def plotPC(PC1, PC2, labelList):
"""Plots a scatter plot of the any 2 specified dimensions after running PCA."""
pc1 = [[], [], [], [], [], [], [], [], [], []]
pc2 = [[], [], [], [], [], [], [], [], [], []]
for l in range(len(labelList)):
# l returns a number within a numpy array
actualNum = labelList[l][0]
pc1[actualNum].append(PC1[l])
pc2[actualNum].append(PC2[l])
fig = plt.figure()
ax = fig.add_subplot(111)
colorList = [
"red", "green", "blue", "black", "gray", "yellow", "cyan", "magenta",
"burlywood", "purple"
]
for count in range(10):
plt.scatter(pc1[count],
pc2[count],
c=colorList[count],
lw=0,
label=str(count))
plt.legend(scatterpoints=1)
ax.set_xlabel("PC1")
ax.set_ylabel("PC2")
fig.savefig("2D_10MNistGraph.png")
plt.close()
def plot_comparison(self, x_data, x_variable, y1_data, y1_variable, y2_data, y2_variable):
import matplotlib as plt
x, r1, r2, diff, combined, colors = self.compare_results(
x_data,x_variable,
y1_data, y1_variable,
y2_data, y2_variable)
plt.scatter(x, r1, c=colors)
def plot_decision_regions(X, y, classifier, resolution=0.02):
# prepare marker and color map
markers = ('s', 'x', 'o', '^', 'v')
colors = ('red', 'blue', 'lightgreen', 'gray', 'cyan')
cmap = ListedColormap(colors[:len(np.unique(y))])
# plot decision regions
x1_min, x1_max = X[:, 0].min() - 1, X[:, 0].max() + 1
x2_min, x2_max = X[:, 1].min() - 1, X[:, 1].max() + 1
# generate grid point
xx1, xx2 = np.meshgrid(np.arange(x1_min, x1_max, resolution),
np.arange(x2_min, x2_max, resolution))
# translate features into array and predict
Z = classifier.predict(np.array([xx1.ravel(), xx2.ravel()]).T)
# translate result to grid point
Z = Z.reshape(xx1.shape)
# plot contour line of grid point
plt.contourf(xx1, xx2, Z, alpha=0.4, cmap=cmap)
plt.xlim(xx1.min(), xx1.max())
plt.ylim(xx2.min(), xx2.max())
# plot sample by each class
for idx, cl in enumerate(np.unique(y)):
plt.scatter(x=X[y == cl, 0], y=X[y == cl, 1], alpha=0.8, c=cmap(idx),
marker=markers[idx], label=cl)
def plot_boundary(model, x, y, **kwargs):
assert (x.shape[-1] == 2)
cmap_light = ListedColormap(['#FFAAAA', '#AAFFAA', '#AAAAFF'])
cmap_bold = ListedColormap(['#FF0000', '#00FF00', '#0000FF'])
if 'h' in kwargs:
h = kwargs['h']
else:
h = 0.1
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
x_grid, y_grid = np.meshgrid(np.arange(x_min, x_max, h),
np.arange(y_min, y_max, h))
Z = model.predict(np.c_[x_grid.ravel(), y_grid.ravel()])
# Put the result into a color plot
Z = Z.reshape(x_grid.shape)
plt.figure()
plt.pcolormesh(x_grid, y_grid, Z, cmap=cmap_light)
# Plot also the training points
plt.scatter(x[:, 0], x[:, 1], c=y, cmap=cmap_bold, edgecolor='k', s=20)
plt.xlim(x_grid.min(), x_grid.max())
plt.ylim(y_grid.min(), y_grid.max())
if 'title' in kwargs:
plt.suptitle(kwargs['title'])
if 'accuracy' in kwargs:
plt.title("Accuracy: %.1f%%" % (kwargs['accuracy'] * 100), fontsize=10)
plt.show()
def evaluate_prediction():
#Accuracy measure
sklearn.metrics.stocker.confusion_matrix(
Stockname.Startdate('2017-03-27'),
Stockname.Startdate('2018-03-27'))
Startdate = random.StockName.date()
Enddate = random.StockName.date(after=Startdate)
plt.scatter(dates, prices, color='black', label='Data')
plt.plot(StockName.dates,
StockName.predict(dates),
color='black',
label='Observations')
plt.plot(StockName.dates,
StockName.predict(dates),
color='black',
label='Observations')
plt.plot(StockName.dates,
StockName.predict(dates),
color='blue',
label='Predicted',
attr='bold')
plt.plot(StockName.dates,
StockName.predict(dates),
color='yellow',
label='Confidence Interval',
attr='block')
plt.plot(StockName.midpoint.random(dates),
label='Prediction Start',
color='red',
attr='dotted')
plt.xlabel('Date')
plt.ylabel('Price $')
plt.title(StockName, 'Model Evaluation from ', Startdate, 'to ',
Enddate)
def plot_scatter(self, dataframe, x, y, title, xlable, ylable, kurs):
plt.scatter(x, y)
#plt.title(title)
plt.xlabel(xlable)
plt.ylabel(ylable)
plt.savefig('./PDFcreater/Plots/{}/{}.png'.format(kurs, title))
plt.show()
def plotinter(self, pts=1000):
t0 = time.time()
dt = 1 / pts
t = arange(self.pts[0], self.pts[-1] + dt, dt)
plt.plot(self.x(t), self.y(t))
plt.scatter(self.interx, self.intery, color="red")
print(time.time() - t0)
def __init__(self, x, y):
self.x = x
self.y = y
n = len(x) # cantidad de datos
xSum = self.suma(x)
ySum = self.suma(y)
xySum = self.columnaXy(x, y, n)
xCuadrado, sumXCuadrado = self.columnaCuadrado(x, n)
xMedia = self.media(xSum, n)
yMedia = self.media(ySum, n)
num = xySum * n - (xSum + ySum)
den = n * sumXCuadrado - (xSum**2)
m = num / den
b = yMedia - (m * xMedia)
#graficar
x1 = np.linspace(min(x) - 1, max(x) + 1)
linea = m * x1 + b
plt.plot(x1, linea)
plt.scatter(x, y)
plt.xlabel('x')
plt.ylabel('y')
plt.grid(True)
plt.show()
def tsne_plot(model):
"Creates and TSNE model and plots it"
labels = []
tokens = []
total_size = len(model.wv.vocab)
probability = 200.0 / total_size
# r =
for word in model.wv.vocab:
tokens.append(model[word])
labels.append(word)
tsne_model = TSNE(perplexity=40,
n_components=2,
init='pca',
n_iter=2500,
random_state=23)
new_values = tsne_model.fit_transform(tokens)
x = []
y = []
for value in new_values:
x.append(value[0])
y.append(value[1])
plt.figure(figsize=(16, 16))
for i in range(len(x)):
plt.scatter(x[i], y[i])
plt.annotate(labels[i],
xy=(x[i], y[i]),
xytext=(5, 2),
textcoords='offset points',
ha='right',
va='bottom')
plt.show()
def graph():
#Sets some values.
x1 = datlo['ligand_rms_no_super_X']
y1 = datlo['interface_delta_X']
x2 = dathi['ligand_rms_no_super_X']
y2 = dathi['interface_delta_X']
#Calls actual max values for ligand_rms_no_super_X and interface_delta_X
maxrmsd = data['ligand_rms_no_super_X'].max()
minrmsd = data['ligand_rms_no_super_X'].min()
maxint = data['interface_delta_X'].max()
minint = data['interface_delta_X'].min()
#Following lines define everything about the actual figure
plt.figure(figsize=[16,9])
plt.xlim(xmin = minrmsd, xmax = maxrmsd)
plt.ylim(ymin = minint, ymax = maxint)
plot1 = plt.scatter(x1,y1, s=4, c='Blue', marker='o')
plot2 = plt.scatter(x2,y2, s=4, c='Red', marker='o')
plt.tick_params(axis='both',direction='inout',width=1,length=6,labelsize=13,pad=4)
plt.title('interface_delta_x vs ligand_rms_no_super_X', size=16)
plt.xlabel("ligand_rms_no_super_X", fontsize=13)
plt.ylabel("interface_delta_X", fontsize=13)
plt.legend(['total_score <= average', 'total_score > average'], markerscale=5, fontsize=12)
#Prompts user to decide on whether to export png file
printfile()
#Displays plot
plt.show()
def Exchange_rates(Base, Destination):
data =requests.get('https://api.cryptonator.com/api/full/{}-{}'.format(Base, Destination))
Data = (data.json()['ticker']['markets'])
market = []
price = []
volume = []
for A in range(len(Data)):
market.append(Data[A]['market'])
price.append(Data[A]['price'])
volume.append(Data[A]['volume'])
Difference = float(max(price))-float(min(price))
print("Minimum Price is \t",max(price)," \tat ", market[price.index(max(price))],
" \nMaximum Price is \t",min(price)+" \tat ", market[price.index(min(price))],
"\ndifference \t is\t", Difference,Destination)
numbers = (0, len(market))
plt.scatter(numbers, market, color='red')
for i, txt in enumerate(price):
plt.annotate(txt, (numbers[i], market[i]))
plt.title('ARBITRAGE')
plt.ylabel('#PRICE')
plt.show()
def volumeScatter(df):
# scatter plot shows ranges of music volumes at different stress levels
plt.figure()
plt.scatter(df["Stress"], df["DB"])
plt.xlabel('Stress levels')
plt.ylabel('Music volume')
plt.show()
def predict_prices(dates, prices, x):
dates = np.reshape(dates, (len(dates), 1))
svr_lin = SVR(kernel='linear', C=1e3)
svr_poly = SVR(kernel='poly', C=1e3, degree=2)
svr_rbf = SVR(kernel='rbf', C=1e3, gamma=0.1)
svr_lin.fit(dates, prices)
svr_poly.fit(dates, prices)
svr_rbf.fit(dates, prices)
plt.scatter(dates, prices, color='black', label='Data')
plt.plot(dates, svr_rbf.predict(dates), color='red', label='RBF model')
plt.plot(dates,
svr_lin.predict(dates),
color='green',
label='Linear model')
plt.plot(dates,
svr_poly.predict(dates),
color='blue',
label='Polynomial model')
plt.xlabel('Date')
plt.ylabel('Price')
plt.title('Support Vector Regression')
plt.legend()
plt.show()
return svr_rbf.predict(x)[0], svr_lin.predict(x)[0], svr_poly.predict(x)[0]
def scatter_plot(P, L, pcIdx1, pcIdx2, letterList, rev):
fig = plt.figure()
# following the convention in lecture note ScatterPlot.html
colors = ["r", "lime", "b", "y", "c", "m", "k", "tan", "pink", "darkred"]
for i, letter in enumerate(letterList):
plt.scatter(P[L == letter, pcIdx2],
P[L == letter, pcIdx1],
s=0.1,
c=colors[i],
label=letter)
plt.axes().set_aspect('equal')
#plt.axes().set_aspect('equal', 'datalim')
plt.xlabel("Principle Component {}".format(pcIdx2))
plt.ylabel("Principle Component {}".format(pcIdx1))
plt.axhline(0, color='grey')
plt.axvline(0, color='grey')
plt.ylim([-5000, 5000])
plt.xlim([-5000, 5000])
plt.legend()
plt.gca().invert_yaxis()
fig.set_size_inches(8, 8)
fName = os.path.join(
pDir, 'scatter_PC{}_PC{}_{}_{}.png'.format(pcIdx1, pcIdx2,
"".join(letterList), rev))
savefig(fName, bbox_inches='tight')
plt.show()
def show_graph(x_list, y_list, width, height):
""" x_list, y_list = x- & y-coordinates to plot
width, height = size of plot
"""
plt.figure(figsize=[width, height]) # [width, height]
plt.scatter(x_list, y_list, marker='.', s=5)
plt.show()
return
def tsne_plot(embedding, expression_value, cmaps="PuRd"):
plt.scatter(embedding[:, 0],
embedding[:, 1],
lw=0.1,
c=expression_value,
cmap=plt.cm.get_cmap('PuRd'))
plt.colorbar(label='expression value')
plt.show()
def plot_line(x, y, y_hat, line_color='blue'):
# Plot outputs
plt.scatter(x, y, color='black')
plt.plot(x, y_hat, color=line_color, linewidth=3)
plt.xticks(())
plt.yticks(())
plt.show()
def plotPredictions(yActualTrain, yActualVal, yPredTrain, yPredVal): ''' Plot both train and validation predictions ''' plt.figure(figsize=(6, 3)) plt.subplot(131) plt.scatter(yActualTrain, yPredTrain, s=1) plt.subplot(132) plt.scatter(yActualVal,yPredVal, s=1) plt.show()
def plot_data(X, y, theta=np.array([])):
""" Plot student admission data on a graph """
# Set y and x axis labels for scatter plot
plt.ylabel('Exam 2 score')
plt.xlabel('Exam 1 score')
admitted = np.where(y == 1)[0]
not_admitted = np.where(y == 0)[0]
# Plot all admitted students
plt.scatter(X[admitted, :1],
X[admitted, 1:],
marker='+',
label='Admitted',
c='black')
# Plot all non-admitted students
plt.scatter(X[not_admitted, :1],
X[not_admitted, 1:],
marker='o',
label='Not admitted',
c='yellow',
edgecolors='black')
# Set legend for scatter plot
plt.legend(loc='upper right', fontsize=8)
# Show best fit line
if theta.size != 0:
if theta.size <= 3:
x_coords = np.array([np.min(X[:, 1]), np.max(X[:, 1])])
y_coords = (-1 / theta[2]) * (theta[0] + theta[1] * x_coords)
plt.plot(x_coords, y_coords, 'b-', label='Decision boundary')
else:
# Here is the grid range
u = np.linspace(-1, 1.5, 50)
v = np.linspace(-1, 1.5, 50)
z = np.zeros((u.size, v.size))
# Evaluate z = theta*x over the grid
for i, ui in enumerate(u):
for j, vj in enumerate(v):
z[i, j] = np.dot(mapFeature(ui, vj), theta)
z = z.T # important to transpose z before calling contour
# print(z)
# Plot z = 0
pyplot.contour(u, v, z, levels=[0], linewidths=2, colors='g')
pyplot.contourf(u,
v,
z,
levels=[np.min(z), 0, np.max(z)],
cmap='Greens',
alpha=0.4)
plt.show()
def pca_plot(self):
label = np.unique(self.label)
with plt.style.context("seaborn-darkgrid"):
for l in label:
plt.scatter(self.Y[y == l, 0], self.Y[y == l, 1], label=l)
plt.xlabel("PC 1")
plt.ylabel("PC 2")
plt.legend()
plt.show()
def scatter_chart(plt, col1, col2, Title="Scatter Plot"):
color = ['r']
results = linregress(col1,col2)
print results
plt.scatter(col1,col2)
plt.plot(col1, col1*results[0] + results[1])
plt.ylabel(col2.name)
plt.xlabel(col1.name)
plt.title(Title)
def makePlot(muDistr, AiArray, Ai, num):
#plt.scatter(muDistr,AiArray)
if (num == 17):
plt.scatter(muDistr, AiArray)
title = "P(alpha|x,I) "
plt.ylabel("Normalized Probability")
plt.xlabel('x')
plt.title(title)
plt.show()
def plotPredictions(clf):
xx, yy = np.meshgrid(np.arange(0, 250000, 10), np.arange(10, 70, 0.5))
Z = clf.predict(np.c_[xx.ravel(), yy.ravel()])
plt.figure(figsize=(8, 6))
Z = Z.reshape(xx.shape)
plt.contourf(xx, yy, Z, cmap=plt.cm.Paired, alpha=0.8)
plt.scatter(X[:, 0], X[:, 1], c=y.astype(np.float))
plt.show()
def main():
#Before anything happens, number of command-line arguments is checked and appropriate action taken.
argumnumber()
if (len(sys.argv) < 2):
file = raw_input("Please provide a sorted_models file: ")
else:
file = sys.argv[1]
#Prompts user to provide maxtot and maxinter before progam continues.
global maxtot
maxtot = float(raw_input("Please enter maximum total_score: "))
global maxinter
maxinter = float(raw_input("Please enter maximum interface_delta_X: "))
#Imports DataFrame and filters based on max values provided.
models_raw = pd.read_csv(
file, sep=' ', names=['model', 'total_score', 'interface_delta_X'])
models = models_raw.loc[(models_raw['total_score'] <= maxtot)
& (models_raw['interface_delta_X'] <= maxinter)]
sumavrg = (
(np.sum(models['total_score']) + np.sum(models['interface_delta_X'])) /
(len(models['total_score'])))
#Appends a column to models that contains the sum of total_score and interface_delta_X
sumarr = (models['total_score'] + models['interface_delta_X'])
models['add'] = sumarr
#Finds values with lowest sum
modhi = models.loc[models['add'] > sumavrg]
modlo = models.loc[models['add'] <= sumavrg]
minidx = models['add'].idxmin()
xmin = models.iloc[minidx]['total_score']
ymin = models.iloc[minidx]['interface_delta_X']
#Creates the plot.
x1 = modlo['total_score']
y1 = modlo['interface_delta_X']
x2 = modhi['total_score']
y2 = modhi['interface_delta_X']
plt.figure(figsize=[16, 9])
plot1 = plt.scatter(x1, y1, s=2, c='Green', marker='.')
plot2 = plt.scatter(x2, y2, s=2, c='Red', marker='.')
plt.tick_params(axis='both',
direction='inout',
width=1,
length=6,
labelsize=13,
pad=4)
plt.title('interface_delta_x vs total_score', size=16)
plt.xlabel("total_score", fontsize=13)
plt.ylabel("interface_delta_X", fontsize=13)
plt.legend(['Sum <= average', 'Sum > average'], markerscale=7, fontsize=12)
plt.annotate(xy=(xmin, ymin),
s="Lowest sum: total_score: " + str(xmin) +
"; interface_delta_X: " + str(ymin),
textcoords='axes fraction',
xytext=(0.6, 0.05))
printtofile()
plt.show()
def mandlebrot(x, y):
for xval in range(x):
for yval in range(y):
val = 0
iteration = 0
while val in range(20):
val = val * val + x + y * 1j
iteration = iteration + 1
plt.scatter(x, y, color=(0, 0, 255, iteration))
plt.show
def feature_summary(x_col, y_col, show_r2=False):
"""Gives a summary of a feature
:return:
"""
# Preparation
x_name = x_col.name
y_name = y_col.name
df = pd.concat([x_col, y_col], axis=1).sort_index()
plt.rcParams["figure.figsize"] = (10, 7)
breaks(1)
print("%s" % x_name)
print('Quantile:\n', x_col.quantile([0.0, 0.1, 0.25, 0.5, 0.75, 1.0]))
# Histogram
plt.subplot(221)
try:
plt.hist(x_col, bins=30)
plt.xlabel(x_name)
plt.title('Histogram (CF GHP): %s' % x_name)
except ValueError:
print("No histogram for %s available" % x_name)
# Correlation
if y_name != x_name:
df = df.sort_values(x_name)
# df[x_name + "_2"] = df[x_name] * df[x_name]
# df[x_name + "_3"] = df[x_name] * df[x_name] * df[x_name]
x = df.drop(y_name, 1)
reg = linear_model.LinearRegression(normalize=True)
reg.fit(x, df[y_name])
# Plot
plt.subplot(222)
plt.scatter(df[x_name], df[y_name])
plt.plot(df[x_name], reg.predict(x), color='g')
plt.xlabel(x_name)
plt.xlim([df[x_name].min(), df[x_name].max()])
plt.title('x:%s / y:%s ' % (x_name, y_name))
plt.ylabel("Target function: %s" % y_name)
if show_r2:
print("R²:", r2_score(df[y_name], reg.predict(x)))
print(feature_importance(x, reg.coef_))
# Show plots
plt.show()
# Timeline
x_col.rolling(window=10,
center=False).mean().plot(title='%s: Timeline' % x_name,
figsize=(10, 2),
xlim=(170000, 175000))
plt.show()
plt.close('all')
return " "
def plot_various_trial_analyses(self,neuron_ind, var_level):
plt.figure(figsize=(16, 5))
#the first thing we want to do is just plot the data average
#so first get the data for all trials
neuron_i_data_by_trial = self.by_trial_IT_Neural_Data_objmeans_sorted_by_category[var_level][:, :, neuron_ind]
#now take the mean over the second dimension -- the trial dimension
neuron_i_data_trial_mean = neuron_i_data_by_trial.mean(1)
#for convenience, let's compute the min and max values of the neural response
minval = neuron_i_data_trial_mean.min()
maxval = neuron_i_data_trial_mean.max()
#now let's plot the responses across objects
plt.plot(neuron_i_data_trial_mean)
#and block stuff to make the categories easier to see
plt.fill_between(np.arange(64), minval, maxval,
where=(np.arange(64) / 8) % 2, color='k', alpha=0.2)
plt.xticks(np.arange(0, 64, 8) + 4, self.unique_categories, rotation=30);
plt.ylabel('Neural Response of neuron %d' % neuron_ind)
plt.ylim(minval, maxval)
plt.xlabel('Responses for Variation %s images' % var_level)
#now let's look at two trials -- the first and 6th ones, for example
t1 = 0; t2 = 5
t1_data = neuron_i_data_by_trial[:, t1]
t2_data = neuron_i_data_by_trial[:, t2]
plt.figure(figsize=(12, 5))
plt.subplot(1, 2, 1)
plt.plot(t1_data)
plt.xticks(np.arange(0, 64, 8), self.unique_categories, rotation=30);
plt.title('Neuron %d, trial %d, var %s' % (neuron_ind, t1, var_level))
plt.subplot(1, 2, 2)
plt.plot(t2_data)
plt.xticks(np.arange(0, 64, 8), self.unique_categories, rotation=30);
plt.title('Neuron %d, trial %d, var %s' % (neuron_ind, t2, var_level))
#let's do a scatter plot of the responses to one trial vs the other
plt.figure()
plt.scatter(t1_data, t2_data)
plt.xlabel('responses of neuron %d, trial %d, %s'% (neuron_ind, t1, var_level))
plt.ylabel('responses of neuron %d, trial %d, %s'% (neuron_ind, t2, var_level))
#how correlated are they exactly between trials? let's use pearson correlation
rval = stats.pearsonr(t1_data, t2_data)[0]
plt.title('Correlation for varlevel %s images = %.3f' % (var_level, rval))
#in fact, let's have a look at the correlation for all pairs of trials
fig = plt.figure(figsize = (7, 7))
#the numpy corrcoef function basically gets the pairwise pearson correlation efficiently
corrs = np.corrcoef(neuron_i_data_by_trial.T)
#now let's plot the matrix of correlations using the matshow function
plt.colorbar(fig.gca().matshow(corrs))
plt.xlabel('trials of neuron %d' % neuron_ind)
plt.ylabel('trials of neuron %d' % neuron_ind)
plt.title('Between-trial correlations for varlevel %s' % var_level)
def plot_regression_line(x, y, b):
plt.scatter(x, y, color="m", marker="o", s=30)
y_pred = b[0] + b[1] * x
plt.plot(x, y_pred, color="g")
plt.xlabel('x')
plt.ylabel('y')
plt.show()
def plot(x, y, **kwargs):
"""can only do 2D plot right now"""
assert (x.shape[-1] == 2)
color = (y + 2) / 5
if 'accuracy' in kwargs:
accuracy = kwargs['accuracy']
plt.figure()
plt.scatter(x[:, 0], x[:, 1], c=color)
if 'title' in kwargs:
plt.suptitle(kwargs['title'])
if 'accuracy' in kwargs:
plt.title("Accuracy: %.1f%%" % (kwargs['accuracy'] * 100), fontsize=10)
plt.show()
def plot_points(self):
points = self.points
x_pts = [pt[0] for pt in points]
y_pts = [pt[1] for pt in points]
col = [pt[3] for pt in points]
plt.figure()
plt.scatter(x_pts, y_pts, c=col)
# plt.axes([0, 10, 0, 10])
plt.ylim(-15, 15)
plt.xlim(0, 15)
# plt.axes(xlim=(-5, 5), ylim=(0, 3.5))
plt.show()
def scatterPlot(self):
axis = [
min(self.tdata[:, 0]) - 1,
max(self.tdata[:, 0]) + 1,
min(self.tdata[:, 1]) - 1,
max(self.tdata[:, 1]) + 1
]
setx = np.linspace(axis[0], axis[1])
plt.scatter(self.tdata[:, 0], self.tdata[:, 1])
plt.plot(setx, self.modelFunction(setx))
plt.axis(axis)
plt.show()
def print_scatter_data():
import matplotlib.pylab as plt
filename = Par.dirname + ('/Scatter.dat')
fitnesses = []
self_reliences = []
life_times = []
self_reliences_dead = []
for Agent in Par.Agents:
if Agent.dead != True:
fitnesses.append(Agent.fitness)
Needs = Agent.needs
Production = Agent.production
selfReli = [0.0]*Par.num_resources
for i in range(Par.num_resources):
selfReli[i] = Production[i]*Needs[i]
self_reliences.append(abs(sum(selfReli)))
else:
life_time = Agent.t_death - Agent.t_discovery
life_times.append(life_time)
Needs = Agent.needs
Production = Agent.production
selfReli = [0.0]*Par.num_resources
for i in range(Par.num_resources):
selfReli[i] = Production[i]*Needs[i]
self_reliences_dead.append(abs(sum(selfReli)))
file =open(filename, 'w')
for i in range(len(fitnesses)):
s= str(fitnesses[i]) +' '+ str(self_reliences[i])
file.write(s)
file.write('\n')
file.close()
plt.scatter(self_reliences, fitnesses)
plt.ylabel('Fitness')
plt.xlabel('self_reliences')
plt.savefig('FitnessVSR.png')
plt.close()
plt.scatter(self_reliences_dead, life_times)
plt.ylabel('LifeTimes')
plt.xlabel('self_reliences')
plt.savefig('LifeTimeVSR.png')
plt.close()
import matplotlib as plt
import numpy as np
import pandas as pd
dat=pd.read_csv('Voters.csv').as_matrix()
x=dat[:,0]
y=dat[:,1]
plt.scatter(x,y)
plt.show()
plt.hist(x)
plt.hist(y,bins=15)
#images
train=pd.read_csv('test.csv')
M=train.as_matrix()
im=M[0,1:]
im=im.reshape(28,28)
M=train.as_matrix()
plt.imshow(im)
plt.show()
plt.imshow(im,cmap="gray")
from scipy.stats import norm
norm.pdf(0)
norm.pdf(0,loc=5, scale=10)
r=np.random.randn(10)
norm.pdf(r)
norm.cdf(r)
r=10*np.random.randn(10000)+5
df = pd.DataFrame(ground_cricket_data)
# instantiate LinearRegression class
regr = linear_model.LinearRegression()
# define variables
x = df['Ground Temperature']
# pandas.Series.to_frame() returns a data frame
x = x.to_frame()
y = df['Chirps/Second']
# fit the object to the data
regr.fit(x, y)
# plot using equation
plt.scatter(x, y)
# use attributes to plot linear regression equation
# y = β0 + β1x where β0 is intercept and β1 is coefficient
plt.plot(x, (regr.intercept_ + (regr.coef_ * x)))
# plot using max/min as data for prediction
# create a new data frame of min and max feature values
df_new = pd.DataFrame({'Ground Temp': [df['Ground Temperature'].min(),
df['Ground Temperature'].max()]})
plt.scatter(x, y)
# plot the new frame against the prediction
plt.plot(df_new, regr.predict(df_new))
# calculate the r-squared score (or coefficient of determination)
regr.score(x, y)
###Note, this function will auto change, it acts global.
seqDB, data_genes, data_isoforms = qcf.bioReplicateSelfCorrelate(seqDB,data_genes, data_isoforms,
excludeSelf=1) ###Exclude self avoids self comparison
#
pairs = np.zeros([len(seqDB),2])
#xToPlot= 'pearsonCorrToMTT'
#yToPlot = 'pearsonCorrToMeanReplicate'
xToPlot= 'spearmanCorrToMeanReplicate'
yToPlot = 'pearsonCorrToMeanReplicate'
for rowId in range(len(seqDB)):
pairs[rowId,0] = seqDB.loc[rowId,xToPlot] #seqDB['num_cells'] ###X AXIS
pairs[rowId,1] = seqDB.loc[rowId,yToPlot] ####Y AXIS
plt.scatter(pairs[:,0],pairs[:,1])
plt.xlabel(xToPlot)
plt.ylabel(yToPlot)
axes = plt.gca()
axes.set_xlim([0.8,1.05])
axes.set_ylim([0.8,1.05])
fig = plt.gcf()
fig.set_size_inches(15,10)
# In[12]:
seqDB
# In[21]:
# In[67]:
#4
categoricalFreq_rel=categoricalFreq.div(categoricalFreq.sum(1).astype(float))
categoricalFreq_rel
categoricalFreq_rel.plot(kind='barh', stacked=True)
title('MPG by Efficiency(stacked)')
savefig('stacked', dpi=400, bbox_inches='tight')
# In[64]:
#5
plt.scatter(carData['barrels08'], carData['highway08'])
plt.title('Barrel Consumption vs Highway MPG')
# In[2]:
#Part 2
import scipy as sp
import sklearn as sk
# In[3]:
#2
medicalData=pd.read_table('Medical.csv', header=False, sep=',')
medicalData
import numpy as np
import matplotlib as plt
import sys, string, os
n_archivos = len(sys.argv)
for i in range(n_archivos)
datos = np.loadtxt(sys.argv[i])
N = np.shape(datos)[0]
for i in range(N):
plt.scatter(datos[i,0],datos[i,1])
plt.show()
df["time"] = [t[11:13] + t[14:16] for t in df["lastupdated"]]
df["day"] = [date2int(t) for t in df["lastupdated"]] # day 0 is May 17, 2014
df["dayofwk"] = [(t+6)%7 for t in df["day"]] # 0 indexed Sunday
df.head()
# <codecell>
plt.figure(figsize=(10,15))
im = plt.imread('chicago.png')
implot = plt.imshow(im)
x = (df['west'] - df['west'].min())*477/(df['east'].max() - df['west'].min())
y = 798-(df['north'] - df['south'].min())*798/(df['north'].max() - df['south'].min())
s = df['currentspeed'] / df['currentspeed'].max()
plt.scatter(x,y,c=s,linewidth=0,s=1000,alpha=0.1)
#x0 = (df.ix[0]['west'] - df['west'].min())*477/(df['east'].max() - df['west'].min())
#y0 = 798-(df.ix[0]['north'] - df['south'].min())*798/(df['north'].max() - df['south'].min())
#plt.scatter(x0,y0,c='r',s=2000)
#x0 = (df.ix[0]['east'] - df['west'].min())*477/(df['east'].max() - df['west'].min())
#y0 = 798-(df.ix[0]['south'] - df['south'].min())*798/(df['north'].max() - df['south'].min())
#plt.scatter(x0,y0,c='r',s=2000)
plt.xlim(0,477)
plt.ylim(798,0)
plt.xticks([])
plt.yticks([])
#plt.plot([df['west'],df['west'],df['east'],df['east'],df['west']],[df['south'],df['north'],df['north'],df['south'],df['south']],linewidth=20,alpha=0.2)
# <codecell>
plt.show()
# Dendrogram
from scipy.spatial.distance import pdist
from scipy.cluster.hierarchy import linkage, dendrogram, fcluster, fclusterdata
distanceMatrix = pdist(data)
dend = dendrogram(linkage(distanceMatrix, method='complete'), color_threshold=2, leaf_font_size=10, labels = df.yearID.tolist())
assignments = fcluster(linkage(distanceMatrix, method = 'complete'), 2, 'distance')
cluster_output = pandas.DataFrame({'team':df.yearID.tolist(), 'cluster':assignments})
cluster_output
plt.scatter(df.total_salaries, df.total_runs, s=60, c=cluster_output.cluster)
# Got the following code when I tried to improve the plot
# AttributeError: 'int' object has no attribute 'view'
#colors = cluster_output.cluster
#colors[colors == 1] = 'b'
#colors[colors == 2] = 'g'
#colors[colors == 3] = 'r'
#
#plt.scatter(df.total_salaries, df.total_runs, s=100, c=colors, lw=0)
############################################################################
# Principal component analysis
def plotDistribution(dist): for k in dist.index: alpha = np.array([dist[x][k] for x in dist])*100 x = [k for x in np.arange(0,len(alpha))] y = dist.columns plt.scatter(x,y,c=alpha,marker='s',linewidths=0,cmap='Oranges',norm=pltcolors.Normalize(vmin=0,vmax=1),vmin=0,vmax=1,edgecolors=None)
pd.set_option('display.max_rows', 3000)
pd.set_option('display.width', 100000)
df = pd.read_csv('../input/2013_NCAA_Game.csv')
pd.scatter_matrix(df)
pd.scatter_matrix(df, diagonal='kde')
hist(df['Team Avg Scoring Margin'])
plt.scatter(df['Team Score'], df['Team Margin'])
pf = pd.read_csv('../input/clean_player_data.csv')
pf = pf.drop_duplicates()
tt = pf.groupby('Team').mean()
import sys
import numpy as np
import matplotlib as plt
import math
a=sys.argv[1]
data=np.loadtxt(a)
x=data[:,3]
y=data[:,4]
figura=plt.polyfit(x,y,1)
plt.scatter(x,y)
plt.plot(x,y*figura[0]*(y**4) + figura[i]*(y**3), figura[2]*(y**2), figura[3]*y + fit[4])
plt.xlabel("Pasos (x)", frontsize=20)
plt.ylabel("Distancia (y)", frontsize =20)
plt.tittle("Numero de Pasos VS Distancia con la Regresion", frontsize =15)
plt.savefig('ajuste.png')
initialCon.append(-0.01 / 300.0 * x)
# Ensuring boundary conditions
#initialCon[0] = 0
#initialCon[-1] = 0
yPrev = initialCon
yCurrent = initialCon
sample = []
for n in range(0,10):
for i in range(0,len(x)):
if i !=0 and i != 649:
yNew = ((2 - 2*r**2 - 6 * eps * r**2 * N**2)*yCurrent[i]
- yPrev[i] + r**2*(1 + 4*eps*N**2)*(yCurrent[i+1]
+ yCurrent[i-1]) - eps*r**2*N**2 *(yCurrent[i+2]
+ yCurrent[i-2]))
yPrev = copy(yCurrent)
yCurrent = copy(yNew)
plt.scatter(yNew)
plt.draw()
plt.pause()
plt.clf()
#%% USPS version
pca = PCA(n_components=5)
X_trans = pca.fit_transform(X)
data = np.hstack((X_trans, np.matrix(y).T))
#%%
np.random.shuffle(data)
sample = data[:500,:]
#%%
pl.figure()
for i in range(5):
for j in range(5):
try:
#pl.subplot(5,5,((j)*5)+i)
pl.figure()
pl.scatter(sample[:,i].A1, sample[:,j].A1, 20, sample[:,5].A1)
pl.show()
except IndexError:
print i,j
plt.hist(data.year, bins=np.arange(1950, 2013), color='#cccccc')
plt.xlabel("Release Year")
remove_border()
# Received following message:
# Traceback (most recent call last):
# File "<stdin>", line 1, in <module>
# AttributeError: 'module'object has not attribute 'hist'
# AND
# AttributeError: 'module'object has not attribute 'xlabel'
plt.hist(data.score, bins=20, color='#cccccc')
plt.xlabel("IMDB rating")
remove_border()
# Again, I'm receiving AttributeError messages. Is there an issue with the matplotlib that is not allowing me to produce a histogram?
plt.scatter(data.year, data.score, lw=0, alpha=.08, color='k')
plt.xlabel("Year")
plt.ylabel("IMDB Rating")
remove_border()
# Again, I'm receiving AttributeError message.
data[(data.votes > 9e4) & (data.score < 5)][['title', 'year', 'score', 'votes', 'genres']]
data[data.score == data.score.min()][['title', 'year', 'score', 'votes', 'genres']]
data[data.score == data.score.max()][['title', 'year', 'score', 'votes', 'genres']]
genre_count = np.sort(data[genres].sum())[::-1]
pd.DataFrame({'Genre Count': genre_count})
# The genres were not listed alongside the counts
print r("summary(rdata)")
r("?princomp")
r("p = princomp(rdata)")
print r("names(p)")
print r("head(p$scores, n=6")
irisPd = pd.DataFrame(r.get("p$scores"),columns=['pc1','pc2','pc3','pc4','pc5'])
irisPd.head()
mat.scatter(irisPY.Comp1,irisPY.Comp2).
title('Iris').
xlabel('Primary Component 1').
ylabel('Primary Component 2')
mat.show()
colors = ['red', 'green', 'blue']
labels = ['Setosa', 'Virginica', 'Versicolor']
fig = mat.figure()
ax = mat.add_subplot(1, 1, 1)
ax.set_xlabel('Primary Component 1')
ax.set_ylabel('Primary Component 2')
ax.set_title('Species Data')
tama = []
tam = 0
clustersx = np.empty((0))
clustersy = np.empty((0))
for i in range(n_centros):
arr_x = np.empty((0))
arr_y = np.empty((0))
for j in range(n_puntos):
if (int(minimos[j])==i):
arr_x = np.append(arr_x,posx[j])
arr_y = np.append(arr_y,posy[j])
tam += np.size(arr_x)
tama.append(tam)
clustersx = np.append(clustersx,arr_x)
clustersy = np.append(clustersy,arr_y)
clustersx = np.split(clustersx,tama)
clustersy = np.split(clustersy,tama)
for i in range(n_centros):
plt.xlabel("Puntos en x")
plt.ylabel("Puntos en y")
plt.title("K-means clustering")
plt.scatter(clustersx[i],clustersy[i],c=colores[i])
plt.scatter(centrosx[i],centrosy[i],c=colores[i],s=110)
plt.show()
import numpy as np import matplotlib as pl n = 1024 X = np.random.normal(0,1,n) Y = np.random.normal(0,1,n) pl.scatter(X,Y)
import matplotlib as plt
import numpy as np
from sklearn import datasets, linear_model
def generate_data():
np.random.seed(0)
X, y = datasets.make_moons(200, noise=0.20)
return X, y
class Config:
nn_input_dim = 2
nn_output_dim = 2
epsilon = 0.01
reg_lambda = 0.01
def visualize(X, y, model):
plot_decision_boundary(lambda x: predict(model, x), X, y)
plt.title("Logistic regression")
def plot_decision_boundary(pred_func, X, y):
pass
if __name__ == "__mail__":
X, y = generate_data()
plt.scatter(X[:,0], X[:,1], s=40, c=y, cmap=plt.cm.Spectral)
plt.show()
def read():
pickle_file = open("pickled_data.pkl", "r")
t = pickle.load(pickle_file)
v = pickle.load(pickle_file)
print t
print v
initialize(v, s, t, dt, n)
calculate(v, s, t, dt, n)
store(v, t, n)
#plot
plt.figure(1)
plt.subplot(211)
plt.plot(t, v,"g-", linewidth=2.0)
plt.scatter(t, v)
plt.title('The Velocity of a Free Falling Object')
plt.xlabel('Time($t$)', fontsize=14)
plt.ylabel('Velocity($m/s$)', fontsize=14)
plt.text(3,-60,r'$g = 9.8 m/s^2$', fontsize=16)
plt.grid(True)
plt.subplot(212)
plt.plot(t, s,"g-", linewidth=2.0)
plt.scatter(t, s)
plt.title('The Displacement of a Free Falling Object')
plt.xlabel('Time($t$)', fontsize=14)
plt.ylabel('Displacement($m$)', fontsize=14)
plt.text(3,-300,r'$g = 9.8 m/s^2$', fontsize=16)
plt.grid(True)
