + finalname, entropyImage)
a = np.empty_like(E)
a[:, :] = E
a = np.flipud(a)
fig = plt.figure()
plt.imshow(a, cmap=plt.get_cmap("jet"), origin="lower")
plt.xlabel('Entropy in 10x10 neighborhood')
plt.colorbar()
plt.savefig('color_' + finalname, bbox_inches='tight')
plt.imshow(E, cmap=plt.get_cmap("jet"), origin="lower")
plt.plot()
htmlname = newname + '_frame_' + str(frame) + '.html'
mpld3.save_html(fig, htmlname)
# mpld3.fig_to_html(fig, template_type="simple")
print 'finished!'
cap.release()
def colormagMPLD3(tabfile, bfilter, rfilter):
import matplotlib.pyplot as plt
import mpld3
coldict = dict(B=0, V=1, R=2, J=3, K=4)
photdata = getdata(tabfile)
cp = [cleandata(i) for i in photdata]
colorarray = colexces(cp[coldict[bfilter]], cp[coldict[rfilter]])
fig, ax = plt.subplots()
scatter = ax.scatter(colorarray[3], colorarray[2] - colorarray[3], c=colorarray[1], s=40)
ax.axes.invert_xaxis()
ax.axes.set_xlabel(rfilter)
ax.axes.set_ylabel(bfilter + " - " + rfilter)
labels = [str(colorarray[1][i]) for i in range(0, len(colorarray[1]))]
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig, tooltip)
mpld3.save_html(fig, "mpld3color.html")
return
def construct_plot(self, save_template=False, template_name="model.html"):
# build plot data
fig, ax = plt.subplots(subplot_kw=dict(axisbg='#EEEEEE'))
scatter = ax.scatter(self.model_data[self.target].values,
self.model_data['prediction'].values.astype(int),
c= 'r',
cmap=plt.cm.jet)
ax.grid(color='white', linestyle='solid')
ax.set_title("Actual (target) vs. prediction", size=20)
plt.ylabel('prediction')
plt.xlabel('actual')
# create interactive tooltip, save as HTML
tooltip = mpld3.plugins.PointLabelTooltip(scatter)
mpld3.plugins.connect(fig, tooltip)
if save_template:
mpld3.save_html(fig, template_name)
return fig
def generate_plots(image_filename=None, html_filename=None):
"""Generate static and/or dynamic plots for sources count metric"""
if not (image_filename or html_filename):
return
data_set = get_data_set()
dates = [item["date"] for item in data_set]
fig, ax = pyplot.subplots()
ax.set_title("Sources count")
for i, vcs in enumerate(VCS_TYPES):
col = get_rgb_color(i * 1.0 / len(VCS_TYPES))
ax.plot(dates, [item[vcs] for item in data_set], color=col, label=vcs)
ax.legend(loc="upper left")
if image_filename:
# Save static plot as image
pyplot.savefig(image_filename)
if html_filename:
# Save dynamic plot as html document
save_html(fig, html_filename)
def lightcurveMPLD3(tabfile, filters):
import matplotlib.pyplot as plt
import mpld3
fig = plt.figure()
numplots = len(filters)
coldict = dict(B=0, V=1, R=2, J=3, K=4)
photdata = getdata(tabfile)
photdatatrim = [photdata[coldict[j]] for j in filters]
cp = [cleandata(k) for k in photdatatrim]
for i in range(0, len(filters)):
a = fig.add_subplot(numplots, 1, i + 1)
a.scatter(cp[i][0], cp[i][1])
a.axes.invert_yaxis()
a.axes.set_xlabel("Julian Date")
a.axes.set_ylabel(filters[i] + " magnitude")
mpld3.plugins.connect(fig, mpld3.plugins.Zoom(button=False, enabled=True))
mpld3.save_html(fig, "mpld3lc.html")
return
def vis_data(post_data):
# Use Mpld3 to visualize data
# CSS for labels
css = """
body {
background-color: #E0E4CC
}
iframe {
width: 80%
height: 900%
text-align: left
}
table, th, td, iframe
{
font-family: Arial, Helvetica, sans-serif;
text-align: right;
color: #000000;
background-color: #A7DBD8;
border: none;
border-spacing: 0;
padding: 0;
}
"""
pd.set_option('display.max_colwidth', -1)
size = []
for likes in post_data['likes']:
if likes > 1:
size.append(likes * 10)
else:
size.append(9)
data = pd.DataFrame({
'Color': post_data['tones']
})
labels = []
for i in range(len(post_data['ids'])):
label = data.ix[[i], :].T
label.columns = ['Post {0}'.format(i + 1)]
labels.append((label.to_html()))
fig, ax = plt.subplots()
scatter = ax.scatter(matplotlib.dates.date2num(post_data['times']),
post_data['follower_counts'],
c=post_data['tones'],
s=size,
alpha=0.7,
cmap=plt.cm.jet)
ax.grid(color='white', linestyle='solid')
ax.set_title('#{0} Trends'.format(hash_tag), size=40)
green = mpatches.Patch(color='green', label='Positive')
gray = mpatches.Patch(color='gray', label='Neutral')
red = mpatches.Patch(color='red', label='Negative')
plt.legend(handles=[green, gray, red], ncol=3, framealpha=0.5)
plt.xlabel('Time', size=25)
plt.ylabel('Number of Followers the Poster has', size=25)
frame = plt.gca()
frame.axes.get_xaxis().set_ticks([])
frame.axes.get_yaxis().set_ticks([])
tooltip = mpld3.plugins.PointHTMLTooltip(scatter, labels, css=css)
mpld3.plugins.connect(fig, tooltip)
fig.set_size_inches(8.5, 6.5)
mpld3.save_html(fig, '{0}-graph.html'.format(hash_tag))
from pylab import show, figure
import ShapelyChipDesigns as SD
import mpld3
n1 = 3
n2 = 2
wfinger = 3
lfinger = 90
wgap = 3
ltaper = 100
wc = 10
wGgap = 4.5
CAP = SD.MakeFingercapacitor(n1, n2,
wfinger, lfinger, wgap, ltaper,
wc, wGgap)
fig = figure()
CAP.show_info()
SD.mouseshow()
mpld3.save_html(fig, "_img/test_finger_capacitor.html")
fig2 = pl.figure(2)
ax2 = fig2.add_axes([0.1,0.15,0.8,0.8])
percent_growth = (records['data2'] - records['data1'])*100./records['data1']
scatter = ax2.scatter(records['data1'], percent_growth, s = 100., alpha = 0.4, c = records['lat']*20, cmap = pl.cm.Reds)
ax2.set_xlim(0,20000)
pl.xticks(size = 16)
pl.yticks(size = 16)
pl.ylabel('% Increase in population (2000-10)', size = 18)
pl.xlabel('Population in year 2000 in 000s', size = 18)
labels = [i for i in records['keys']]
#fig2.plugins = [plugins.PointLabelTooltip(scatter, labels)]
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig2, tooltip)
mpld3.save_html(fig2, 'mpld3_test.html')
#pl.show()
#mpld3.show()
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
fig3 = pl.figure(3)
map = Basemap(projection='merc', lat_0 = 20, lon_0 = 80,
resolution = 'h', area_thresh = 1.,
llcrnrlon=68.0, llcrnrlat=8.0,
urcrnrlon=95.0, urcrnrlat=37.0)
map.drawmapboundary(fill_color='#1E90FF')
map.fillcontinents(color='#ddaa66',lake_color='#1E90FF')
map.drawcoastlines()
map.drawcountries()
dx = xmax - xmin
ddx=0.1*dx
dy = ymax - ymin
ddy=0.1*dy
plt.hold(False)
plt.xlim(xmin-ddx,xmax+ddx)
plt.ylim(ymin-ddy,ymax+ddy)
plt.title('Bibliography Graph %s' %year_iter)
plt.axis('off')
plt.savefig("../output/bib-graph%s.png" %year_iter) # save as png
fig = plt.figure(1, figsize=(10, 10))
plt.axis('off')
pos=nx.drawing.nx_agraph.graphviz_layout(bib_graph)
node_color=[c*10 for c in nx.core_number(bib_graph).values()]
# for node in bib_graph:
# pos[node]=(pos[node][0]*10, pos[node][1]*10)
nx.draw_networkx(bib_graph, pos, node_size=node_weight, node_color=node_color, edge_color=edge_weight, alph=0.5, cmap=plt.cm.OrRd, font_size=11, font_family='arial')
plt.title('Bibliography Graph %s' %year_iter)
mpld3.plugins.connect(fig)
mpld3.save_html(fig, html_fig)
# Uncomment for more output formats
#nx.write_graphml(bib_graph, './output/biblio-perso-globale%s.graphml' %year_iter)
#nx.write_gml(bib_graph, './output/biblio-perso-globale.gml')
#nx.write_graphml(bib_graph, './output/biblio-perso-globale.graphml')
#plt.show() # display
input = "../output/bib-graph????.png"
output = "../output/bib-animation.gif"
os.system("convert -delay 100 -loop 0 %s %s" % (input, output))
html_fig.close()
normalize(df, 'v-relative', 'v-relative-normalized')
normalize(df, 'minimum-AU-distance', 'minimum-AU-distance-normalized')
df['mining-index'] = .8 * df['v-relative-normalized'] + .2 * df['minimum-AU-distance-normalized'] # lower is better
df['close-approach-date'] = pd.to_datetime(df['close-approach-date'], coerce=True)
df = df[['close-approach-date', 'mining-index', 'object', 'minimum-AU-distance-normalized', 'v-relative']]
for year in range(2025, 2201):
first_date = str(year)+'-01-01'
last_date = str(year)+'-12-31'
df_copy = df[(df['close-approach-date'] >= first_date) & (df['close-approach-date'] <= last_date)]
df_copy.set_index(['close-approach-date'], inplace=True)
fig, ax = plt.subplots(subplot_kw=dict(axisbg="#FFFFFF"), figsize=(15,7))
ax.text
scatter = ax.scatter(df_copy.index, df_copy['mining-index'], c=df_copy['mining-index'], s=30)
ax.set_xlabel('Month', fontsize=18)
ax.set_ylabel('Extraction Index', fontsize=18, family='sans-serif', weight='bold')
ax.set_title('Element Extraction from Close Asteroids in ' + str(year), fontsize=24)
ax.set_xlim(datetime.date(year, 1, 1), datetime.date(year, 12, 31))
ax.set_ylim(0.0, 1.0)
ax.tick_params(axis='both', which='major', pad=15, labelsize=10)
df_copy['formatted'] = df_copy.index
df_copy['formatted'] = df_copy['formatted'].apply(lambda x: x.strftime('%b %d, %Y'))
labels = ['<table><tr><th>Object</th><td>{0}</td></tr><tr><th>Velocity</th><td>{1} km/s</td></tr><tr><th>Distance</th><td>{2} AU</td></tr><tr><th>Date</th><td>{3}</td></tr></table>'.format(i[0], i[1], i[2], i[3]) for i in df_copy[['object', 'v-relative', 'minimum-AU-distance-normalized', 'formatted']].as_matrix()]
tooltip = mpld3.plugins.PointHTMLTooltip(scatter, labels=labels, css=css)
mpld3.plugins.connect(fig, tooltip)
mpld3.save_html(fig, str(year)+'_scatter')
#mpld3.show()
Use the toolbar buttons at the bottom-right of the plot to enable zooming
and panning, and to reset the view.
"""
import matplotlib.pyplot as plt
import numpy as np
import mpld3
fig, ax = plt.subplots(subplot_kw=dict(axisbg='#EEEEEE'))
N = 100
scatter = ax.scatter(np.random.normal(size=N),
np.random.normal(size=N),
c=np.random.random(size=N),
s=1000 * np.random.random(size=N),
alpha=0.3,
cmap=plt.cm.jet)
ax.grid(color='white', linestyle='solid')
ax.set_title("Scatter Plot (with tooltips!)", size=20)
labels = ['point {0}'.format(i + 1) for i in range(N)]
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig, tooltip)
plt.savefig("E:/IPython2/141007 Sphinx and ShapelyChipDesigns/try4/docs/pyplots/img/scatter_plot.png")
plt.savefig("scatter_plot.png")
mpld3.save_html(fig, "E:/IPython2/141007 Sphinx and ShapelyChipDesigns/try4/docs/pyplots/img/scatter_plot.html")
#mpld3.save_html(fig, "E:/IPython2/141007 Sphinx and ShapelyChipDesigns/try4/docs/_build/html/_images/scatter_plot.html")
mpld3.save_html(fig, "E:/IPython2/141007 Sphinx and ShapelyChipDesigns/try4/docs/pyplots/scatter_plot.html")
mpld3.save_html(fig, "scatter_plot.html")
mpld3.save_html(fig, "_img/scatter_plot.html")
def plot_intra_obs_dy_dz(self):
# Make a table with the max delta chipx and chipy during each obsid.
# First get the mins, maxes, means for each obsid by grouping.
obsids = self.asol.group_by('obsid')['obsid', 'year', 'dy', 'dz']
mins = obsids.groups.aggregate(np.minimum)
maxes = obsids.groups.aggregate(np.maximum)
means = obsids.groups.aggregate(np.mean)
t = Table([means['year'],
(maxes['dy'] - mins['dy']) * 20,
(maxes['dz'] - mins['dz']) * 20],
names=('year', 'dy', 'dz'))
t['ybin'] = np.trunc((t['year'] - t['year'][-1] - 0.0001) * 4.0)
# Now group the dx and dy vals in 3-month intervals and find the 50th
# and 90th percentile within each time bin. This again using aggregation,
# but this time in a trickier way by returning a Column object as the
# aggregation object instead of a single value.
t_bin = t.group_by('ybin')
i_sorts = t_bin.groups.aggregate(np.argsort)
outs = {}
for col in ('dy', 'dz'):
for perc in (50, 90, -5):
rows = []
for group, i_sort in izip(t_bin.groups, i_sorts[col]):
if perc < 0:
for row in group[i_sort[perc:]]:
rows.append(row)
else:
ii = (int(perc) * (len(group) - 1)) // 100
rows.append(group[i_sort[ii]])
outs[str(perc) + col] = Table(rows=rows, names=t_bin.colnames)
plt.close(1)
fig, axes = plt.subplots(nrows=2, ncols=1, sharex=True, num=1)
for col, ax in izip(('dy', 'dz'), axes):
for perc, color in izip((50, 90, -5), ('b', 'm', 'r')):
t = outs[str(perc) + col]
if perc < 0:
ax.plot(t['year'], t[col], '.', color=color, markersize=5,
label='Outliers')
else:
ax.plot(t['year'], t[col], color=color, label='{}th percentile'.format(perc))
ax.fill_between(t['year'], t[col], color=color, alpha=0.3)
ax.grid()
ax.set_ylabel(col.upper() + ' (arcsec)')
ylims = [axes[i].get_ylim()[1] for i in (0, 1)]
for ii in (0, 1):
axes[ii].set_ylim(0, max(ylims))
axes[0].set_title('Intra-observation aimpoint drift (spacecraft coordinates)')
axes[0].legend(loc='upper left', fontsize='small', title='')
axes[1].set_xlabel('Year')
mpld3.plugins.connect(fig, mpld3.plugins.MousePosition(fmt='.1f'))
outroot = os.path.join(opt.data_root, 'intra_obs_dy_dz')
logger.info('Writing plot files {}.png,html'.format(outroot))
mpld3.save_html(fig, outroot + '.html')
fig.patch.set_visible(False)
plt.savefig(outroot + '.png', frameon=False)
def plot_chip_x_y(self, info_det):
"""
Make 3-panel plot showing CHIPX vs. CHIPY, CHIPX vs. time, CHIPY vs. time.
:param det: detector
:param info_det: dict of relevant information for plot
:returns: None
"""
# Gather plot data from percentile tables
years = []
chipxs = []
chipys = []
for perc in (0, 10, 50, 90, 100):
for xy in ('x', 'y'):
dat = getattr(self, 'p{}_{}{}'.format(perc, self.chip_col, xy))
years.append(dat['year'])
chipxs.append(dat[self.chipx_col])
chipys.append(dat[self.chipy_col])
year = np.concatenate(years)
chipx = np.concatenate(chipxs)
chipy = np.concatenate(chipys)
# Open three plot axes for CHIPX vs CHIPY, CHIPX vs time and CHIPY vs Time
plt.close(1)
fig = plt.figure(1, figsize=(10, 5))
ax1 = plt.subplot2grid((2, 4), (0, 0), colspan=2, rowspan=2)
ax2 = plt.subplot2grid((2, 4), (0, 2), colspan=2)
ax3 = plt.subplot2grid((2, 4), (1, 2), colspan=2, sharex=ax2)
cm = matplotlib.cm.get_cmap('YlOrRd')
# Make the N-month bounding box
asol = self.asol
iok = np.searchsorted(asol['year'], asol['year'][-1] - float(opt.box_duration) / 12)
asol = self.asol[iok:]
x0, x1 = info_det['chipx']['min'], info_det['chipx']['max']
y0, y1 = info_det['chipy']['min'], info_det['chipy']['max']
dx = x1 - x0
dy = y1 - y0
year0 = asol['year'][0]
dyear = asol['year'][-1] - year0
ax1.add_patch(Rectangle((x0, y0), dx, dy,
facecolor='#fff8f8', edgecolor='k',
zorder=-100))
ax2.add_patch(Rectangle((year0, x0), dyear, dx,
facecolor='#fff8f8', edgecolor='k',
zorder=-100))
ax3.add_patch(Rectangle((year0, y0), dyear, dy,
facecolor='#fff8f8', edgecolor='k',
zorder=-100))
pogx = POG[self.det][0]
pogy = POG[self.det][1]
ax1.plot([pogx], [pogy], '*r', ms=15, zorder=100)
ax2.plot([POG['year']], [pogx], '*r', ms=15, zorder=100)
ax3.plot([POG['year']], [pogy], '*r', ms=15, zorder=100)
plot_opt = dict(c=year, cmap=cm, alpha=0.8, s=6.0, linewidths=0.5, zorder=10)
points = ax1.scatter(chipx, chipy, **plot_opt)
ax1.set_xlabel('CHIPX')
ax1.set_ylabel('CHIPY')
ax1.set_title('{} aimpoint position (CCD {})'.format(self.det, self.ccd))
ax1.set_aspect('equal', 'datalim')
ax1.grid()
ax2.scatter(year, chipx, **plot_opt) # points =
ax2.set_ylabel('CHIPX')
ax2.yaxis.tick_right()
ax2.grid()
ax3.scatter(year, chipy, **plot_opt) # points =
ax3.set_xlabel('Year')
ax3.set_ylabel('CHIPY')
ax3.yaxis.tick_right()
ax3.grid()
plt.show()
mpld3.plugins.connect(fig, mpld3.plugins.LinkedBrush(points))
mpld3.plugins.connect(fig, mpld3.plugins.MousePosition(fmt='.1f'))
outroot = os.path.join(opt.data_root, 'chip_x_y_{}'.format(self.det_title))
logger.info('Writing plot files {}.png,html'.format(outroot))
mpld3.save_html(fig, outroot + '.html')
fig.patch.set_visible(False)
plt.savefig(outroot + '.png', frameon=False)
def create_plot(players, defaults=PLOT_DEFAULTS, plot='all'):
title = defaults[plot]['title']
x_var = defaults[plot]['x_var']
y_var = defaults[plot]['y_var']
y_var2 = defaults[plot]['y_var2']
y_err_regex = defaults[plot]['y_err_regex']
group = defaults[plot]['group']
drafted = defaults[plot]['drafted']
save_file = defaults[plot]['save_file']
if 'type' in defaults[plot]:
type = defaults[plot]['type']
else:
type = None
if 'undrafted_x_var' in defaults[plot]:
undrafted_x_var = defaults[plot]['undrafted_x_var']
else:
undrafted_x_var = None
print('creating plot {}'.format(plot))
if drafted == False:
show_draft = False
drafted = 'drafted'
else:
show_draft = True
player_list = []
for player in players:
player_list.append(player.flatten())
df = DataFrame(player_list)
df = df.sort(y_var, ascending=False)
fig, ax = plt.subplots()
elements = []
labels=[]
for name, big_group in df.groupby(group):
positions = []
color=next(ax._get_lines.color_cycle)
for drafted_name, group in big_group.groupby(drafted):
x = group[x_var]
y = group[y_var]
y2 = group[y_var2]
yerr = [group[y_var] - group.filter(regex=y_err_regex).min(axis=1),
group.filter(regex=y_err_regex).max(axis=1) - group[y_var]]
if drafted_name:
if show_draft:
element = ax.scatter(x,y, color=color,
s=60, alpha=0.6, marker='D')
ax.errorbar(x,y,yerr=yerr, linestyle="None", lw='1',color=color, )
positions.append(element)
if type != 'price':
element2 = ax.scatter(x,y2, color=color,
s=90, alpha=0.5, marker='+')
positions.append(element2)
players = list(group.apply(lambda x: PLOT_TOOLTIP.format(**x),axis=1))
mpld3.plugins.connect(fig, mpld3.plugins.PointHTMLTooltip(element, players,
voffset=-75, hoffset=10))
else:
if undrafted_x_var: #special x var for undrafted price
x = group[undrafted_x_var]
element = ax.scatter(x,y, color=color,
s=90, alpha=0.2, marker='o')
ax.errorbar(x,y,yerr=yerr, linestyle="None", lw='1',color=color, )
positions.append(element)
if type != 'price':
element2 = ax.scatter(x,y2, color=color,
s=90, alpha=0.5, marker='+')
positions.append(element2)
players = list(group.apply(lambda x: PLOT_TOOLTIP.format(**x),axis=1))
mpld3.plugins.connect(fig, mpld3.plugins.PointHTMLTooltip(element, players,
voffset=-75, hoffset=10))
elements.append(positions)
labels.append(name)
ax.set_title(title)
if type == 'price':
ax.set_xlim((df[x_var].max()+1), 0) # hard axis on price, reversed
else:
ax.set_xlim(0,(df[x_var].max() + 10))
mpld3.plugins.connect(fig, mpld3.plugins.InteractiveLegendPlugin(elements, labels))
mpld3.save_html(fig, PLOT_SAVE_DIR + '/' + save_file)
return save_file
column_rename_map = {'season': 'Season',
'number': 'Episode',
'rating' : 'Rating',
'votes' : 'Votes',
'first_aired' : 'Air date',
'overview' : 'Synopsis'}
for i in range(len(df)):
label = df.iloc[[i]][columns_for_labels].T
label.columns = df.iloc[[i]].title
labels.append(label.rename(column_rename_map).to_html())
# Plot scatter points
c = (df.season-1).map(pd.Series(list(sns.color_palette(n_colors=len(df.season.value_counts())))))
points = ax.scatter(df.number_abs, df.rating, alpha=.99, c=c, zorder=2)
ax.set_ylim(5,10)
ax.set_xlim(0,main_episodes.number_abs.max()+1)
ax.set_ylabel('Trakt.tv Episode Rating')
ax.set_xlabel('Episode number')
fig.set_size_inches(12, 6)
ax.set_title(show_summary.title[0], size=20)
tooltip = plugins.PointHTMLTooltip(points, labels,
voffset=10, hoffset=10, css=css)
plugins.connect(fig, tooltip)
mpld3.save_html(fig, str(show_summary.title[0] + ".html"))
mpld3.display()
def getHTML(self, params):
# print(params)
global current_gene
data_max = 0
fig = plt.figure(figsize=(9, 7))
gs = gridspec.GridSpec(4, 1, height_ratios=[6, 1, 1, 1])
gene = params["freq"].upper()
range_ext = int(params["range"])
searched = "False"
lines = []
if gene.startswith("CHR"):
temp = gene.split(":")
current_gene = ["Region", temp[0][3:], int(temp[1]), int(temp[2]), "+"]
else:
for item in genes:
if item[0] == gene:
current_gene = item
break
else:
temp_gene = self.search_SGD(gene)
print(temp_gene)
searched = "True"
for item in genes:
if item[0] == temp_gene[0]:
current_gene = item
break
else:
current_gene = temp_gene
print(gene)
# Todo add possibility to search SGD defaulting to SGD coordinates
print(
"*" * 40
+ "\nQuery by user:"******";\nrange extension:"
+ str(range_ext)
+ " ;Checked Boxes:"
+ str(params["check_boxes"])
+ ";SGD used:"
+ searched
+ "\n"
+ "*" * 40
)
# print(params)
splt1 = plt.subplot(gs[0, :])
splt1.set_title(
"{}-Chromosome {}:{}:{}, strand:{}".format(
current_gene[0], current_gene[1], current_gene[2], current_gene[3], current_gene[4]
),
size=20,
)
# splt1.set_xlabel('Distance from TSS (nt)')
splt1.axes.xaxis.set_ticklabels([])
splt1.set_ylabel("Normalized counts per million reads\n ", size=16, labelpad=15)
n = 0
fill_colors = [
"#921B16",
"#D6701C",
"#251F47",
"#68A691",
"#68A691",
"#447604",
"#232621",
"#0BBE30",
"#BC3908",
"#191923",
"#391923",
"#591923",
]
for item in params["check_boxes"]:
if current_gene[4] == "+":
data = data_sets[data_sets_names[int(item)]][current_gene[1]][
current_gene[2] - range_ext : current_gene[3] + range_ext
]
factor = 100.0 / len(data)
data = ndimage.interpolation.zoom(data, factor)
_ = splt1.plot(data, label=data_sets_legend[int(item)], color=fill_colors[n], alpha=0.3, lw=3)
lines.extend(_)
splt1.fill_between(range(0, len(data)), 0, data, alpha=0.2, color=fill_colors[n])
if current_gene[4] == "-":
data = data_sets[data_sets_names[int(item)]][current_gene[1]][
current_gene[2] - range_ext : current_gene[3] + range_ext
]
factor = 100.0 / len(data)
data = ndimage.interpolation.zoom(data[::-1], factor)
print(data)
_ = splt1.plot(data, label=data_sets_legend[int(item)], color=fill_colors[n], alpha=0.3, lw=3)
lines.extend(_)
splt1.fill_between(range(0, len(data)), 0, data, alpha=0.2, color=fill_colors[n])
if np.max(data) > data_max:
data_max = np.max(data)
n += 1
# plot2
if current_gene[4] == "+":
y_values1 = data_sets["genes"][current_gene[1]][
0, current_gene[2] - range_ext : current_gene[3] + range_ext
]
y_values2 = data_sets["genes"][current_gene[1]][
1, current_gene[2] - range_ext : current_gene[3] + range_ext
]
else:
y_values1 = data_sets["genes"][current_gene[1]][
0, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
y_values2 = data_sets["genes"][current_gene[1]][
1, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
# splt2.plot(y_values, 'grey', linewidth=2)
factor = 100.0 / len(y_values1)
splt2 = plt.subplot(gs[1, :])
y_values1 = ndimage.interpolation.zoom(y_values1, factor)
y_values2 = ndimage.interpolation.zoom(y_values2, factor)
x_values = range(0, len(y_values1))
splt2.plot([0, len(y_values1)], [0, 0], "black", linewidth=1.5)
splt2.fill_between(x_values, y_values1 / 4.0, y_values1, color="#FFB30F")
splt2.fill_between(x_values, y_values2 / 4.0, y_values2, color="#FD151B")
splt2.set_ylim(-1.5, 1.5)
splt2.text(1.01, 0.5, "GENES", fontsize=12, transform=splt2.transAxes, verticalalignment="center")
splt2.yaxis.set_tick_params(color="w")
splt2.set_yticks([-0.5, 0.5])
splt2.spines["left"].set_position(("outward", 10))
splt2.set_yticklabels([])
splt2.axes.xaxis.set_ticklabels([])
# plot3
if current_gene[4] == "+":
y_values1 = data_sets["CUTS"][current_gene[1]][0, current_gene[2] - range_ext : current_gene[3] + range_ext]
y_values2 = data_sets["CUTS"][current_gene[1]][1, current_gene[2] - range_ext : current_gene[3] + range_ext]
else:
y_values1 = data_sets["CUTS"][current_gene[1]][
0, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
y_values2 = data_sets["CUTS"][current_gene[1]][
1, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
# splt2.plot(y_values, 'grey', linewidth=2)
factor = 100.0 / len(y_values1)
splt3 = plt.subplot(gs[2, :])
y_values1 = ndimage.interpolation.zoom(y_values1, factor)
y_values2 = ndimage.interpolation.zoom(y_values2, factor)
x_values = range(0, len(y_values1))
splt3.plot([0, len(y_values1)], [0, 0], "black", linewidth=1.5)
splt3.fill_between(x_values, y_values1 / 4.0, y_values1, color="#028090")
splt3.fill_between(x_values, y_values2 / 4.0, y_values2, color="#6EEB83")
splt3.set_ylim(-1.5, 1.5)
splt3.text(1.01, 0.5, "CUTS", fontsize=12, transform=splt3.transAxes, verticalalignment="center")
splt3.yaxis.set_tick_params(color="w")
splt3.set_yticks([-0.5, 0.5])
splt3.spines["left"].set_position(("outward", 10))
splt3.set_yticklabels([])
splt3.axes.xaxis.set_ticklabels([])
# plot4
if current_gene[4] == "+":
y_values1 = data_sets["SUTS"][current_gene[1]][0, current_gene[2] - range_ext : current_gene[3] + range_ext]
y_values2 = data_sets["SUTS"][current_gene[1]][1, current_gene[2] - range_ext : current_gene[3] + range_ext]
else:
y_values1 = data_sets["SUTS"][current_gene[1]][
0, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
y_values2 = data_sets["SUTS"][current_gene[1]][
1, current_gene[2] - range_ext : current_gene[3] + range_ext
][::-1]
# splt2.plot(y_values, 'grey', linewidth=2)
factor = 100.0 / len(y_values1)
splt4 = plt.subplot(gs[3, :])
y_values1 = ndimage.interpolation.zoom(y_values1, factor)
y_values2 = ndimage.interpolation.zoom(y_values2, factor)
x_values = range(0, len(y_values1))
splt4.plot([0, len(y_values1)], [0, 0], "black", linewidth=1.5)
splt4.fill_between(x_values, y_values1 / 4.0, y_values1, color="#028090")
splt4.fill_between(x_values, y_values2 / 4.0, y_values2, color="#6EEB83")
splt4.set_ylim(-1.5, 1.5)
splt4.text(1.01, 0.5, "SUTS", fontsize=12, transform=splt4.transAxes, verticalalignment="center")
splt4.yaxis.set_tick_params(color="w")
splt4.set_yticks([-0.5, 0.5])
splt4.spines["left"].set_position(("outward", 10))
splt4.set_yticklabels([])
splt4.axes.xaxis.set_ticklabels([])
leg = splt1.legend(ncol=3)
leg.set_title("")
for legobj in leg.legendHandles:
legobj.set_linewidth(3.0)
size = (current_gene[3] + range_ext) - (current_gene[2] - range_ext)
splt1.set_ylim(0, np.max(data_max) * 1.3)
# print(str(plt.ylim()[1] - 5))
splt1.text(0.02, 0.02, "Luis Soares", fontsize=6, transform=splt1.transAxes, verticalalignment="top")
leg_line = leg.get_lines()
number_of_samples = len(leg_line)
class HighlightLines(plugins.PluginBase):
"""A plugin to highlight lines on hover"""
JAVASCRIPT = """
mpld3.register_plugin("linehighlight", LineHighlightPlugin);
LineHighlightPlugin.prototype = Object.create(mpld3.Plugin.prototype);
LineHighlightPlugin.prototype.constructor = LineHighlightPlugin;
LineHighlightPlugin.prototype.requiredProps = ["legend_ids","line_ids"];
LineHighlightPlugin.prototype.defaultProps = {alpha_bg:0.3, alpha_fg:1.0}
function LineHighlightPlugin(fig, props){
mpld3.Plugin.call(this, fig, props);
};
LineHighlightPlugin.prototype.draw = function(){
var obj=[]
for(var i=0; i<this.props.legend_ids.length; i++){
obj=obj.concat([mpld3.get_element(this.props.legend_ids[i], this.fig),
mpld3.get_element(this.props.line_ids[i], this.fig)]);
alpha_fg = this.props.alpha_fg;
alpha_bg = this.props.alpha_bg;
}
%s
}
""" % (
create_java(number_of_samples * 2)
)
def __init__(self, legend, lines, samples):
self.lines = lines
self.legend = legend
self.dict_ = {
"type": "linehighlight",
"legend_ids": [utils.get_id(line) for line in legend],
"line_ids": [utils.get_id(line) for line in lines],
"alpha_bg": lines[0].get_alpha(),
"alpha_fg": 1.0,
}
class TopToolbar(plugins.PluginBase):
"""Plugin for moving toolbar to top of figure"""
JAVASCRIPT = """
mpld3.register_plugin("toptoolbar", TopToolbar);
TopToolbar.prototype = Object.create(mpld3.Plugin.prototype);
TopToolbar.prototype.constructor = TopToolbar;
function TopToolbar(fig, props){
mpld3.Plugin.call(this, fig, props);
};
TopToolbar.prototype.draw = function(){
// the toolbar svg doesn't exist
// yet, so first draw it
this.fig.toolbar.draw();
// then change the y position to be
// at the top of the figure
this.fig.toolbar.toolbar.attr("y", 2);
// then remove the draw function,
// so that it is not called again
this.fig.toolbar.draw = function() {}
}
"""
def __init__(self):
self.dict_ = {"type": "toptoolbar"}
plugins.clear(fig)
plugins.connect(
fig, TopToolbar(), HighlightLines(leg_line, lines, number_of_samples), plugins.Reset(), plugins.BoxZoom()
)
file = cStringIO.StringIO()
mpld3.save_html(fig, file)
return file.getvalue()