Plotting

Plotting with Python

Matplotlib is a Python plotting library, which is inspired by the MATLAB plotting
functionality, so the commands used are similar to those used in MATLAB.
Pyplot is a shell like interface to Matplotlib to make it easier to use. It is a collection of
command style functions that make Matplotlib work like MATLAB plotting functionality.
The text talks about Pylab, which combines both the Pyplot and NumPy packages into
a single namespace, to make it easier to import.

Source: https://matplotlib.org/users/pyplot_tutorial.html

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 Note about Plotting with Spyder
Depending on the Spyder default settings, plots may appear in a figure window or
in the iPython console.
To open plots in a figure window, per session, you should type the command:
%matplotlib qt (resets when session ends)
To open plots in a figure window by default across sessions, go to:
Tools->Preferences, select iPython Console ->Graphics
then set Graphics Backend to Automatic

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 Plotting with pyplot
The pyplot package contains several commands used for creating and formatting plots in
Python.
Each pyplot function makes some change to a figure: e.g., creates a figure, creates a
plotting area in a figure, plots some lines in a plotting area, decorates the plot with labels.
In matplotlib.pyplot various states are preserved across function calls, so that it keeps
track of things like the current figure and plotting area, and the plotting functions are directed
to the current plot axes.
Pyplot summary: https://matplotlib.org/api/pyplot_summary.html

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Basic Plotting Functions
The plot function has different forms, depending on the input arguments.
If y is a list, plot(y) produces a piecewise graph of the elements of (y) versus the index
of the elements of (y).
Since Python ranges start with 0, the default x list has the same length as y but starts
with 0. Hence the x data are [0,1,2,3].
If you specify two lists as arguments, plot(x,y) produces a graph of y versus x.
Both lists must have the same number of elements

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 Creating plots with pyplot
plot() is a versatile command and will take
an arbitrary number of arguments.
For example, to plot x versus y, you can
issue the command:
plot([1, 2, 3, 4], [1, 4, 9, 16])

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 Creating plots with pyplot
For every x, y pair of arguments, there is an optional third argument which is the format
string that indicates the color and line type of the plot.
The letters and symbols of the format string are from MATLAB, and you concatenate a
color string with a line style string.
The default format string is ‘b-‘, which is a solid blue line. For example, to plot the above
with red circles, you would issue the command:
plot([1,2,3,4], [1,4,9,16], 'ro')

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Plotting Format Options
line color line marker line style
b blue . point - solid
g green o circle : dotted
r red x x-mark -. dashdot
c cyan + plus -- dashed
m magenta * star
y yellow s square
k black d diamond
v triangle (down)
^ triangle (up)
< triangle (left)
> triangle (right)
p pentagram
h hexagram

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Formatting Plots with pyplot
The result of a plot function call is not a finished product, since there are no titles,
axis labels, or grid lines on the plot.
The details can be added with the functions:
◦ title,
◦ xlabel,
◦ ylabel,
◦ grid
◦ legend
◦ axis
◦ etc…

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Formatting with pyplot – numpy arrays
from matplotlib.pyplot import *
from numpy import *
clf()
x = arange(1,11)
y = x**2

plot(x,y)
xlabel('x')
ylabel('y')
title('y is equal to x squared')
legend(['y = x**2'])

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Creating plots with pyplot - axis
from matplotlib.pyplot import *

#clears the current figure window

clf()

#creates the plot with x, y values red

circle markers
plot([1,2,3,4], [1,4,9,16], 'ro')

#changes the limits of the x and y axis

#[xmin, xmax, ymin, ymax]
axis([0, 6, 0, 20])

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Displaying Multiple Plots in One
Figure

subplot(m,n,p)
This splits the figure window into an m-by-n matrix of small subplots and selects the pth
subplot for the current plot.

For example, the command subplot(3,2,1) creates six

areas arranged in three rows and two columns as shown, and
makes the upper left subplot current.

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Plotting: Subplots
clf()
x = arange(1,11)
y = x**2
subplot(2,1,1)
plot(x,y,'r:*')
xlabel('x')
ylabel('y')
title('y is equal to x squared')
legend(['y = x**2'])
subplot(2,1,2)
plot(x,y,'k-.>')
xlabel('x')
ylabel('y')
title('y is equal to x squared')
legend(['y = x**2'])
grid('on')
grid('off')
See:11_plot5.py

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Question:
Write a script to initialize two numpy arrays, max_temp (with random integers between 1 and 45] and
min_temp (with random integers between -20 and 20] for the maximum temperatures and minimum
temperatures of all months in a year, respectively.
Calculate the absolute temperature differences for each month (difference between maximum and
minimum temperatures) and store in numpy array, diff_temp.
Find the average temperature (average) of the diff_temp array
Display the month numbers of those months whose temperature difference is more than average
Plot the maximum and minimum temperatures in the first chart and the temperature differences in the
second chart as given below. Put the titles and axis labels of the charts as below.
Arrange the axis limits appropriately (x axis will have the bounds: the month numbers in both charts and
y axis will have the bounds: the maximum value of maximum temperatures list and the minimum value
of the minimum temperatures list, in the first chart and the maximum value of temperature differences
and the minimum value of the temperature differences in the second chart.
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 Output:
Plot:

Sample Output:
[43, 34, 15, 1, 36, 3, 26, 33, 38, 20, 4, 45]
[-19, 20, -13, 16, -20, 15, -9, -14, 15, -20, -10, 9]
Monthly differences: [62, 14, 28, 15, 56, 12, 35, 47, 23, 40, 14, 36]
Average difference: 31.833333333333332
Months with difference above average:
[1 5 7 8 10 12]
See: 11_plotQuestion.py

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Pie Charts
from matplotlib.pyplot import *

clf()

# Pie chart,slices will be ordered,

# plotted counter-clockwise:

labels = 'Frogs', 'Hogs', 'Dogs', ‘Cats'

sizes = [15, 30, 45, 10]

# only "explode" the 2nd slice(i.e. 'Hogs')

explode = (0, 0.1, 0, 0)

pie(sizes, explode=explode,
labels=labels,autopct='%1.1f%%')

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Bar Charts
from matplotlib.pyplot import *
from numpy import *

clf()
n_groups = 5
index = arange(n_groups)

means_men = (20, 35, 30, 35, 27)

means_women = (25, 32, 34, 20, 25)

bar_width = 0.25
bar(index,means_men, bar_width,align='edge')
bar(index,means_women, -bar_width,align='edge')

xlabel('Group')
ylabel('Scores')
title('Scores by group and gender')
legend(['Men', 'Women'])
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Histogram
Often you want to get an understanding of the distribution of certain numerical variables within it
when exploring a dataset.
One way of visualizing the distribution of a single numerical variable is by using a histogram.
A histogram divides the values within a numerical variable into “bins” and counts the number of
observations that fall into each bin.
By visualizing these binned counts in a columnar fashion, we can obtain an understanding of the
distribution of values within a variable.
A histogram can only be used to plot numerical values and it is usually used for large data sets. It is
useful for detecting outliers and/or gaps in the data set.

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 Histogram – Creating Manually
Example: We want to construct a histogram of the following scores in a math exam where the maximum possible mark is 20.
Scores:
[2, 4, 14, 14, 16, 17, 13, 16, 7,2, 4, 14, 14, 16, 17, 13, 16, 7,8, 9, 10, 11, 19, 18,
15, 15, 16,8, 9, 10, 11, 19, 18, 15, 15, 16,13, 12, 7, 8, 9, 12, 11, 18]

1. First order the data to make it easier to group.

[2, 2, 4, 4, 7, 7, 7, 8, 8, 8, 9, 9, 9, 10, 10, 11, 11, 11, 12, 12, 13, 13, 13, 14, 14, 14,
14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 17, 17, 18, 18, 18, 19, 19]

1. Next, look at the data and find the minimum and maximum values to choose the width of each ‘bucket’. The minimum is 2
and the maximum is 19. Let’s choose a width of 4. So there will be 5 buckets: [2-5.4), [5.4-8.8), [8.8 - 12.2), [12.2-15.6),
[15.6-19].

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Histogram – Creating Manually
3) Next, calculate the number of each values in 4) Finally, create a histogram that displays
each bucket. the frequency data.

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Histogram – Example with Scores

See: 11_histogram_scores.py

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Additional Details:
For more information about plotting in Python:
https://matplotlib.org/api/pyplot_summary.html

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Question 1:
Plot the function y=3x3 – 26x + 10, and first and second derivatives, for -2<=x<=4,
(increment by 0.1) all in the same plot.

See: 11_Q1.py

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Question 2:
Make two separate plots on the same figure window for the function
f(x)= (x-3)(x+2)(4x-0.75)-e1/2/2,
one plot for -2<=x<=1 and one for -4<=x<=4 (increment by 0.1).

See: 11_Q2.py

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Steps to Understanding Experimental Data

Conduct an experiment to gather data

Physical(e.g.), in a biology lab
Social(e.g. questionnaires)
Use theory to generate some questions
Design a computation to help answer questions about the data.

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Example - Springs
When springs are compressed or stretched by some force, they store
energy.
When the force is no longer applied they release the stored energy.
Imagine an experiment where a weight is hung from the bottom of a
spring, stretching the spring.
The data we obtain is the difference between the un-stretched and
the stretched spring length vs. the mass applied to the spring.

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Hooke’s Law
The theory that we are going to use to analyse the data is Hooke’s law of
elasticity.
The force F stored in a spring is linearly related to the distance the spring is
compressed/stretched.

Holds for a variety of materials and systems but does not hold for very large force.

All springs have an elastic limit beyond which they cannot be stretched.

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Hooke’s Law
The formula is:
F = -kx
F: represents the force
x: is the stretched distance
k: is the spring constant If the spring is stiff k is large, if the spring is weak, k is small.
Force: (mass * gravity)
F = m * 9.81
Spring constant(k):
k = -(m*g)/ x -> (Newtons/meter)

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Data:
Distance (m) Mass (kg)
0.0865 0.1
0.1015 0.15
0.1106 0.2
0.1279 0.25
0.1892 0.3
0.2695 0.35
0.2888 0.4
0.2425 0.45
0.3465 0.5
0.3225 0.55
0.3764 0.6
0.4263 0.65
0.4562 0.7

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The Program:
⮚The following function read distance and mass data from a text into two lists, and returns the
lists containing the data.

import pylab
def getData(filename):
dataFile = open(filename, 'r')
distances = []
masses = []
dataFile.readline()
for line in dataFile:
d,m = line.split(' ')
distances.append(float(d))
masses.append(float(m))
dataFile.close()
return(masses, distances)

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Plotting the Data:
The following function gets the experimental data from the file, calculates the force from the data,
and produces a plot of the data.

def plotData(inputfile):
masses, distances = getData(inputfile)
forces = []
for m in masses:
#9.81 represents gravitational force
forces.append(m * 9.81)
pylab.plot(forces, distances, 'ro')
pylab.title('Measured Displacement of Spring')
pylab.xlabel('Force(newtons)')
pylab.ylabel('Distance(meters)')

plotData('11_springData.txt')

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The Plot:
The plot shown is not what Hooke’s law predicts.
Hooke’s law tells us that the distance should increase linearly with the mass. I.e. the
points should lie on a straight line.

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Experimental Error
When we take real measurements, the experimental data are rarely a perfect match
for the theory.

Measurement error is to be expected, so we should expect the points to lie around a

line rather than on a line.

It would be nice to have a line that represents our best guess of where the points would
have been if we had no measurement error.

The usual way to do this is to fit a line to the data, called linear interpolation.

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Fitting the Data
Fitting analytical curves to experimental data is a common task in engineering.
To fit a curve, linear regression is used.
The function used in linear regression is the least squares function.

Let observed and predicted be vectors of equal length where observed contains the
measured points and predicted the corresponding data points on the proposed fit.

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polyfit function
Pylab/NumPy provide built-in functions to find a polynomial fit for the data points.
np.polyfit(observedX, observedY, n )

Finds coefficients of a polynomial of degree n, that provides a best least squares fit
for the observed data.
▪ n = 1 -> best line y = ax + b
▪ n = 2 -> best parabola y = ax2 + bx + c

Polyfit returns coefficients a,b for a polynomial with degree of 1. We can find
the predicted distances using these values.

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Fitting the Data with polyfit
The program below fits the data using the polyfit function and plots both the measured points and
the linear model.

def fitData(inputfile):
masses, distances = getData(inputfile)
forces = []
for m in masses:
#9.81 represents gravitational force
forces.append(m * 9.81) plot(forces, distances, 'ro',label = 'Measured Displacements')
title('Measured Displacement of Spring')
xlabel('|Force|(newtons)')
ylabel('Distance(meters)')

#find linear fit

a,b = polyfit(forces, distances, 1)
predictedDistances = []
for f in forces:
predictedDistances.append(a*f+b)

plot(forces, predictedDistances,
label = 'Displacements predicted by '\
'linear fit')
legend(loc = 'best')

fitData('11_springData.txt')

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The Plot:

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Polyval Function (NumPy package)
polyval(p,x) evaluates the polynomial p at each point in x. p is a vector of length n+1
whose elements are the coefficients of an nth degree polynomial.

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polyval
def fitData(inputfile):
masses, distances = getData(inputfile)
forces = []
for m in masses:
#9.81 represents gforce
forces.append(m * 9.81)
plot(forces, distances, 'ro',label = 'Measured Displacements')
title('Measured Displacement of Spring')
xlabel('|Force|(newtons)')
ylabel('Distance(meters)')

#find linear fit using polyfit/polyval

fit = polyfit(forces, distances, 1)
predictedDistances = polyval(fit, forces)

plot(forces, predictedDistances,
label = 'Displacements predicted by '\
'linear fit')
legend(loc = 'best')

clf()
fitData('11_springData.txt')

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Terms of Use
⮚ This presentation was adapted from lecture materials provided in MIT Introduction to
Computer Science and Programming in Python.
⮚ Licenced under terms of Creative Commons License.

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