[SciPy-Dev] Issues Inserting Graphical Overlay Using Matplotlib Patches

Thu Oct 1 09:19:07 EDT 2020

Hello All,

For your information, I managed to rectify the code to incorporate my ellipse onto one plot.  I used some of Dominick's suggestions, but I also moved the 'fig,graph = plt.subplots(figsize=(6,6))' line just below the ellipse syntax i.e. 'ellipse = patches.Ellipse([mean[0], mean [1]], std_dev[0]*2, std_dev[1]*2, alpha=0.25)'. This had made all the difference.

Thanks for all your input.

#statistical analysis using mean and standard deviation

import matplotlib.patches as patches

mean = np.mean(data, 0)
std_dev = np.std(data, 0)

ellipse = patches.Ellipse([mean[0], mean [1]], std_dev[0]*2, std_dev[1]*2, alpha=0.25)

fig,graph = plt.subplots(figsize=(6,6))
graph.scatter(data.iloc[:, 0], data.iloc[:, 1])
graph.scatter(mean[0],mean[1])

plt.xlabel('V1')
plt.ylabel('V2')
plt.title('Visualization of raw data');

graph.add_patch(ellipse)
________________________________
From: SciPy-Dev <scipy-dev-bounces+stephen_malcolm=hotmail.com at python.org> on behalf of Andrea Gavana <andrea.gavana at gmail.com>
Sent: 01 October 2020 10:42
To: SciPy Developers List <scipy-dev at python.org>
Subject: Re: [SciPy-Dev] Issues Inserting Graphical Overlay Using Matplotlib Patches

import matplotlib.pyplot as plt?

On Thu, 1 Oct 2020 at 11.49, Stephen Malcolm <stephen_malcolm at hotmail.com<mailto:stephen_malcolm at hotmail.com>> wrote:

Hi Dominik,

Thanks for the feedback. Ok, so I ran your code.

However, I'm getting an error which is highlighted below the code.  Hoping you can shed some light? Appreciate your help on this.

import matplotlib.patches as patches

fig,graph = plt.subplots(figsize=(6, 6))

# just a single subplots call at the beginning as you want it all on a single image

plt.xlabel('V1')

plt.ylabel('V2')

plt.title('Visualization of raw data');

plt.scatter(data.iloc[:, 0], data.iloc[:, 1])

plt.scatter(mean[0],mean[1])

# remove plt.figure(figsize=(6, 6)) here

graph.add_patch(ellipse)

plt.show()

**

Error is:

NameError                                 Traceback (most recent call last)
<ipython-input-4-bd49ad8e0a12> in <module>()
      3 import matplotlib.patches as patches
      4
----> 5 fig,graph = plt.subplots(figsize = (6, 6))
      6 # just a single subplots call at the beginning as you want it all on a single image
      7 plt.xlabel('V1')

NameError: name 'plt' is not defined

________________________________

From: SciPy-Dev <scipy-dev-bounces+stephen_malcolm=hotmail.com at python.org<mailto:hotmail.com at python.org>> on behalf of Dominik Stańczak <stanczakdominik at gmail.com<mailto:stanczakdominik at gmail.com>>

Sent: 01 October 2020 04:04

To: SciPy Developers List <scipy-dev at python.org<mailto:scipy-dev at python.org>>

Subject: Re: [SciPy-Dev] Issues Inserting Graphical Overlay Using Matplotlib Patches

Hey,

Subplots already includes a call to figure, which creates a new active graph as you put it. This is the empty one that pops out. I'd do this:

fig,graph = plt.subplots(figsize=(6, 6))

# just a single subplots call at the beginning as you want it all on a single image

plt.xlabel('V1')

plt.ylabel('V2')

plt.title('Visualization of raw data');

plt.scatter(data.iloc[:, 0], data.iloc[:, 1])

plt.scatter(mean[0],mean[1])

# remove plt.figure(figsize=(6, 6)) here

graph.add_patch(ellipse)

plt.show()

I expect that to work, or at least to head in the right direction :)

Cheers,

Dominik

On Wed, Sep 30, 2020, 19:55 Stephen Malcolm <stephen_malcolm at hotmail.com<mailto:stephen_malcolm at hotmail.com>> wrote:

Hello All,

I'm having some trouble adding a graphical overlay i.e. an ellipse onto my plot.

I wish to do this, as I need to explain/ portray the mean, standard deviation and outliers. And hence evaluate the suitability of the dataset.

Could you please let me know what code I'm missing/ or need to add, in order to insert this ellipse?

I have no trouble plotting the data points and the mean using this code, however, the ellipse (width and height/ standard deviation) doesn't appear.

I have no errors, instead, I'm getting a separate graph (without data points or ellipse) below the plotted one.

Please find my code below:

#pandas used to read dataset and return the data

#numpy and matplotlib to represent and visualize the data

#sklearn to implement kmeans algorithm

import pandas as pd

import numpy as np

import matplotlib.pyplot as plt

from sklearn.cluster import KMeans

#import the data

data = pd.read_csv('banknotes.csv')

#extract values

x=data['V1']

y=data['V2']

#print range to determine normalization

print ("X_max : ",x.max())

print ("X_min : ",x.min())

print ("Y_max : ",y.max())

print ("Y_min : ",y.min())

#normalize values

mean_x=x.mean()

mean_y=y.mean()

max_x=x.max()

max_y=y.max()

min_x=x.min()

min_y=y.min()

for i in range(0,x.size):

    x[i] = (x[i] - mean_x) / (max_x - min_x)

for i in range(0,y.size):

    y[i] = (y[i] - mean_y) / (max_y - min_y)

#statistical analyis using mean and standard deviation

import matplotlib.patches as patches

mean = np.mean(data, 0)

std_dev = np.std(data, 0)

ellipse = patches.Ellipse([mean[0], mean [1]], std_dev[0]*2, std_dev[1]*2, alpha=0.25)

plt.xlabel('V1')

plt.ylabel('V2')

plt.title('Visualization of raw data');

plt.scatter(data.iloc[:, 0], data.iloc[:, 1])

plt.scatter(mean[0],mean[1])

plt.figure(figsize=(6, 6))

fig,graph = plt.subplots()

graph.add_patch(ellipse)

Kind Regards,

Stephen

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