I am programming in Python 3 and I have data structured like this:
coordinates = [(0.15,0.25),(0.35,0.25),(0.55,0.45),(0.65,0.10),(0.15,0.25)]
These are coordinates. Within each pair, the first number is the x coordinate and the second one the y coordinate. Some of the coordinates repeat themselves. I want to plot these data like this:
The coordinates that are most frequently found should appear either as higher intensity (i.e., brighter) points or as points with a different color (for example, red for very frequent coordinates and blue for very infrequent coordinates). Don't worry about the circle and semicircle. That's irrelevant. Is there a matplotlib plot that can do this? Scatter plots do not work because they do not report on the frequency with which each coordinate is found. They just create a cloud.
The answer is:
import matplotlib.pyplot as plt
from scipy.stats import kde
import numpy as np
xvalues = np.random.normal(loc=0.5,scale=0.01,size=50000)
yvalues = np.random.normal(loc=0.25,scale=0.1,size=50000)
nbins=300
k = kde.gaussian_kde([xvalues,yvalues])
xi, yi = np.mgrid[0:1:nbins*1j,0:1:nbins*1j]
zi = k(np.vstack([xi.flatten(),yi.flatten()]))
fig, ax = plt.subplots()
ax.pcolormesh(xi, yi, zi.reshape(xi.shape), shading='auto', cmap=plt.cm.hot)
x = np.arange(0.0,1.01,0.01,dtype=np.float64)
y = np.sqrt((0.5*0.5)-((x-0.5)*(x-0.5)))
ax.axis([0,1,0,0.55])
ax.set_ylabel('S', fontsize=16)
ax.set_xlabel('G', fontsize=16)
ax.tick_params(labelsize=12, width=3)
ax.plot(x,y,'w--')
plt.show()
Related
Question background: I am trying to make two geometries in a one plot in python. I have made one geometry which is an object having mesh as shown in figure below. The respective code is also mentioned here.
df_1_new = pd.DataFrame()
df_1_new['X_coordinate']=pd.Series(x_new)
df_1_new['Y_coordinate']=pd.Series(y_new)
df_1_new['node_number'] = df_1_new.index
df_1_new = df_1_new[['node_number','X_coordinate','Y_coordinate']]
plt.scatter(x_new, y_new)
plt.show
The second geometry, which is a circle and I made this geometry running below code.
from matplotlib import pyplot as plt, patches
plt.rcParams["figure.figsize"] = [9.00, 6.50]
plt.rcParams["figure.autolayout"] = True
fig = plt.figure()
ax = fig.add_subplot()
circle1 = plt.Circle((2, 2), radius=5, fill = False)
ax.add_patch(circle1)
ax.axis('equal')
plt.show()
My question: How can I combine both geometries mentioned above in a one plot. I would like to place my circle around my geometry (object). Geometry has a centroid (2, 2) and I want to place my circle's centroid exactly on the centroid of geometry therefore I will be having a circle around my geometry. What code I should write. Kindly help me on this.
For your reference: I want my plot just like in below picture.
you need to do all the plotting between the subplot creation and before you issue the plt.show() command, as any command after it will create a new figure.
from matplotlib import pyplot as plt, patches
plt.rcParams["figure.figsize"] = [9.00, 6.50]
plt.rcParams["figure.autolayout"] = True
fig = plt.figure()
ax = fig.add_subplot()
# other plt.scatter or plt.plot here
plt.scatter([3,4,5,6,4],[5,4,2,3,2]) # example
circle1 = plt.Circle((2, 2), radius=5, fill = False)
ax.add_patch(circle1)
ax.axis('equal')
plt.show()
image example
to get the points inside the circle, you need to play with the circle radius and center till you get it right.
something you can do is to make the circle at the np.median of your x and y values, so you are sure about the center position.
I am trying to fill the area between two vertical curves(RHOB and NPHI) using matplotlib.pyplot. Both RHOB and NPHI are having different scale of x-axis.
But when i try to plot i noticed that the fill_between is filling the area between RHOB and NPHI in the same scale.
#well_data is the data frame i am reading to get my data
#creating my subplot
fig, ax=plt.subplots(1,2,figsize=(8,6),sharey=True)
ax[0].get_xaxis().set_visible(False)
ax[0].invert_yaxis()
#subplot 1:
#ax01 to house the NPHI curve (NPHI curve are having values between 0-45)
ax01=ax[0].twiny()
ax01.set_xlim(-15,45)
ax01.invert_xaxis()
ax01.set_xlabel('NPHI',color='blue')
ax01.spines['top'].set_position(('outward',0))
ax01.tick_params(axis='x',colors='blue')
ax01.plot(well_data.NPHI,well_data.index,color='blue')
#ax02 to house the RHOB curve (RHOB curve having values between 1.95,2.95)
ax02=ax[0].twiny()
ax02.set_xlim(1.95,2.95)
ax02.set_xlabel('RHOB',color='red')
ax02.spines['top'].set_position(('outward',40))
ax02.tick_params(axis='x',colors='red')
ax02.plot(well_data.RHOB,well_data.index,color='red')
# ax03=ax[0].twiny()
# ax03.set_xlim(0,50)
# ax03.spines['top'].set_position(('outward',80))
# ax03.fill_betweenx(well_data.index,well_data.RHOB,well_data.NPHI,alpha=0.5)
plt.show()
ax03=ax[0].twiny()
ax03.set_xlim(0,50)
ax03.spines['top'].set_position(('outward',80))
ax03.fill_betweenx(well_data.index,well_data.RHOB,well_data.NPHI,alpha=0.5)
above is the code that i tried, but the end result is not what i expected.
it is filling area between RHOB and NPHI assuming RHOB and NPHI is in the same scale.
How can i fill the area between the blue and the red curve?
Since the data are on two different axes, but each artist needs to be on one axes alone, this is hard. What would need to be done here is to calculate all data in a single unit system. You might opt to transform both datasets to display-space first (meaning pixels), then plot those transformed data via fill_betweenx without transforming again (transform=None).
import numpy as np
import matplotlib.pyplot as plt
y = np.linspace(0, 22, 101)
x1 = np.sin(y)/2
x2 = np.cos(y/2)+20
fig, ax1 = plt.subplots()
ax2 = ax1.twiny()
ax1.tick_params(axis="x", colors="C0", labelcolor="C0")
ax2.tick_params(axis="x", colors="C1", labelcolor="C1")
ax1.set_xlim(-1,3)
ax2.set_xlim(15,22)
ax1.plot(x1,y, color="C0")
ax2.plot(x2,y, color="C1")
x1p, yp = ax1.transData.transform(np.c_[x1,y]).T
x2p, _ = ax2.transData.transform(np.c_[x2,y]).T
ax1.autoscale(False)
ax1.fill_betweenx(yp, x1p, x2p, color="C9", alpha=0.4, transform=None)
plt.show()
We might equally opt to transform the data from the second axes to the first. This has the advantage that it's not defined in pixel space and hence circumvents a problem that occurs when the figure size is changed after the figure is created.
x2p, _ = (ax2.transData + ax1.transData.inverted()).transform(np.c_[x2,y]).T
ax1.autoscale(False)
ax1.fill_betweenx(y, x1, x2p, color="grey", alpha=0.4)
I am trying to plot a normal distribution curve in Python using matplotlib. I followed the accepted answer in the post python pylab plot normal distribution in order to generate the graph.
I would like to know if there is a way of projecting the mu - 3*sigma, mu + 3*sigma and the mean values on both the x-axis and y-axis.
Thanks
EDIT 1
Image for explaining projection
example_image.
In the image, I am trying to project the mean value on x and y-axis. I would like to know if there is a way I can achieve this along with obtaining the values (the blue circles on x and y-axis) on x and y-axis.
The following script shows how to achieve what you want:
import matplotlib.pyplot as plt
import numpy as np
import scipy.stats as stats
mu = 2
variance = 9
sigma = np.sqrt(variance)
x = np.linspace(mu - 3*sigma, mu + 3*sigma, 500)
y = stats.norm.pdf(x, mu, sigma)
fig, ax = plt.subplots()
ax.plot(x, y)
ax.set_xlim([min(x), max(x)])
ax.set_ylim([min(y), max(y)+0.02])
ax.hlines(y=max(y), xmin=min(x), xmax=mu, color='r')
ax.vlines(x=mu, ymin=min(y), ymax=max(y), color='r')
plt.show()
The produced plot is
If you are familiar with the properties of normal distribution, it is easy to know intersection with x axis is just mu, i.e., the distribution mean. Intersection with y axis is just the maximum value of y, i.e, max(y) in the code.
I have a list of x,y,z points and a list of values assigned to each 3D point.
Now the question is, how can I color each point in a 3D scatter plot according to the list of values ?
The colors should be typical engineering -> RGB -> lowest blue to highest red
Thanks a lot
Basically I am searching for an equivalent to: scatter3(X,Y,Z,S,C)
See here: https://ch.mathworks.com/help/matlab/ref/scatter3.html
I tried:
col = [i/max(values)*255 for i in values]
ax.scatter(sequence_containing_x_vals, sequence_containing_y_vals, sequence_containing_z_vals,c=col, marker='o')
pyplot.show()
..but I don't get the desired result
Note the recommended way of producing scatters with colors is to supply the values directly to c:
ax.scatter(x, y, z, c=values, marker='o', cmap="Spectral")
Minimal example:
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
x = y = z = values = [1,2,3,4,5]
ax = plt.subplot(projection="3d")
sc = ax.scatter(x, y, z, c=values, marker='o', s=100, cmap="Spectral")
plt.colorbar(sc)
plt.show()
I'm struggling to draw a power law graph for Facebook Data that I found online. I'm using Networkx and I've found how to draw a Degree Histogram and a degree rank. The problem that I'm having is I want the y axis to be a probability so I'm assuming I need to sum up each y value and divide by the total number of nodes? Can anyone please help me do this? Once I've got this I'd like to draw a log-log graph to see if I can obtain a straight line. I'd really appreciate it if anyone could help! Here's my code:
import collections
import networkx as nx
import matplotlib.pyplot as plt
from networkx.algorithms import community
import math
import pylab as plt
g = nx.read_edgelist("/Users/Michael/Desktop/anaconda3/facebook_combined.txt","r")
nx.info(g)
degree_sequence = sorted([d for n, d in g.degree()], reverse=True)
degreeCount = collections.Counter(degree_sequence)
deg, cnt = zip(*degreeCount.items())
fig, ax = plt.subplots()
plt.bar(deg, cnt, width=0.80, color='b')
plt.title("Degree Histogram for Facebook Data")
plt.ylabel("Count")
plt.xlabel("Degree")
ax.set_xticks([d + 0.4 for d in deg])
ax.set_xticklabels(deg)
plt.show()
plt.loglog(degree_sequence, 'b-', marker='o')
plt.title("Degree rank plot")
plt.ylabel("Degree")
plt.xlabel("Rank")
plt.show()
You seem to be on the right tracks, but some simplifications will likely help you. The code below uses only 2 libraries.
Without access your graph, we can use some graph generators instead. I've chosen 2 qualitatively different types here, and deliberately chosen different sizes so that the normalization of the histogram is needed.
import networkx as nx
import matplotlib.pyplot as plt
g1 = nx.scale_free_graph(1000, )
g2 = nx.watts_strogatz_graph(2000, 6, p=0.8)
# we don't need to sort the values since the histogram will handle it for us
deg_g1 = nx.degree(g1).values()
deg_g2 = nx.degree(g2).values()
# there are smarter ways to choose bin locations, but since
# degrees must be discrete, we can be lazy...
max_degree = max(deg_g1 + deg_g2)
# plot different styles to see both
fig = plt.figure()
ax = fig.add_subplot(111)
ax.hist(deg_g1, bins=xrange(0, max_degree), density=True, histtype='bar', rwidth=0.8)
ax.hist(deg_g2, bins=xrange(0, max_degree), density=True, histtype='step', lw=3)
# setup the axes to be log/log scaled
ax.set_yscale('log')
ax.set_xscale('log')
ax.set_xlabel('degree')
ax.set_ylabel('relative density')
ax.legend()
plt.show()
This produces an output plot like this (both g1,g2 are randomised so won't be identical):
Here we can see that g1 has an approximately straight line decay in the degree distribution -- as expected for scale-free distributions on log-log axes. Conversely, g2 does not have a scale-free degree distribution.
To say anything more formal, you could look at the toolboxes from Aaron Clauset: http://tuvalu.santafe.edu/~aaronc/powerlaws/ which implement model fitting and statistical testing of power-law distributions.