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

[Andrea Gavana]

import matplotlib.pyplot as plt?

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

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> Hi Dominik,
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> Thanks for the feedback. Ok, so I ran your code.
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> However, I'm getting an error which is highlighted below the code.  Hoping
> you can shed some light? Appreciate your help on this.
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> import matplotlib.patches as patches
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> fig,graph = plt.subplots(figsize=(6, 6))
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> # just a single subplots call at the beginning as you want it all on a
> single image
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> plt.xlabel('V1')
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> plt.ylabel('V2')
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> plt.title('Visualization of raw data');
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> plt.scatter(data.iloc[:, 0], data.iloc[:, 1])
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> plt.scatter(mean[0],mean[1])
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> # remove plt.figure(figsize=(6, 6)) here
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> graph.add_patch(ellipse)
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> plt.show()
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> **
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> Error is:
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> 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')
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> NameError: name 'plt' is not defined
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> ------------------------------
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> *From:* SciPy-Dev <scipy-dev-bounces+stephen_malcolm=
> hotmail.com at python.org> on behalf of Dominik Stańczak <
> stanczakdominik at gmail.com>
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> *Sent:* 01 October 2020 04:04
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> *To:* SciPy Developers List <scipy-dev at python.org>
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> *Subject:* Re: [SciPy-Dev] Issues Inserting Graphical Overlay Using
> Matplotlib Patches
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> Hey,
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> 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:
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> fig,graph = plt.subplots(figsize=(6, 6))
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> # just a single subplots call at the beginning as you want it all on a
> single image
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> plt.xlabel('V1')
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> plt.ylabel('V2')
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> plt.title('Visualization of raw data');
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> plt.scatter(data.iloc[:, 0], data.iloc[:, 1])
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> plt.scatter(mean[0],mean[1])
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> # remove plt.figure(figsize=(6, 6)) here
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> graph.add_patch(ellipse)
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> plt.show()
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> I expect that to work, or at least to head in the right direction :)
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> Cheers,
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> Dominik
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> On Wed, Sep 30, 2020, 19:55 Stephen Malcolm <stephen_malcolm at hotmail.com>
> wrote:
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> Hello All,
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> I'm having some trouble adding a graphical overlay i.e. an ellipse onto my
> plot.
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> 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.
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> Could you please let me know what code I'm missing/ or need to add, in
> order to insert this ellipse?
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> 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.
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> I have no errors, instead, I'm getting a separate graph (without data
> points or ellipse) below the plotted one.
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> Please find my code below:
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> #pandas used to read dataset and return the data
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> #numpy and matplotlib to represent and visualize the data
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> #sklearn to implement kmeans algorithm
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> import pandas as pd
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> import numpy as np
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> import matplotlib.pyplot as plt
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> from sklearn.cluster import KMeans
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> #import the data
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> data = pd.read_csv('banknotes.csv')
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> #extract values
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> x=data['V1']
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> y=data['V2']
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> #print range to determine normalization
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> print ("X_max : ",x.max())
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> print ("X_min : ",x.min())
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> print ("Y_max : ",y.max())
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> print ("Y_min : ",y.min())
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> #normalize values
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> mean_x=x.mean()
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> mean_y=y.mean()
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> max_x=x.max()
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> max_y=y.max()
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> min_x=x.min()
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> min_y=y.min()
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> for i in range(0,x.size):
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>     x[i] = (x[i] - mean_x) / (max_x - min_x)
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> for i in range(0,y.size):
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>     y[i] = (y[i] - mean_y) / (max_y - min_y)
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> #statistical analyis using mean and standard deviation
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> import matplotlib.patches as patches
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> mean = np.mean(data, 0)
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> std_dev = np.std(data, 0)
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> ellipse = patches.Ellipse([mean[0], mean [1]], std_dev[0]*2, std_dev[1]*2,
> alpha=0.25)
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> plt.xlabel('V1')
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> plt.ylabel('V2')
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> plt.title('Visualization of raw data');
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> plt.scatter(data.iloc[:, 0], data.iloc[:, 1])
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> plt.scatter(mean[0],mean[1])
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> plt.figure(figsize=(6, 6))
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> fig,graph = plt.subplots()
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> graph.add_patch(ellipse)
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> Kind Regards,
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> Stephen
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