def sb_violinplot(series, dataframe=None, groupCol=None, **kwargs):
import pandas as pd
import seaborn as sns
if not groupCol:
assert isinstance(series, pd.Series)
return to_bokeh(sns.violinplot(x=series, **kwargs).figure)
else:
assert dataframe and groupCol
assert isinstance(series, str)
return to_bokeh(
sns.violinplot(x=groupCol, y=series, data=dataframe,
**kwargs).figure)
def mc_results(self):
# Compute Monte Carlo results
Y = self.Y.as_matrix()
Y0 = float(self.ticker4_1)
hist_point = int(self.ticker4)
num_paths = int(self.ticker3)
center_point = np.mean(Y[hist_point,:])
stkgrid = np.linspace(0.5*center_point,1.5*center_point,100)
meanlst = np.array([])
stdlst = np.array([])
paylst = np.array([])
for stk in stkgrid:
meanlst = np.append(meanlst, np.mean(payoff(Y[hist_point,:],stk)))
stdlst = np.append(stdlst,np.std(payoff(Y[hist_point,:],stk))/np.sqrt(num_paths))
plt.plot(stkgrid,meanlst+2*stdlst, 'g-')
plt.plot(stkgrid,meanlst-2*stdlst,'g-',label='2-Sig Error')
plt.plot(stkgrid,meanlst+stdlst,'r-')
plt.plot(stkgrid,meanlst-stdlst,'r-',label='1-Sig Error')
plt.plot(stkgrid,meanlst,'b',label='Mean')
plt.title('MC Option Price (Blue) with 1-Sig (Red) and 2-Sig (Green) Errors')
plt.xlabel('Strike')
plt.ylabel('Value')
p = mpl.to_bokeh()
p.title_text_font_size= str(TITLE_SIZE)+'pt'
return p
def initialize_plot(self, ranges=None, plot=None, plots=None):
element = self.hmap.last
key = self.keys[-1]
self.mplplot.initialize_plot(ranges)
plot = mpl.to_bokeh(self.mplplot.state)
self.handles['plot'] = plot
return plot
def initialize_plot(self, ranges=None, plot=None, plots=None):
element = self.hmap.last
key = self.keys[-1]
self.mplplot.initialize_plot(ranges)
plot = mpl.to_bokeh(self.mplplot.state)
self.handles['plot'] = plot
return plot
def test(datasets="", genes=None, samples=None, chart_type=None, scale=None):
data = get_demo_normalized_set()
sns.set_style("whitegrid")
if chart_type is None or chart_type == "box":
data.transpose().boxplot(column=[1, 2, 3], return_type="axes")
elif chart_type == "scatter":
pass
return to_bokeh(name="descriptive")
def acid_violin(acid):
olives = pd.read_sql('olives', db.engine, columns=['region', 'area_main', acid])
sns.set_style("whitegrid")
sns.mpl.rc("figure", figsize=(15, 6))
ax = sns.violinplot(data=olives,
x="area_main",
y=acid,
cut=0.1,
scale='count',
title=acid + " acid distribution")
bh = mpl.to_bokeh(ax.figure)
return bh
def makeplot(dataframe):
plt.figure(figsize=(11,8))
dataframe.plot()#df plot function
# ax.legend(bbox_to_anchor=(1,1),bbox_transform=plt.gcf().transFigure)
plt.legend(fontsize=20,bbox_to_anchor=(1.05,1),loc=2)
plt.ylabel('Closing Price',fontsize=15)
plt.xlabel('Day',fontsize=15)
# fig.savefig('AAPL.png')
# output_file("templates/plot.html",title="test")
output_file("templates/plot.html",title="closingPrices")
# show(mpl.to_bokeh())
save(mpl.to_bokeh())
def update_frame(self, key, ranges=None, plot=None, element=None, empty=False):
self.mplplot.update_frame(key, ranges)
reused = isinstance(self.hmap, DynamicMap) and self.overlaid
if not reused and element is None:
element = self._get_frame(key)
else:
self.current_key = key
self.current_frame = element
plot = mpl.to_bokeh(self.mplplot.state)
update_plot(self.handles['plot'], plot)
if not self.overlaid:
self._update_plot(key, self.handles['plot'], element)
def initialize_plot(self, ranges=None, plot=None, plots=None):
self.mplplot.initialize_plot(ranges)
plot = plot if plot else self.handles.get('plot')
new_plot = mpl.to_bokeh(self.mplplot.state)
if plot:
update_plot(plot, new_plot)
else:
plot = new_plot
self.handles['plot'] = plot
if not self.overlaid:
self._update_plot(self.keys[-1], plot, self.hmap.last)
return plot
def initialize_plot(self, ranges=None, plot=None, plots=None):
self.mplplot.initialize_plot(ranges)
plot = plot if plot else self.handles.get('plot')
new_plot = mpl.to_bokeh(self.mplplot.state)
if plot:
update_plot(plot, new_plot)
else:
plot = new_plot
self.handles['plot'] = plot
if not self.overlaid:
self._update_plot(self.keys[-1], plot, self.hmap.last)
return plot
def update_frame(self, key, ranges=None, plot=None, element=None, empty=False):
self.mplplot.update_frame(key, ranges)
reused = isinstance(self.hmap, DynamicMap) and self.overlaid
if not reused and element is None:
element = self._get_frame(key)
else:
self.current_key = key
self.current_frame = element
plot = mpl.to_bokeh(self.mplplot.state)
update_plot(self.handles['plot'], plot)
if not self.overlaid:
self._update_plot(key, self.handles['plot'], element)
def plot_pulses2(self, km=False):
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from bokeh.resources import CDN
from bokeh.embed import components
from bokeh.mpl import to_bokeh
from bokeh.models.tools import WheelZoomTool, ResetTool, PanTool, HoverTool, SaveTool
lines = self.get_lines()
N = len(lines)
npoints = self.total_units / self.km2unit if km else self.total_units
fig = plt.figure(figsize=(12, 2 + N * 0.5))
ax = fig.add_subplot(111)
labels = ['IPP']
for i, line in enumerate(lines):
labels.append(line.get_name(channel=True))
l = ax.plot((0, npoints), (N - i - 1, N - i - 1))
points = [(tup[0], tup[1] - tup[0])
for tup in line.pulses_as_points(km=km) if tup != (0, 0)]
ax.broken_barh(points, (N - i - 1, 0.5),
edgecolor=l[0].get_color(),
facecolor='none')
n = 0
f = ((self.ntx + 50) / 100) * 5 if (
(self.ntx + 50) / 100) * 10 > 0 else 2
for x in np.arange(0, npoints,
self.ipp if km else self.ipp * self.km2unit):
if n % f == 0:
ax.text(x, N, '%s' % n, size=10)
n += 1
labels.reverse()
ax.set_yticks(range(len(labels)))
ax.set_yticklabels(labels)
ax.set_xlabel = 'Units'
plot = to_bokeh(fig, use_pandas=False)
plot.tools = [
PanTool(dimensions=['width']),
WheelZoomTool(dimensions=['width']),
ResetTool(),
SaveTool()
]
plot.toolbar_location = "above"
return components(plot, CDN)
def plot_comparison(dataset_identifiers, features, type="boxplot"):
sns.set_style("whitegrid")
sns.set_palette("deep")
generator = "matplot"
f, axes = plt.subplots(1, 2)
# dataset_identifiers = ['DESeq_1_18_0_umc_read_counts_table_without_8433',
# 'DESeq_1_18_0_genentech_read_counts_table']
# features = ["ENSG00000002549"]
path = APP_CONFIG["application_files_location"] + APP_CONFIG["application_store_name"]
i = 0
subset = None
print features
for d in dataset_identifiers:
dataset = dr.get_data_frame_from_hdf(d, path)
if type != "pca":
subset = dataset.ix[features, :]
if type == "boxplot":
axes[i].boxplot(subset)
create_csv_version(subset.transpose(), d, type, subset.columns)
if type == "scatter":
generator = "matplot"
#print len(subset.ix[0, :])
t = axes[i].plot(subset.transpose(), 'o')
create_csv_version(subset.transpose(), d, type, subset.columns)
plugins.connect(f, plugins.PointLabelTooltip(t[0], labels=(list(subset.columns))))
if type == "pca":
print(type)
pca = PCA(n_components=2)
t_data = dataset.transpose()
pca_result = pca.fit(t_data)
pca_transformed = pca_result.transform(t_data)
t = axes[i].plot(pca_transformed[:, 0], pca_transformed[:, 1], 'o')
create_csv_version(pca_transformed, d, type, dataset.columns)
plugins.connect(f, plugins.PointLabelTooltip(t[0], labels=(list(dataset.columns))))
axes[i].set_xlabel(d)
axes[i].set_ylabel(str(features))
i += 1
if generator == "bokeh":
bk = to_bokeh(name="descriptive")
else:
bk = plt.gcf()
sz = bk.get_size_inches()
bk.set_size_inches((sz[0]*2.5, sz[1]*2))
return bk
def plot_multiple_agents(results_path, results_name, num_workers):
def _get_data_from_files():
dfs = []
for i_work in range(num_workers):
dfs.append(
pd.read_json(os.path.abspath(files_name.format(i_work)),
lines=True))
df = pd.DataFrame()
df['epoch'] = dfs[0]['epoch']
columns = list(dfs[0].columns.values)
columns.remove('epoch')
columns.remove('time')
columns.remove('step')
# ensure all matrices of the same size,
# since not all agents necessarily reached the same epoch
max_epochs = 0
for d in dfs:
epochs = d.shape[0]
max_epochs = max(max_epochs, epochs)
data = {}
for c in columns:
data[c] = np.vstack([df[c].as_matrix() for df in dfs])
return data, columns
files_name = os.path.join(results_path, results_name)
plot_path = '{}.{}'.format(files_name, 'html')
files_name += '_{}.json'
data, columns = _get_data_from_files()
figs = []
for i, col in enumerate(columns):
fig = plt.figure(i)
axis = sns.tsplot(data=data[col], err_style="unit_traces")
# axis = sns.tsplot(data=data[c], ci=[50, 70, 90], legend=True)
axis.set_title(col)
axis.set_xlabel('epochs')
axis.set_ylabel(col)
fig.add_axes(axis)
figs.append(to_bokeh(fig))
plot = column(Div(text='<h1 align="center">{}</h1>'.format(results_name)),
*figs)
output_file(plot_path, title=results_name)
save(plot)
def hist_den_plot(self):
Y = self.Y.as_matrix()
hist_point = int(self.ticker4)
delta_t = float(self.ticker3_2)
data = Y[hist_point,:]
sns.distplot(data, color='k', hist_kws={"color":"b"}, norm_hist=True)
#sns.distplot(data, color='k', hist_kws={"color":"b"})
plt.hist(data)
plt.title('Distribution at T = ' + str(np.round(delta_t*hist_point,4)) + ' with Mean: ' +str(np.round(np.mean(data),4)) + ' and Std Dev: ' + str(np.round(np.std(data),4)))
plt.xlabel('Price Bins')
plt.ylabel('Bin Count')
p = mpl.to_bokeh()
p.title_text_font_size= str(TITLE_SIZE)+'pt'
return p
def bokeh_frisbee(i):
""" Creates a bokeh html file of the 3D plot """
from bokeh import mpl
from bokeh.plotting import output_file, save
fig = plt.figure()
fig.canvas.set_window_title('Frisbee Simulation HTML')
ax = fig.gca(projection='3d')
ax.plot(mat_z[0:i], mat_x[0:i], mat_y[0:i], label='Frisbee Flight')
plt.ylabel("X distance (m)")
plt.xlabel("Z distance (m)")
if absmax(mat_z) < 1:
ax.set_xlim(-1, 1)
output_file("online_fig.html")
save(mpl.to_bokeh(fig))
return
def figtoHTML(figure, pathName):
'''
For a given figure object (matplotlib), saves it a specified file path as an HTML file (bokeh format).
Args:
figure: A matplotlib figure object to save.
pathName: Path of file to save figure to.
Returns:
1 if successful, 0 if not successful.
'''
try:
output_file(pathName)
bfig = to_bokeh(figure)
except:
print('Failed to save figure to {}'.format(pathName))
return 0
return 1
def updateFigure():
filename = str(selectFile.value)
allData = []
data = []
with open(filePath, 'r') as csvfile:
next(csvfile)
allData = csv.reader(csvfile, delimiter=',')
##Making word cloud for the selected file
data = [row for row in allData if row[1] == filename]
print(data)
words = []
for row in data:
words.append(row[2])
print(words[0])
csvfile.close()
wordcloud = WordCloud(background_color="white",
max_font_size=40).generate(words[0])
plt.imshow(wordcloud) #, interpolation="bilinear"
plt.axis("off")
plt.show()
fig = mpl.to_bokeh(plt.figure())
return fig
def visualize_data():
data_file = parse(MY_FILE, "~")
counter = Counter(item["Product"] for item in data_file)
data_list = [
counter["P-HYP"],
counter["RTVAST"],
counter["A-MKHYP"],
counter["P-HYPL"],
]
labels_tuple = tuple(["P-HYP", "RTVAST", "A-MKHYP", "P-HYPL"])
plt.title("Test")
plt.plot(data_list)
plt.xticks(range(len(labels_tuple)), labels_tuple)
#Save to bokeh
plot = mpl.to_bokeh(name='test')
bpl.show(plot)
output_file("test1.html")
plt.clf()
def path_plot(self):
num_paths_plot = min(50,int(self.ticker3))
hist_point = int(self.ticker4)
#print 'Hist Point ', hist_point
Y = self.Y.as_matrix()
pltdat = Y[:,0:num_paths_plot]
mY, MY = min(Y[hist_point,:]), max(Y[hist_point,:])
plt.plot(pltdat, alpha=0.1, linewidth=1.8)
sns.tsplot(pltdat.T,err_style='ci_band', ci=[68,95,99], alpha=1, \
linewidth = 2.5, color='indianred')
#sns.tsplot(pltdat.T,err_style='ci_band', ci=[68,95,99,99.99999], alpha=1, \
# linewidth = 2.5, condition='Mean Path', color='indianred')
plt.plot([hist_point, hist_point], [0.99*mY, 1.01*MY], 'k-',label='Time Series Histogram')
plt.xlabel('Time Step')
plt.ylabel('Price')
#plt.legend()
p = mpl.to_bokeh()
p.title = 'Mean Path (Red), MC Paths (Background) and Density Line (Black)'
p.title_text_font_size= str(TITLE_SIZE)+'pt'
return p
def plot_left_right(df,
colors,
plot_column='right',
grouping_column='party',
folder=RESULT_FOLDER,
plot_suffix=""):
# median-centered per domain right position
df[plot_column] = df[plot_column] - df[plot_column].median()
ax = sns.violinplot(x=plot_column,
y=grouping_column,
data=df[[plot_column, grouping_column]],
palette=sns.color_palette(colors),
split=True,
scale="count",
inner="stick",
saturation=0.5)
ax.set_xlim([0, 1])
ax.set_xticks(np.arange(0, 1, .1))
ax.set_xlabel("links-rechts Index")
ax.set_ylabel("Partei")
ax.set_facecolor("white")
ax.set_title(plot_suffix)
output_file(os.path.join(folder, "violinPlot-%s.html" % plot_suffix))
show(mpl.to_bokeh())
import numpy as np
import pandas as pd
from bokeh import mpl
from bokeh.plotting import show
ts = pd.Series(np.random.randn(1000),
index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
p = ts.plot()
show(mpl.to_bokeh(name="series"))
import numpy as np
import pandas as pd
from bokeh import mpl
ts = pd.Series(np.random.randn(1000),
index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
df = pd.DataFrame(np.random.randn(1000, 4),
index=ts.index,
columns=list('ABCD'))
df = df.cumsum()
df.plot(legend=False)
mpl.to_bokeh(name="dataframe")
# a "waterfall" plot or a "stagger" plot.
nverts = 60
ncurves = 20
offs = (0.1, 0.0)
rs = np.random.RandomState([12345678])
yy = np.linspace(0, 2 * np.pi, nverts)
ym = np.amax(yy)
xx = (0.2 + (ym - yy) / ym)**2 * np.cos(yy - 0.4) * 0.5
segs = []
for i in range(ncurves):
xxx = xx + 0.02 * rs.randn(nverts)
curve = list(zip(xxx, yy * 100))
segs.append(curve)
colors = [(1.0, 0.0, 0.0, 1.0), (0.0, 0.5, 0.0, 1.0), (0.0, 0.0, 1.0, 1.0),
(0.0, 0.75, 0.75, 1.0), (0.75, 0.75, 0, 1.0), (0.75, 0, 0.75, 1.0),
(0.0, 0.0, 0.0, 1.0)]
col = LineCollection(segs, linewidth=5, offsets=offs)
ax = plt.axes()
ax.add_collection(col, autolim=True)
col.set_color(colors)
ax.set_title('Successive data offsets')
fig = plt.gcf()
show(mpl.to_bokeh(name="lc_offsets"))
import numpy as np
import matplotlib.pyplot as plt
from bokeh import mpl
from bokeh.plotting import show
x = np.linspace(-2 * np.pi, 2 * np.pi, 100)
y = np.sin(x)
z = np.cos(x)
plt.plot(x, y, "r-", marker='o')
plt.title("Matplotlib Figure in Bokeh")
# dashed lines work
plt.plot(x, z, "g-x", linestyle="-.")
#show(mpl.to_bokeh())
#show(mpl.to_bokeh(name="test"))
show(mpl.to_bokeh(plt.gcf(), name="test"))
#show(mpl.to_bokeh(plt.gcf(), server="default"))
#show(mpl.to_bokeh(plt.gcf(), name="test", server="default"))
verts = np.swapaxes(verts, 0, 1)
# In your case, "verts" might be something like:
# verts = zip(zip(lon1, lat1), zip(lon2, lat2), ...)
# If "data" in your case is a numpy array, there are cleaner ways to reorder
# things to suit.
facecolors = ['red', 'green', 'blue', 'cyan', 'yellow', 'magenta', 'black']
edgecolors = ['cyan', 'yellow', 'magenta', 'black', 'red', 'green', 'blue']
widths = [5, 10, 20, 10, 5]
# Make the collection and add it to the plot.
col = PolyCollection(verts,
facecolor=facecolors,
edgecolor=edgecolors,
linewidth=widths,
linestyle='--',
alpha=0.5)
ax = plt.axes()
ax.add_collection(col)
plt.xlim([-60, 60])
plt.ylim([-60, 60])
plt.title("MPL-PolyCollection support in Bokeh")
output_file("polycollection.html", title="polycollection.py example")
show(mpl.to_bokeh())
plt.setp(plt.gca(), xticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('I', fontsize=20)
plt.subplot(222)
plt.plot(x, y2, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(),
xticklabels=[],
yticks=(4, 8, 12),
yticklabels=[],
xticks=(0, 10, 20))
plt.ylabel('II', fontsize=20)
plt.subplot(223)
plt.plot(x, y3, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.ylabel('III', fontsize=20)
plt.setp(plt.gca(), yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.subplot(224)
xfit = np.array([np.amin(x4), np.amax(x4)])
plt.plot(x4, y4, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(), yticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('IV', fontsize=20)
# We create the figure in matplotlib and then we "pass it" to Bokeh
mpl.to_bokeh(name="subplots")
import numpy as np
import matplotlib.pyplot as plt
from bokeh import mpl
from bokeh.plotting import show
x = np.linspace(-2 * np.pi, 2 * np.pi, 100)
y = np.sin(x)
z = np.cos(x)
plt.plot(x, y, "r-", marker='o')
plt.title("Matplotlib Figure in Bokeh")
# dashed lines work
plt.plot(x, z, "g-x", linestyle="-.")
#show(mpl.to_bokeh())
#show(mpl.to_bokeh(name="sincos"))
show(mpl.to_bokeh(plt.gcf(), name="sincos"))
#show(mpl.to_bokeh(plt.gcf(), server="default"))
#show(mpl.to_bokeh(plt.gcf(), name="sincos", server="default"))
from ggplot import *
from bokeh import mpl
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
df = pd.DataFrame({
"x": range(100),
"y": np.random.choice([-1, 1], 100)
})
df.y = df.y.cumsum()
g = ggplot(aes(x='x', y='y'), data=df) + \
geom_step()
g.draw()
plt.title("Step ggplot-based plot in Bokeh.")
mpl.to_bokeh(name="step")
ax.plot(sel_by_wave1[j].wave.iloc[i],
sel_by_wave1[j].abs_cal.iloc[i],
marker='',
color=colors[i],
lw=0.1) for i in range(len(sel_by_wave1[j].wave))
] for j in range(len(sel_by_wave1))]
ax.set_xlabel(u'Wavelength [\AA]')
ax.set_ylabel(u'abs\_cal [erg s$^{-1}$ cm$^{-2}$ \AA$^{-1}$]')
# USING BOKEH
TOOLS = 'pan, box_zoom, wheel_zoom, hover, resize, undo, redo, reset, save'
# x = sel_by_wave1[0].wave.iloc[0]
# y = sel_by_wave1[0].abs_cal.iloc[0]
# # output_file('delOri.html')
# p = figure(tools=TOOLS)
#
# [p.line(x, y, color=color) for x, y, color in zip(sel_by_wave1[0].wave, sel_by_wave1[0].abs_cal, ['red', 'green'])]
#
# session = push_session(curdoc())
#
# session.show(p)
# session.loop_until_closed()
output_file('delOri.html')
show(to_bokeh(fig, tools=TOOLS))
fig.savefig('./RESULTS/spec_l1240.pdf')
plt.clf()
plt.close('all')
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from scipy import optimize
from bokeh import mpl
# Set the palette colors.
sns.set(palette="Set2")
# Build the sin wave
def sine_wave(n_x, obs_err_sd=1.5, tp_err_sd=.3):
x = np.linspace(0, (n_x - 1) / 2, n_x)
y = np.sin(x) + np.random.normal(0, obs_err_sd) + np.random.normal(0, tp_err_sd, n_x)
return y
sines = np.array([sine_wave(31) for _ in range(20)])
# Generate the Seaborn plot with "ci" bars.
ax = sns.tsplot(sines, err_style="ci_bars", interpolate=False)
xmin, xmax = ax.get_xlim()
x = np.linspace(xmin, xmax, sines.shape[1])
out, _ = optimize.leastsq(lambda p: sines.mean(0) - (np.sin(x / p[1]) + p[0]), (0, 2))
a, b = out
xx = np.linspace(xmin, xmax, 100)
plt.plot(xx, np.sin(xx / b) + a, c="#444444")
plt.title("Seaborn tsplot with CI in bokeh.")
mpl.to_bokeh(name="sinerror")
def plot_2d_graph(self, data_frame, gp, chart_type):
if gp is None: gp = GraphProperties()
if gp.chart_type is None and chart_type is None: chart_type = 'line'
if gp.resample is not None: data_frame = data_frame.asfreq(gp.resample)
self.apply_style_sheet(gp)
# create figure & add a subplot
fig = plt.figure(figsize = ((gp.width * gp.scale_factor)/gp.dpi,
(gp.height * gp.scale_factor)/gp.dpi), dpi = gp.dpi)
ax = fig.add_subplot(111)
if gp.x_title != '': ax.set_xlabel(gp.x_title)
if gp.y_title != '': ax.set_ylabel(gp.y_title)
plt.xlabel(gp.x_title)
plt.ylabel(gp.y_title)
fig.suptitle(gp.title, fontsize = 14 * gp.scale_factor)
# format Y axis
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset = False)
ax.yaxis.set_major_formatter(y_formatter)
# create a second y axis if necessary
ax2 = []
if gp.y_axis_2_series != []:
ax2 = ax.twinx()
# do not use a grid with multiple y axes
ax.yaxis.grid(False)
ax2.yaxis.grid(False)
# matplotlib 1.5
try:
cyc = matplotlib.rcParams['axes.prop_cycle']
color_cycle = [x['color'] for x in cyc]
except KeyError:
# pre 1.5
pass
# color_cycle = matplotlib.rcParams['axes.color_cycle']
bar_ind = np.arange(0, len(data_frame.index))
# for bar charts, create a proxy x-axis (then relabel)
xd, bar_ind, has_bar, no_of_bars = self.get_bar_indices(data_frame, gp, chart_type, bar_ind)
# plot the lines (using custom palettes as appropriate)
try:
# get all the correct colors (and construct gradients if necessary eg. from 'blues')
color_spec = self.create_color_list(gp, data_frame)
# for stacked bar
yoff_pos = np.zeros(len(data_frame.index.values)) # the bottom values for stacked bar chart
yoff_neg = np.zeros(len(data_frame.index.values)) # the bottom values for stacked bar chart
zeros = np.zeros(len(data_frame.index.values))
# for bar chart
bar_space = 0.2
bar_width = (1 - bar_space) / (no_of_bars)
bar_index = 0
has_matrix = False
# some lines we should exclude from the color and use the default palette
for i in range(0, len(data_frame.columns.values)):
if gp.chart_type is not None:
if isinstance(gp.chart_type, list):
chart_type = gp.chart_type[i]
else:
chart_type = gp.chart_type
if chart_type == 'heatmap':
# TODO experimental!
# ax.set_frame_on(False)
ax.pcolor(data_frame, cmap=plt.cm.Blues, alpha=0.8)
# plt.colorbar()
has_matrix = True
break
label = str(data_frame.columns[i])
ax_temp = self.get_axis(ax, ax2, label, gp.y_axis_2_series)
yd = data_frame.ix[:,i]
if color_spec[i] is None:
color_spec[i] = color_cycle[i % len(color_cycle)]
if (chart_type == 'line'):
linewidth_t = self.get_linewidth(label,
gp.linewidth, gp.linewidth_2, gp.linewidth_2_series)
if linewidth_t is None: linewidth_t = matplotlib.rcParams['axes.linewidth']
ax_temp.plot(xd, yd, label = label, color = color_spec[i],
linewidth = linewidth_t)
elif(chart_type == 'bar'):
# for multiple bars we need to allocate space properly
bar_pos = [k - (1 - bar_space) / 2. + bar_index * bar_width for k in range(0,len(bar_ind))]
ax_temp.bar(bar_pos, yd, bar_width, label = label, color = color_spec[i])
bar_index = bar_index + 1
elif(chart_type == 'stacked'):
bar_pos = [k - (1 - bar_space) / 2. + bar_index * bar_width for k in range(0,len(bar_ind))]
yoff = np.where(yd > 0, yoff_pos, yoff_neg)
ax_temp.bar(bar_pos, yd, label = label, color = color_spec[i], bottom = yoff)
yoff_pos = yoff_pos + np.maximum(yd, zeros)
yoff_neg = yoff_neg + np.minimum(yd, zeros)
# bar_index = bar_index + 1
elif(chart_type == 'scatter'):
ax_temp.scatter(xd, yd, label = label, color = color_spec[i])
if gp.line_of_best_fit is True:
self.trendline(ax_temp, xd.values, yd.values, order=1, color= color_spec[i], alpha=1,
scale_factor = gp.scale_factor)
# format X axis
self.format_x_axis(ax, data_frame, gp, has_bar, bar_ind, has_matrix)
except: pass
if gp.display_source_label == True:
ax.annotate('Source: ' + gp.source, xy = (1, 0), xycoords='axes fraction', fontsize=7 * gp.scale_factor,
xytext=(-5 * gp.scale_factor, 10 * gp.scale_factor), textcoords='offset points',
ha='right', va='top', color = gp.source_color)
if gp.display_brand_label == True:
self.create_brand_label(ax, anno = gp.brand_label, scale_factor = gp.scale_factor)
leg = []
leg2 = []
loc = 'best'
# if we have two y-axis then make sure legends are in opposite corners
if ax2 != []: loc = 2
try:
leg = ax.legend(loc = loc, prop={'size':10 * gp.scale_factor})
leg.get_frame().set_linewidth(0.0)
leg.get_frame().set_alpha(0)
if ax2 != []:
leg2 = ax2.legend(loc = 1, prop={'size':10 * gp.scale_factor})
leg2.get_frame().set_linewidth(0.0)
leg2.get_frame().set_alpha(0)
except: pass
try:
if gp.display_legend is False:
if leg != []: leg.remove()
if leg2 != []: leg.remove()
except: pass
try:
plt.savefig(gp.file_output, transparent=False)
except: pass
####### various matplotlib converters are unstable
# convert to D3 format with mpld3
try:
# output matplotlib charts externally to D3 based libraries
import mpld3
if gp.display_mpld3 == True:
mpld3.save_d3_html(fig, gp.html_file_output)
mpld3.show(fig)
except: pass
# FRAGILE! convert to Bokeh format
# better to use direct Bokeh renderer
try:
if (gp.convert_matplotlib_to_bokeh == True):
from bokeh.plotting import output_file, show
from bokeh import mpl
output_file(gp.html_file_output)
show(mpl.to_bokeh())
except: pass
# FRAGILE! convert matplotlib chart to Plotly format
# recommend using AdapterCufflinks instead to directly plot to Plotly
try:
import plotly.plotly as py
import plotly
import plotly.tools as tls
if gp.convert_matplotlib_to_plotly == True:
plotly.tools.set_credentials_file(username = gp.plotly_username,
api_key = gp.plotly_api_key)
py_fig = tls.mpl_to_plotly(fig, strip_style = True)
plot_url = py.plot_mpl(py_fig, filename = gp.plotly_url)
except:
pass
# display in matplotlib window
try:
if GraphicsConstants.plotfactory_silent_display == True:
return fig
elif gp.silent_display == False:
plt.show()
else:
return fig
except:
pass
import numpy as np
import pandas as pd
from bokeh import mpl
from bokeh.plotting import output_file, show
ts = pd.Series(np.random.randn(1000), index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
df = pd.DataFrame(np.random.randn(1000, 4), index=ts.index, columns=list('ABCD'))
df = df.cumsum()
df.plot(legend=False)
output_file("dataframe.html")
show(mpl.to_bokeh())
# You have several ways to input the colors:
# colors = ['r','g','b','c','y','m','k']
# colors = ['red','green','blue','cyan','yellow','magenta','black']
# colors = ['#ff0000', '#008000', '#0000ff', '#00bfbf', '#bfbf00', '#bf00bf', '#000000']
# colors = [(1.0, 0.0, 0.0, 1.0), (0.0, 0.5, 0.0, 1.0), (0.0, 0.0, 1.0, 1.0), (0.0, 0.75, 0.75, 1.0),
# (0.75, 0.75, 0, 1.0), (0.75, 0, 0.75, 1.0), (0.0, 0.0, 0.0, 1.0)]
colors = ['r', 'g', 'b', 'c', 'y', 'm', 'k']
widths = [5, 10, 20, 40, 20, 10, 5]
segments = make_segments(x, y)
lc = LineCollection(segments, colors=colors, linewidth=widths, alpha=alpha)
ax = plt.gca()
ax.add_collection(lc)
return lc
# Colored sine wave
x = np.linspace(0, 4 * np.pi, 100)
y = np.sin(x)
colorline(x, y)
plt.title("MPL support for ListCollection in Bokeh")
plt.xlim(x.min(), x.max())
plt.ylim(-1.0, 1.0)
mpl.to_bokeh(name="listcollection")
def sample_distribution_for_genes(dataset_identifier, genes, title="", samples=None, unit="zscore", chart_type="heat",
chart_rendering="html"):
try:
generator = None
convert = False
tooltip = False
sns.set(style="whitegrid")
#get path to HDF store from config file
path_to_store = APP_CONFIG["application_files_location"] + APP_CONFIG["application_store_name"]
print("path to store " + path_to_store)
print(genes)
#get data set as a pandas frame
dataset = dr.get_data_frame_from_hdf(dataset_identifier, path_to_store)
tooltip = None
#filter selected genes
gene_list = dataset.loc[genes, :]
labels = list(gene_list.columns)
#matplotlib settings
ax = None
fig = None
#heatmap
#html = dynamic plot
#pdf = pdf file
if chart_type == "heat":
if chart_rendering == "html":
print("bokeh heatmap")
sns.set()
title += " heatmap"
generator = "bokeh"
print("sns heatmap")
fig = HeatMap(gene_list.dropna(), title=title)
elif chart_rendering == "pdf":
plt.switch_backend('Agg')
title += " heatmap pdf"
sns.set_context("paper", font_scale=0.8)
generator = "matplot"
ax = sns.heatmap(gene_list)
#adapt label fontsize
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(2.0)
# tick.label.set
print("axis loaded")
print("heatmap with bokeh")
elif chart_type == "box":
#boxplot charts
title += " boxplot"
generator = "bokeh"
# convert = True
TOOLS = "resize,crosshair,pan,wheel_zoom,box_zoom,reset,previewsave,hover"
print("creating box plot")
# new_z_set = pd.DataFrame(stats.zscore(gene_list), index=gene_list.index, columns=gene_list.columns)
t_genes = gene_list.transpose()
# sns.boxplot(t_genes, color="coolwarm_r", names=t_genes.columns)
fig = BoxPlot(t_genes, legend=True, tools=TOOLS)
hover = fig.select(dict(type=HoverTool))
hover.tooltips = [
("sample", "$index")
]
elif chart_type == "scatter":
if chart_rendering == "html":
title += " scatter"
generator = "bokeh"
# tooltip = True
TOOLS = "resize, crosshair, pan, wheel_zoom, box_zoom,reset, previewsave, hover"
fig = bpl.figure(title=title, tools=TOOLS)
current_palette = sns.color_palette()
i = 0
colors = bp.Spectral10
# fig.scatter(dc, dc["index"])
for e in gene_list.iterrows():
val = [v for v in e[1]]
idx = range(0, len(val))
col_data_source = ColumnDataSource(dict(
x=idx,
y=val,
sample=gene_list.columns[idx],
))
fig.scatter('x', 'y', color=colors[i], legend=e[0], source=col_data_source)
i += 1
hover = fig.select(dict(type=HoverTool))
hover.tooltips = [
("sample", "@sample"),
("count", "$y")
]
elif chart_rendering == "pdf":
plt.switch_backend('PDF')
sns.color_palette("deep")
title += " scatter pdf"
generator = "matplot"
print("starting with matplot")
transposed_data = gene_list.transpose()
ax = transposed_data.plot(style='o')
legend = plt.legend(frameon=1)
frame = legend.get_frame()
frame.set_edgecolor('blue')
coll_len = len(gene_list.columns)
for idx, gene in enumerate(gene_list.index):
for x, y in zip(range(0, coll_len), gene_list.iloc[idx, :]):
if y > gene_list.iloc[idx, :].quantile(0.99):
ax.annotate(labels[x], xy=(x, y), textcoords='data')
# grid.add_legend(labels)
print("plotted with matplot")
if ax is not None:
if generator == "matplot" and (title is not None):
ax.set_title(title)
elif generator == "matplot" and ax is not None:
ax.set_title(title)
if generator == "matplot":
fig = plt.gcf()
if convert is True and generator == "bokeh":
fig = plt.gcf()
fig = mpl.to_bokeh(fig)
return {"generator": generator, "chart": fig}
except BaseException as e:
print(e.__str__())
def exoctk_tot_results():
exo_dict = ExoCTK.tot.transit_obs.load_exo_dict()
inst_dict = ExoCTK.tot.transit_obs.load_mode_dict('WFC3 G141')
# Get the input from the form
exo_dict['star']['hmag'] = float(
request.form['hmag']) # H-band magnitude of the system
exo_dict['planet']['exopath'] = request.form[
'exopath'] # filename for model spectrum [wavelength, flux]
exo_dict['planet']['w_unit'] = request.form[
'w_unit'] # wavelength unit (um or nm)
exo_dict['planet']['f_unit'] = request.form[
'f_unit'] # flux unit (fp/f* or (rp/r*)^2)
exo_dict['planet'][
'depth'] = 4.0e-3 # Approximate transit/eclipse depth for plotting purposes
exo_dict['planet']['i'] = float(
request.form['i']) # Orbital inclination in degrees
exo_dict['planet']['ars'] = float(
request.form['ars']
) # Semi-major axis in units of stellar radii (a/R*)
exo_dict['planet']['period'] = float(
request.form['period']) # Orbital period in days
# Detector and Observation inputs (Make these form inputs!)
exo_dict['calculation'] = 'scale'
inst_dict['configuration']['detector'][
'subarray'] = 'GRISM256' # Subarray size, GRISM256 or GRISM512
inst_dict['configuration']['detector']['nsamp'] = 10 # WFC3 NSAMP, 1..15
inst_dict['configuration']['detector'][
'samp_seq'] = 'SPARS5' # WFC3 SAMP-SEQ, SPARS5, SPARS10, or SPARS25
exo_dict['observation'][
'transit_duration'] = 4170 # Full transit/eclipse duration in seconds
exo_dict['observation']['norbits'] = 4 # Number of HST orbits per visit
exo_dict['observation']['noccultations'] = 5 # Number of transits/eclipses
exo_dict['observation'][
'nchan'] = 15 # Number of spectrophotometric channels
exo_dict['observation'][
'scanDirection'] = 'Forward' # Spatial scan direction, Forward or Round Trip
exo_dict['observation'][
'schedulability'] = '30' # % time HST can observe target (30 or 100)
# Run PandExo
deptherr, rms, ptsOrbit = ExoCTK.tot.transit_obs.run_pandexo(
exo_dict, inst_dict, output_file='wasp43b_G141.p')
# Plot the model spectrum with simpulated data and uncertainties
specfile = exo_dict['planet']['exopath']
w_unit = exo_dict['planet']['w_unit']
grism = inst_dict['configuration']['instrument']['disperser']
nchan = exo_dict['observation']['nchan']
binspec = ExoCTK.tot.transit_obs.plot_PlanSpec(
specfile,
w_unit,
grism,
deptherr,
nchan,
smooth=10,
labels=['Model Spectrum', 'Simulated Obs.'])
# Make the matplotlib plot into a Bokeh plot
plt.savefig('static/plots/sim.png')
sim_plot = mpl.to_bokeh(plt.gcf())
output_file('test_sim.html')
save(sim_plot)
plt.close()
xmin, xmax = (1.125, 1.650)
ymin, ymax = (np.min(binspec) - 2 * deptherr,
np.max(binspec) + 2 * deptherr)
sim_plot.y_range = Range1d(ymin, ymax)
sim_plot.x_range = Range1d(xmin, 6)
# sim_plot.y_axis_label = 'Wavelength (micron)'
sim_script, sim_plot = components(sim_plot)
# Plot the transit curves
numorbits = exo_dict['observation']['norbits']
depth = exo_dict['planet']['depth']
inc = exo_dict['planet']['i']
aRs = exo_dict['planet']['ars']
period = exo_dict['planet']['period']
windowSize = 20 # observation start window size in minutes
minphase, maxphase = ExoCTK.tot.transit_obs.calc_StartWindow('eclipse',
rms,
ptsOrbit,
numorbits,
depth,
inc,
aRs,
period,
windowSize,
ecc=0,
w=90.)
# Make the matplotlib plot into a Bokeh plot
plt.savefig('static/plots/obs.png')
obs_plot = mpl.to_bokeh(plt.gcf())
output_file('test_obs.html')
save(obs_plot)
plt.close()
obs_script, obs_plot = components(obs_plot)
exo_dict['minphase'] = round(minphase, 4)
exo_dict['maxphase'] = round(maxphase, 4)
sim = open('test_sim.html')
lines = sim.readlines()
sim_html = "".join(lines)
sim.close()
obs = open('test_obs.html')
lines = obs.readlines()
obs_html = "".join(lines)
print(obs_html)
html_dict = {'sim': sim_html, 'obs': obs_html}
return render_template('tot_results.html',
exo_dict=exo_dict,
html_dict=html_dict)
import numpy as np
import pandas as pd
from bokeh import mpl
from bokeh.plotting import show
ts = pd.Series(np.random.randn(1000),
index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
df = pd.DataFrame(np.random.randn(1000, 4),
index=ts.index,
columns=list('ABCD'))
df = df.cumsum()
df.plot(legend=False)
show(mpl.to_bokeh(name="dataframe"))
# demo inspired by: http://matplotlib.org/examples/pylab_examples/stem_plot.html
from bokeh import mpl
from bokeh.plotting import output_file, show
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0.1, 2*np.pi, 10)
markerline, stemlines, baseline = plt.stem(x, np.cos(x), '-.')
plt.setp(markerline, 'markerfacecolor', 'b')
plt.setp(baseline, 'color', 'r', 'linewidth', 2)
output_file("mpl_stem.html", title="mpl_stem.py example")
show(mpl.to_bokeh(tools='pan, wheel_zoom, crosshair'))
rasterized=True,
linestyle=next(linecycler))
legend = ax1.legend()
ax1.legend(loc=0)
ax1.minorticks_on()
ax1.set_ylim((0, np.max(new_sigma)))
ax1.set_xlim((0.1, 3.1))
# ax1.set_title(r'$\sigma({0})={1:.1f}\%$'.format(str(label[key_y]), np.abs(sigma_just_CMB_y / fid[key_y] * 100.)))
ax1.set_ylabel(r'sigma(' + label[key_y] + r')')
ax1.set_xlabel(r'prior/sigma(x) old')
plt.title(r'Prior results on ' + label[key_y])
# ============================================
# FINALLY SAVE
# ============================================
# ============================================
# ============================================
output_file("subplots.html")
save(mpl.to_bokeh())
plt.savefig(base_dir +
'data/{}/run{}/output/prior_{}_snow_mass.pdf'.format(
data_type, str(run_idx), str(key_y)),
dpi=400,
papertype='Letter',
format='pdf',
transparent=True,
bbox_inches='tight')
plt.close()
plt.subplot(221)
plt.plot(x, y1, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(), xticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('I', fontsize=20)
plt.subplot(222)
plt.plot(x, y2, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(), xticklabels=[], yticks=(4, 8, 12), yticklabels=[], xticks=(0, 10, 20))
plt.ylabel('II', fontsize=20)
plt.subplot(223)
plt.plot(x, y3, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.ylabel('III', fontsize=20)
plt.setp(plt.gca(), yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.subplot(224)
xfit = np.array([np.amin(x4), np.amax(x4)])
plt.plot(x4, y4, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(), yticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('IV', fontsize=20)
# We create the figure in matplotlib and then we "pass it" to Bokeh
show(mpl.to_bokeh(name="subplots"))
numpoly, numverts = 100, 4
centers = 100 * (np.random.random((numpoly, 2)) - 0.5)
offsets = 10 * (np.random.random((numverts, numpoly, 2)) - 0.5)
verts = centers + offsets
verts = np.swapaxes(verts, 0, 1)
# In your case, "verts" might be something like:
# verts = zip(zip(lon1, lat1), zip(lon2, lat2), ...)
# If "data" in your case is a numpy array, there are cleaner ways to reorder
# things to suit.
facecolors = ['red', 'green', 'blue', 'cyan', 'yellow', 'magenta', 'black']
edgecolors = ['cyan', 'yellow', 'magenta', 'black', 'red', 'green', 'blue']
widths = [5, 10, 20, 10, 5]
ax = plt.axes()
# Make the collection and add it to the plot.
col = PolyCollection(verts, facecolor=facecolors, edgecolor=edgecolors,
linewidth=widths, linestyle='--', alpha=0.5)
ax.add_collection(col)
plt.xlim([-60, 60])
plt.ylim([-60, 60])
plt.title("MPL-PolyCollection support in Bokeh")
mpl.to_bokeh(name="polycollection")
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib as mplc
import matplotlib.pyplot as plt
from bokeh import mpl
from bokeh.plotting import show
# Generate the pandas dataframe
data = np.random.multivariate_normal([0, 0], [[1, 2], [2, 20]], size=100)
data = pd.DataFrame(data, columns=["X", "Y"])
mplc.rc("figure", figsize=(6, 6))
# Just plot seaborn kde
sns.kdeplot(data, cmap="BuGn_d")
plt.title("Seaborn kdeplot in bokeh.")
show(mpl.to_bokeh(name="kde"))
def update_frame(self, key, ranges=None):
if key in self.hmap:
self.mplplot.update_frame(key, ranges)
self.handles['plot'] = mpl.to_bokeh(self.mplplot.state)
# a "waterfall" plot or a "stagger" plot.
nverts = 60
ncurves = 20
offs = (0.1, 0.0)
rs = np.random.RandomState([12345678])
yy = np.linspace(0, 2 * np.pi, nverts)
ym = np.amax(yy)
xx = (0.2 + (ym - yy) / ym) ** 2 * np.cos(yy - 0.4) * 0.5
segs = []
for i in range(ncurves):
xxx = xx + 0.02 * rs.randn(nverts)
curve = list(zip(xxx, yy * 100))
segs.append(curve)
colors = [(1.0, 0.0, 0.0, 1.0), (0.0, 0.5, 0.0, 1.0), (0.0, 0.0, 1.0, 1.0),
(0.0, 0.75, 0.75, 1.0), (0.75, 0.75, 0, 1.0), (0.75, 0, 0.75, 1.0),
(0.0, 0.0, 0.0, 1.0)]
col = LineCollection(segs, linewidth=5, offsets=offs)
ax = plt.axes()
ax.add_collection(col, autolim=True)
col.set_color(colors)
ax.set_title('Successive data offsets')
fig = plt.gcf()
mpl.to_bokeh(name="lc_offsets")
import numpy as np
import pandas as pd
from bokeh import mpl
ts = pd.Series(np.random.randn(1000),
index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
p = ts.plot()
mpl.to_bokeh(name="series")
from ggplot import *
from bokeh import mpl
from bokeh.plotting import show
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
df = pd.DataFrame({
"x": range(100),
"y": np.random.choice([-1, 1], 100)
})
df.y = df.y.cumsum()
g = ggplot(aes(x='x', y='y'), data=df) + \
geom_step()
g.draw()
plt.title("Step ggplot-based plot in Bokeh.")
show(mpl.to_bokeh(name="step"))
def update_frame(self, key, ranges=None):
if key in self.hmap:
self.mplplot.update_frame(key, ranges)
self.handles['plot'] = mpl.to_bokeh(self.mplplot.state)
rs = np.random.RandomState([12345678])
yy = np.linspace(0, 2 * np.pi, nverts)
ym = np.amax(yy)
xx = (0.2 + (ym - yy) / ym) ** 2 * np.cos(yy - 0.4) * 0.5
segs = []
for i in range(ncurves):
xxx = xx + 0.02 * rs.randn(nverts)
curve = list(zip(xxx, yy * 100))
segs.append(curve)
colors = [
(1.0, 0.0, 0.0, 1.0),
(0.0, 0.5, 0.0, 1.0),
(0.0, 0.0, 1.0, 1.0),
(0.0, 0.75, 0.75, 1.0),
(0.75, 0.75, 0, 1.0),
(0.75, 0, 0.75, 1.0),
(0.0, 0.0, 0.0, 1.0),
]
col = LineCollection(segs, linewidth=5, offsets=offs)
ax = plt.axes()
ax.add_collection(col, autolim=True)
col.set_color(colors)
ax.set_title("Successive data offsets")
fig = plt.gcf()
show(mpl.to_bokeh(name="lc_offsets"))
plt.setp(plt.gca(), xticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('I', fontsize=20)
plt.subplot(222)
plt.plot(x, y2, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(),
xticklabels=[],
yticks=(4, 8, 12),
yticklabels=[],
xticks=(0, 10, 20))
plt.ylabel('II', fontsize=20)
plt.subplot(223)
plt.plot(x, y3, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.ylabel('III', fontsize=20)
plt.setp(plt.gca(), yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.subplot(224)
xfit = np.array([np.amin(x4), np.amax(x4)])
plt.plot(x4, y4, 'ks', xfit, fit(xfit), 'r-', lw=2)
plt.axis([2, 20, 2, 14])
plt.setp(plt.gca(), yticklabels=[], yticks=(4, 8, 12), xticks=(0, 10, 20))
plt.ylabel('IV', fontsize=20)
# We create the figure in matplotlib and then we "pass it" to Bokeh
show(mpl.to_bokeh(name="subplots"))
def plot_2d_graph(self, data_frame, gp, chart_type):
if gp is None: gp = GraphProperties()
if gp.chart_type is None and chart_type is None: chart_type = 'line'
if gp.resample is not None: data_frame = data_frame.asfreq(gp.resample)
self.apply_style_sheet(gp)
# create figure & add a subplot
fig = plt.figure(figsize=((gp.width * gp.scale_factor) / gp.dpi,
(gp.height * gp.scale_factor) / gp.dpi),
dpi=gp.dpi)
ax = fig.add_subplot(111)
if gp.x_title != '': ax.set_xlabel(gp.x_title)
if gp.y_title != '': ax.set_ylabel(gp.y_title)
plt.xlabel(gp.x_title)
plt.ylabel(gp.y_title)
fig.suptitle(gp.title, fontsize=14 * gp.scale_factor)
# format Y axis
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset=False)
ax.yaxis.set_major_formatter(y_formatter)
# create a second y axis if necessary
ax2 = []
if gp.y_axis_2_series != []:
ax2 = ax.twinx()
# do not use a grid with multiple y axes
ax.yaxis.grid(False)
ax2.yaxis.grid(False)
# matplotlib 1.5
try:
cyc = matplotlib.rcParams['axes.prop_cycle']
color_cycle = [x['color'] for x in cyc]
except KeyError:
# pre 1.5
pass
# color_cycle = matplotlib.rcParams['axes.color_cycle']
bar_ind = np.arange(0, len(data_frame.index))
# for bar charts, create a proxy x-axis (then relabel)
xd, bar_ind, has_bar, no_of_bars = self.get_bar_indices(
data_frame, gp, chart_type, bar_ind)
# plot the lines (using custom palettes as appropriate)
try:
# get all the correct colors (and construct gradients if necessary eg. from 'blues')
color_spec = self.create_color_list(gp, data_frame)
# for stacked bar
yoff_pos = np.zeros(len(data_frame.index.values)
) # the bottom values for stacked bar chart
yoff_neg = np.zeros(len(data_frame.index.values)
) # the bottom values for stacked bar chart
zeros = np.zeros(len(data_frame.index.values))
# for bar chart
bar_space = 0.2
bar_width = (1 - bar_space) / (no_of_bars)
bar_index = 0
has_matrix = False
# some lines we should exclude from the color and use the default palette
for i in range(0, len(data_frame.columns.values)):
if gp.chart_type is not None:
if isinstance(gp.chart_type, list):
chart_type = gp.chart_type[i]
else:
chart_type = gp.chart_type
if chart_type == 'heatmap':
# TODO experimental!
# ax.set_frame_on(False)
ax.pcolor(data_frame, cmap=plt.cm.Blues, alpha=0.8)
# plt.colorbar()
has_matrix = True
break
label = str(data_frame.columns[i])
ax_temp = self.get_axis(ax, ax2, label, gp.y_axis_2_series)
yd = data_frame.ix[:, i]
if color_spec[i] is None:
color_spec[i] = color_cycle[i % len(color_cycle)]
if (chart_type == 'line'):
linewidth_t = self.get_linewidth(label, gp.linewidth,
gp.linewidth_2,
gp.linewidth_2_series)
if linewidth_t is None:
linewidth_t = matplotlib.rcParams['axes.linewidth']
ax_temp.plot(xd,
yd,
label=label,
color=color_spec[i],
linewidth=linewidth_t)
elif (chart_type == 'bar'):
# for multiple bars we need to allocate space properly
bar_pos = [
k - (1 - bar_space) / 2. + bar_index * bar_width
for k in range(0, len(bar_ind))
]
ax_temp.bar(bar_pos,
yd,
bar_width,
label=label,
color=color_spec[i])
bar_index = bar_index + 1
elif (chart_type == 'stacked'):
bar_pos = [
k - (1 - bar_space) / 2. + bar_index * bar_width
for k in range(0, len(bar_ind))
]
yoff = np.where(yd > 0, yoff_pos, yoff_neg)
ax_temp.bar(bar_pos,
yd,
label=label,
color=color_spec[i],
bottom=yoff)
yoff_pos = yoff_pos + np.maximum(yd, zeros)
yoff_neg = yoff_neg + np.minimum(yd, zeros)
# bar_index = bar_index + 1
elif (chart_type == 'scatter'):
ax_temp.scatter(xd, yd, label=label, color=color_spec[i])
if gp.line_of_best_fit is True:
self.trendline(ax_temp,
xd.values,
yd.values,
order=1,
color=color_spec[i],
alpha=1,
scale_factor=gp.scale_factor)
# format X axis
self.format_x_axis(ax, data_frame, gp, has_bar, bar_ind,
has_matrix)
except:
pass
if gp.display_source_label == True:
ax.annotate('Source: ' + gp.source,
xy=(1, 0),
xycoords='axes fraction',
fontsize=7 * gp.scale_factor,
xytext=(-5 * gp.scale_factor, 10 * gp.scale_factor),
textcoords='offset points',
ha='right',
va='top',
color=gp.source_color)
if gp.display_brand_label == True:
self.create_brand_label(ax,
anno=gp.brand_label,
scale_factor=gp.scale_factor)
leg = []
leg2 = []
loc = 'best'
# if we have two y-axis then make sure legends are in opposite corners
if ax2 != []: loc = 2
try:
leg = ax.legend(loc=loc, prop={'size': 10 * gp.scale_factor})
leg.get_frame().set_linewidth(0.0)
leg.get_frame().set_alpha(0)
if ax2 != []:
leg2 = ax2.legend(loc=1, prop={'size': 10 * gp.scale_factor})
leg2.get_frame().set_linewidth(0.0)
leg2.get_frame().set_alpha(0)
except:
pass
try:
if gp.display_legend is False:
if leg != []: leg.remove()
if leg2 != []: leg.remove()
except:
pass
try:
plt.savefig(gp.file_output, transparent=False)
except:
pass
####### various matplotlib converters are unstable
# convert to D3 format with mpld3
try:
# output matplotlib charts externally to D3 based libraries
import mpld3
if gp.display_mpld3 == True:
mpld3.save_d3_html(fig, gp.html_file_output)
mpld3.show(fig)
except:
pass
# FRAGILE! convert to Bokeh format
# better to use direct Bokeh renderer
try:
if (gp.convert_matplotlib_to_bokeh == True):
from bokeh.plotting import output_file, show
from bokeh import mpl
output_file(gp.html_file_output)
show(mpl.to_bokeh())
except:
pass
# FRAGILE! convert matplotlib chart to Plotly format
# recommend using AdapterCufflinks instead to directly plot to Plotly
try:
import plotly.plotly as py
import plotly
import plotly.tools as tls
if gp.convert_matplotlib_to_plotly == True:
plotly.tools.set_credentials_file(username=gp.plotly_username,
api_key=gp.plotly_api_key)
py_fig = tls.mpl_to_plotly(fig, strip_style=True)
plot_url = py.plot_mpl(py_fig, filename=gp.plotly_url)
except:
pass
# display in matplotlib window
try:
if Constants.plotfactory_silent_display == True:
pass
elif gp.silent_display == False:
plt.show()
except:
pass
def load_spectra():
#'/Users/guillaumeshippee/Desktop/splat-master/reference/Spectra/10001_10443.fits' #change
if request.method == 'GET':
return render_template('input.html', error='')
else:
# for k in list(request.form.keys()):
# print(k,request.form[k])
# search by file "upload"
if request.form['submit'] == 'Load File':
try:
path = request.form['path']
sp = splat.Spectrum(file=str(path))
sp = [sp]
except:
return render_template('input.html', error = "\n\nProblem with file upload button")
# search by file path specification
if request.form['submit'] == 'Load File ':
try:
path = request.form['path']
sp = splat.Spectrum(file=str(path))
sp = [sp]
except:
return render_template('input.html', error = "\n\nProblem with file path specification")
# search by spectrum key
if request.form['submit'] == 'Load by ID':
try:
sp = splat.Spectrum(int(str(request.form['key'])))
sp = [sp]
except:
return render_template('input.html', error = "\n\nProblem with key specification")
# search by date observed
if request.form['submit'] == 'Load by Date':
try:
sp = splat.getSpectrum(date = str(request.form['date']))
except:
return render_template('input.html', error = "\n\nProblem with key specification")
# search by shortname
elif request.form['submit'] == 'Load by Shortname':
try:
sp = splat.getSpectrum(shortname = str(request.form['shortname']))
except:
return render_template('input.html', error = "\n\nProblem with specifying file by shortname")
# search by name
elif request.form['submit'] == 'Load by Name':
try:
sp = splat.getSpectrum(name = str(request.form['name']))
except:
return render_template('input.html', error = "\n\nProblem with specifying file by name")
# search by options
elif request.form['submit'] == 'Load by Options':
sp1 = request.form['sp1']
sp2 = request.form['sp2']
mag1 = request.form['mag1']
mag2 = request.form['mag2']
if sp2 == '':
sp = sp1
elif sp1 == '':
sp2 = sp1
elif sp1 == '' and sp2 == '':
sp = ''
else:
sp = [sp1, sp2]
if mag2 == '':
mag = mag1
elif sp1 == '':
mag2 = mag1
elif sp1 == '' and sp2 == '':
mag = ''
else:
mag = [mag1, mag2]
kwargs = {'spt': sp, 'jmag' : mag, 'snr' : request.form['snr'], 'date' : request.form['date'] }
kwargs = {k: v for k, v in kwargs.items() if v}
try:
sp = splat.getSpectrum(**kwargs)
except:
return render_template('input.html', error = "\n\nProblem with option search")
# lucky pull
elif request.form['submit'] == 'Get Lucky!':
sp = splat.getSpectrum(lucky=True)
if len(sp) == 0:
return render_template('input.html', error = "\n\nNo spectra matched search constratins")
try:
tab = []
for s in sp:
spectral_type = splat.classifyByStandard(s)[0]
mpl_fig = splat.plotSpectrum(s, web=True, uncertainty = True, mdwarf=True)[0]
bokehfig = mpl.to_bokeh(fig=mpl_fig)
bokehfig.set(x_range=Range1d(.8,2.4),y_range=Range1d(0,s.fluxMax().value*1.2))
# sys.stdout = open("out1.txt", "w")
# sys.stdout = sys.__stdout__
# with open("out1.txt", "r") as f:
# content = f.read()
content = s.info(printout=False)
# print(content)
p = Paragraph(text=content)
widget = VBox(bokehfig, p)
tab.append(Panel(child=widget, title=str(s.name)))
# tab.append(Panel(child=widget, title=str(spectral_type)+ " Star"))
plottabs = Tabs(tabs= tab)
script, div_dict = components({"plot" : plottabs})
except:
return render_template('input.html', error = "\n\nProblem Plotting Spectra")
return render_template('out.html', star_type = spectral_type, script=script, div=div_dict)
def make_violin_plot(x,
y,
hue,
data,
plot_type="factor",
palette="GnBu",
width=750,
height=500):
data = data[[x, y, hue]]
sns_palette = sns.color_palette(palette, 2)
sns.set_style("whitegrid")
if plot_type == "factor":
violin_plot_sns = sns.factorplot(x=x,
y=y,
hue=hue,
data=data,
kind="violin",
palette=sns_palette)
else:
violin_plot_sns = sns.violinplot(x=x,
y=y,
hue=hue,
data=data,
palette=sns_palette,
split=True,
scale="area",
inner="box",
orient="v",
bw=.15,
responsive=True)
violin_plot = mpl.to_bokeh()
violin_plot.toolbar_location = "above"
violin_plot.toolbar_sticky = False
violin_plot.grid.grid_line_color = "SlateGray"
violin_plot.grid.grid_line_alpha = .5
violin_plot.grid.minor_grid_line_color = "SlateGray"
violin_plot.grid.minor_grid_line_alpha = .2
violin_plot.plot_height = height
violin_plot.plot_width = width
if "amount" in y:
violin_plot.title.text = "Fare Violin Plot"
violin_plot.yaxis[0].formatter = NumeralTickFormatter(format="$ 0.00")
if "distance" in y:
violin_plot.title.text = "Distance Violin Plot"
violin_plot.yaxis[0].formatter = PrintfTickFormatter(
format="%5.2f miles")
def day_ticker():
days = [
"Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday",
"Sunday"
]
if abs(int(round(tick)) - tick) < .05:
return days[int(round(tick))]
else:
return ""
def month_ticker():
months = [
"January", "February", "March", "April", "May", "June", "July"
]
if abs(int(round(tick)) - tick) < .05:
return months[int(round(tick))]
else:
return ""
if "day" in x:
violin_plot.xaxis[0].formatter = FuncTickFormatter.from_py_func(
day_ticker)
if "month" in x:
violin_plot.xaxis[0].formatter = FuncTickFormatter.from_py_func(
month_ticker)
return violin_plot
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from bokeh import mpl
from bokeh.plotting import show
# In order to efficiently plot many lines in a single set of axes,
# add the lines all at once. Here is a simple example showing how it is done.
N = 50
x = np.arange(N)
# Here are many sets of y to plot vs x
ys = [x + i for i in x]
colors = ['#ff0000', '#008000', '#0000ff', '#00bfbf', '#bfbf00', '#bf00bf', '#000000']
line_segments = LineCollection([list(zip(x, y)) for y in ys], color=colors,
linewidth=(0.5, 1, 1.5, 2), linestyle='dashed')
ax = plt.axes()
ax.add_collection(line_segments)
ax.set_title('Line Collection with dashed colors')
show(mpl.to_bokeh(name="lc_dashed"))
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from bokeh import mpl
from bokeh.plotting import show
# We generated random data
data = 1 + np.random.randn(20, 6)
# And then just call the violinplot from Seaborn
sns.violinplot(data, color="Set3")
plt.title("Seaborn violin plot in bokeh.")
show(mpl.to_bokeh(name="violin"))
from ggplot import *
from bokeh import mpl
import matplotlib.pyplot as plt
g = ggplot(diamonds, aes(x='price', color='cut')) + \
geom_density()
g.draw()
plt.title("Density ggplot-based plot in Bokeh.")
mpl.to_bokeh(name="density")
from ggplot import *
from bokeh import mpl
import matplotlib.pyplot as plt
g = ggplot(diamonds, aes(x='price', color='cut')) + \
geom_density()
g.draw()
plt.title("xkcd-ggplot-mpl based plot in Bokeh.")
mpl.to_bokeh(name="xkcd_density", xkcd=True)
def plot_2d_graph(self, data_frame, gp, chart_type):
if gp.resample is not None: data_frame = data_frame.asfreq(gp.resample)
# set the matplotlib style sheet & defaults
matplotlib.rcdefaults()
# first search PyThalesians styles, then try matplotlib
try:
plt.style.use(Constants().plotfactory_pythalesians_style_sheet[gp.style_sheet])
except:
plt.style.use(gp.style_sheet)
matplotlib.rcParams.update({'font.size': matplotlib.rcParams['font.size'] * gp.scale_factor})
# create figure & add a subplot
fig = plt.figure(figsize = ((gp.width * gp.scale_factor)/gp.dpi,
(gp.height * gp.scale_factor)/gp.dpi), dpi = gp.dpi)
ax = fig.add_subplot(111)
# format Y axis
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset = False)
ax.yaxis.set_major_formatter(y_formatter)
if gp.x_title != '': ax.set_xlabel(gp.x_title)
if gp.y_title != '': ax.set_ylabel(gp.y_title)
# create a second y axis if necessary
ax2 = []
if gp.y_axis_2_series != []:
ax2 = ax.twinx()
# do not use a grid with multiple y axes
ax.yaxis.grid(False)
ax2.yaxis.grid(False)
color_cycle = matplotlib.rcParams['axes.color_cycle']
bar_ind = np.arange(0, len(data_frame.index))
xd, bar_ind, has_bar, no_of_bars = self.get_bar_indices(data_frame, gp, chart_type, bar_ind)
# plot the lines (using custom palettes as appropriate)
try:
# get all the correct colors (and construct gradients if necessary eg. from 'blues')
color_spec = self.create_color_list(gp, data_frame)
# for stacked bar
yoff = np.zeros(len(data_frame.index.values)) # the bottom values for stacked bar chart
# for bar chart
# bar_ind = np.arange(len(data_frame.index))
# has_bar = False
bar_space = 0.2
bar_width = (1 - bar_space) / (no_of_bars)
bar_index = 0
# some lines we should exclude from the color and use the default palette
for i in range(0, len(data_frame.columns.values)):
if chart_type is not None:
if gp.chart_type is not None:
if isinstance(gp.chart_type, list):
chart_type = gp.chart_type[i]
else:
chart_type = gp.chart_type
label = str(data_frame.columns[i])
ax_temp = self.get_axis(ax, ax2, label, gp.y_axis_2_series)
yd = data_frame.ix[:,i]
if (chart_type == 'line'):
linewidth_t = self.get_linewidth(label,
gp.linewidth, gp.linewidth_2, gp.linewidth_2_series)
if linewidth_t is None: linewidth_t = matplotlib.rcParams['axes.linewidth']
ax_temp.plot(xd, yd, label = label, color = color_spec[i],
linewidth = linewidth_t)
elif(chart_type == 'bar'):
bar_pos = [k - (1 - bar_space) / 2. + bar_index * bar_width for k in range(0,len(bar_ind))]
if color_spec[i] is not None:
ax_temp.bar(bar_pos, yd, bar_width, label = label,
color = color_spec[i])
else:
ax_temp.bar(bar_pos, yd, bar_width, label = label,
color = color_cycle[i % len(color_cycle)])
bar_index = bar_index + 1
# bar_ind = bar_ind + bar_width
has_bar = True
elif(chart_type == 'stacked'):
ax_temp.bar(xd, yd, label = label, color = color_spec[i], bottom = yoff)
yoff = yoff + yd
has_bar = True
elif(chart_type == 'scatter'):
ax_temp.scatter(xd, yd, label = label, color = color_spec[i])
if gp.line_of_best_fit is True:
self.trendline(ax_temp, xd.values, yd.values, order=1, color= color_spec[i], alpha=1,
scale_factor = gp.scale_factor)
# format X axis
self.format_x_axis(ax, data_frame, gp, has_bar, bar_ind)
except: pass
plt.xlabel(gp.x_title)
plt.ylabel(gp.y_title)
fig.suptitle(gp.title, fontsize = 14 * gp.scale_factor)
if gp.display_source_label == True:
ax.annotate('Source: ' + gp.source, xy = (1, 0), xycoords='axes fraction', fontsize=7 * gp.scale_factor,
xytext=(-5 * gp.scale_factor, 10 * gp.scale_factor), textcoords='offset points',
ha='right', va='top', color = gp.source_color)
if gp.display_brand_label == True:
self.create_brand_label(ax, anno = gp.brand_label, scale_factor = gp.scale_factor)
leg = []
leg2 = []
loc = 'best'
# if we have two y-axis then make sure legends are in opposite corners
if ax2 != []: loc = 2
try:
leg = ax.legend(loc = loc, prop={'size':10 * gp.scale_factor})
leg.get_frame().set_linewidth(0.0)
leg.get_frame().set_alpha(0)
if ax2 != []:
leg2 = ax2.legend(loc = 1, prop={'size':10 * gp.scale_factor})
leg2.get_frame().set_linewidth(0.0)
leg2.get_frame().set_alpha(0)
except: pass
try:
if gp.display_legend is False:
if leg != []: leg.remove()
if leg2 != []: leg.remove()
except: pass
try:
plt.savefig(gp.file_output, transparent=False)
except: pass
####### various matplotlib converters are unstable
# convert to D3 format with mpld3
try:
if gp.display_mpld3 == True:
mpld3.save_d3_html(fig, gp.html_file_output)
mpld3.show(fig)
except: pass
# FRAGILE! convert to Bokeh format
# better to use direct Bokeh renderer
try:
if (gp.convert_matplotlib_to_bokeh == True):
from bokeh.plotting import output_file, show
from bokeh import mpl
output_file(gp.html_file_output)
show(mpl.to_bokeh())
except: pass
# FRAGILE! convert matplotlib chart to Plotly format
# recommend using AdapterCufflinks instead to directly plot to Plotly
try:
if gp.convert_matplotlib_to_plotly == True:
plotly.tools.set_credentials_file(username = gp.plotly_username,
api_key = gp.plotly_api_key)
py_fig = tls.mpl_to_plotly(fig, strip_style = True)
plot_url = py.plot_mpl(py_fig, filename = gp.plotly_url)
except:
pass
# display in Matplotlib
try:
if gp.silent_display == False: plt.show()
except:
pass