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Extensive Analysis + Visualization with Python

Hello friends,

Heart disease or Cardiovascular disease (CVD) is a class of diseases that involve the heart or blood vessels. Cardiovascular diseases are the
leading cause of death globally. This is true in all areas of the world except Africa. Together CVD resulted in 17.9 million deaths (32.1%) in
2015. Deaths, at a given age, from CVD are more common and have been increasing in much of the developing world, while rates have
declined in most of the developed world since the 1970s.

So, in this kernel, I have conducted Exploratory Data Analysis or EDA of the heart disease dataset. Exploratory Data Analysis or EDA is a
critical first step in analyzing a new dataset. The primary objective of EDA is to analyze the data for distribution, outliers and anomalies in the
dataset. It enable us to direct specific testing of the hypothesis. It includes analysing the data to find the distribution of data, its main
characteristics, identifying patterns and visualizations. It also provides tools for hypothesis generation by visualizing and understanding the
data through graphical representation.

I hope you learn and enjoy this kernel.

So, your upvote would be highly appreciated.

Table of Contents
The table of contents for this project are as follows: -

1. Introduction to EDA
2. Objectives of EDA
3. Types of EDA
4. Import libraries
5. Import dataset
6. Exploratory data analysis

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Check shape of the dataset

Preview the dataset
Summary of dataset
Dataset description
Check data types of columns
Important points about dataset
Statistical properties of dataset
View column names
7. Univariate analysis
Analysis of target feature variable
Findings of univariate analysis
8. Bivariate analysis
Estimate correlation coefficients
Analysis of target and cp variable
Analysis of target and thalach variable
Findings of bivariate analysis
9. Multivariate analysis
Heat Map
Pair Plot
10. Dealing with missing values
Pandas isnull() and notnull() functions
Useful commands to detect missing values
11. Check with ASSERT statement
12. Outlier detection
13. Conclusion
14. References

1. Introduction to EDA
Back to Table of Contents

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Several questions come to mind when we come across a new dataset. The below list shed light on some of these questions:-

• What is the distribution of the dataset?

• Are there any missing numerical values, outliers or anomalies in the dataset?

• What are the underlying assumptions in the dataset?

• Whether there exists relationships between variables in the dataset?

• How to be sure that our dataset is ready for input in a machine learning algorithm?

• How to select the most suitable algorithm for a given dataset?

So, how do we get answer to the above questions?

The answer is Exploratory Data Analysis. It enable us to answer all of the above questions.

2. Objectives of EDA
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The objectives of the EDA are as follows:-

i. To get an overview of the distribution of the dataset.

ii. Check for missing numerical values, outliers or other anomalies in the dataset.

iii.Discover patterns and relationships between variables in the dataset.

iv. Check the underlying assumptions in the dataset.

3. Types of EDA
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EDA is generally cross-classified in two ways. First, each method is either non-graphical or graphical. Second, each method is either univariate
or multivariate (usually bivariate). The non-graphical methods provide insight into the characteristics and the distribution of the variable(s) of
interest. So, non-graphical methods involve calculation of summary statistics while graphical methods include summarizing the data
diagrammatically.

There are four types of exploratory data analysis (EDA) based on the above cross-classification methods. Each of these types of EDA are
described below:-

i. Univariate non-graphical EDA

The objective of the univariate non-graphical EDA is to understand the sample distribution and also to make some initial conclusions about
population distributions. Outlier detection is also a part of this analysis.

ii. Multivariate non-graphical EDA

Multivariate non-graphical EDA techniques show the relationship between two or more variables in the form of either cross-tabulation or
statistics.

iii. Univariate graphical EDA

In addition to finding the various sample statistics of univariate distribution (discussed above), we also look graphically at the distribution of
the sample. The non-graphical methods are quantitative and objective. They do not give full picture of the data. Hence, we need graphical
methods, which are more qualitative in nature and presents an overview of the data.

iv. Multivariate graphical EDA

There are several useful multivariate graphical EDA techniques, which are used to look at the distribution of multivariate data. These are as
follows:-

Side-by-Side Boxplots

Scatterplots

Heat Maps and 3-D Surface Plots

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Enough of theory, now let the journey begin.

The first step in the EDA journey is to import the libraries.

4. Import libraries
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In [1]: # This Python 3 environment comes with many helpful analytics libraries installed
# It is defined by the kaggle/python docker image: https://github.com/kaggle/docker-python
# For example, here's several helpful packages to load in

import numpy as np # linear algebra

import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)

# Input data files are available in the "../input/" directory.

# For example, running this (by clicking run or pressing Shift+Enter) will list all files under the input directory

import os
for dirname, _, filenames in os.walk('/kaggle/input'):
for filename in filenames:
print(os.path.join(dirname, filename))

# Any results you write to the current directory are saved as output.

We can see that the input folder contains one input file named heart.csv .

In [2]: import seaborn as sns

import matplotlib.pyplot as plt
import scipy.stats as st
%matplotlib inline

sns.set(style="whitegrid")

In [3]: # ignore warnings

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import warnings
warnings.filterwarnings('ignore')

I have imported the libraries. The next step is to import the datasets.

5. Import dataset
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I will import the dataset with the usual pandas read_csv() function which is used to import CSV (Comma Separated Value) files.

In [4]: df = pd.read_csv(r"D:\Data Analytics Nit\25th - Seaborn, Eda Practicle\EDA- HEALTHCARE DOMAIN\heart.csv")

6. Exploratory Data Analysis

Back to Table of Contents

The scene has been set up. Now let the actual fun begin.

Check shape of the dataset

It is a good idea to first check the shape of the dataset.

In [5]: # print the shape

print('The shape of the dataset : ', df.shape)

The shape of the dataset : (303, 14)

Now, we can see that the dataset contains 303 instances and 14 variables.

Preview the dataset

In [6]: # preview dataset

df.head()

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Out[6]: age sex cp trestbps chol fbs restecg thalach exang oldpeak slope ca thal target

0 63 1 3 145 233 1 0 150 0 2.3 0 0 1 1

1 37 1 2 130 250 0 1 187 0 3.5 0 0 2 1

2 41 0 1 130 204 0 0 172 0 1.4 2 0 2 1

3 56 1 1 120 236 0 1 178 0 0.8 2 0 2 1

4 57 0 0 120 354 0 1 163 1 0.6 2 0 2 1

Summary of dataset

In [7]: # summary of dataset

df.info()

<class 'pandas.core.frame.DataFrame'>
RangeIndex: 303 entries, 0 to 302
Data columns (total 14 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 age 303 non-null int64
1 sex 303 non-null int64
2 cp 303 non-null int64
3 trestbps 303 non-null int64
4 chol 303 non-null int64
5 fbs 303 non-null int64
6 restecg 303 non-null int64
7 thalach 303 non-null int64
8 exang 303 non-null int64
9 oldpeak 303 non-null float64
10 slope 303 non-null int64
11 ca 303 non-null int64
12 thal 303 non-null int64
13 target 303 non-null int64
dtypes: float64(1), int64(13)
memory usage: 33.3 KB

Dataset description
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The dataset contains several columns which are as follows -

age : age in years

sex : (1 = male; 0 = female)
cp : chest pain type
trestbps : resting blood pressure (in mm Hg on admission to the hospital)
chol : serum cholestoral in mg/dl
fbs : (fasting blood sugar > 120 mg/dl) (1 = true; 0 = false)
restecg : resting electrocardiographic results
thalach : maximum heart rate achieved
exang : exercise induced angina (1 = yes; 0 = no)
oldpeak : ST depression induced by exercise relative to rest
slope : the slope of the peak exercise ST segment
ca : number of major vessels (0-3) colored by flourosopy
thal : 3 = normal; 6 = fixed defect; 7 = reversable defect
target : 1 or 0

Check the data types of columns

The above df.info() command gives us the number of filled values along with the data types of columns.

If we simply want to check the data type of a particular column, we can use the following command.

In [8]: df.dtypes

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Out[8]: age int64

sex int64
cp int64
trestbps int64
chol int64
fbs int64
restecg int64
thalach int64
exang int64
oldpeak float64
slope int64
ca int64
thal int64
target int64
dtype: object

Important points about dataset

sex is a character variable. Its data type should be object. But it is encoded as (1 = male; 0 = female). So, its data type is given as int64.

Same is the case with several other variables - fbs , exang and target .

fbs (fasting blood sugar) should be a character variable as it contains only 0 and 1 as values (1 = true; 0 = false). As it contains
only 0 and 1 as values, so its data type is given as int64.

exang (exercise induced angina) should also be a character variable as it contains only 0 and 1 as values (1 = yes; 0 = no). It also
contains only 0 and 1 as values, so its data type is given as int64.

target should also be a character variable. But, it also contains 0 and 1 as values. So, its data type is given as int64.

Statistical properties of dataset

In [9]: # statistical properties of dataset

df.describe()

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Out[9]: age sex cp trestbps chol fbs restecg thalach exang oldpeak slope

count 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000 303.000000

mean 54.366337 0.683168 0.966997 131.623762 246.264026 0.148515 0.528053 149.646865 0.326733 1.039604 1.399340

std 9.082101 0.466011 1.032052 17.538143 51.830751 0.356198 0.525860 22.905161 0.469794 1.161075 0.616226

min 29.000000 0.000000 0.000000 94.000000 126.000000 0.000000 0.000000 71.000000 0.000000 0.000000 0.000000

25% 47.500000 0.000000 0.000000 120.000000 211.000000 0.000000 0.000000 133.500000 0.000000 0.000000 1.000000

50% 55.000000 1.000000 1.000000 130.000000 240.000000 0.000000 1.000000 153.000000 0.000000 0.800000 1.000000

75% 61.000000 1.000000 2.000000 140.000000 274.500000 0.000000 1.000000 166.000000 1.000000 1.600000 2.000000

max 77.000000 1.000000 3.000000 200.000000 564.000000 1.000000 2.000000 202.000000 1.000000 6.200000 2.000000

Important points to note

The above command df.describe() helps us to view the statistical properties of numerical variables. It excludes character variables.

If we want to view the statistical properties of character variables, we should run the following command -

df.describe(include=['object'])

If we want to view the statistical properties of all the variables, we should run the following command -

df.describe(include='all')

View column names

In [10]: df.columns

Out[10]: Index(['age', 'sex', 'cp', 'trestbps', 'chol', 'fbs', 'restecg', 'thalach',

'exang', 'oldpeak', 'slope', 'ca', 'thal', 'target'],
dtype='object')

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7. Univariate analysis
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Analysis of target feature variable

Our feature variable of interest is target .

It refers to the presence of heart disease in the patient.

It is integer valued as it contains two integers 0 and 1 - (0 stands for absence of heart disease and 1 for presence of heart disease).

So, in this section, I will analyze the target variable.

Check the number of unique values in target variable

In [11]: df['target'].nunique()

Out[11]: 2

We can see that there are 2 unique values in the target variable.

View the unique values in target variable

In [12]: df['target'].unique()

Out[12]: array([1, 0], dtype=int64)

Comment
So, the unique values are 1 and 0. (1 stands for presence of heart disease and 0 for absence of hear disease).

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Frequency distribution of target variable

In [13]: df['target'].value_counts()

Out[13]: target
1 165
0 138
Name: count, dtype: int64

Comment
1 stands for presence of heart disease. So, there are 165 patients suffering from heart disease.

Similarly, 0 stands for absence of heart disease. So, there are 138 patients who do not have any heart disease.

We can visualize this information below.

Visualize frequency distribution of target variable

In [14]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="target", data=df)
plt.show()

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Interpretation
The above plot confirms the findings that -

There are 165 patients suffering from heart disease, and

There are 138 patients who do not have any heart disease.

Frequency distribution of target variable wrt sex

In [15]: df.groupby('sex')['target'].value_counts()

Out[15]: sex target

0 1 72
0 24
1 0 114
1 93
Name: count, dtype: int64

Comment
sex variable contains two integer values 1 and 0 : (1 = male; 0 = female).

target variable also contains two integer values 1 and 0 : (1 = Presence of heart disease; 0 = Absence of heart disease)

So, out of 96 females - 72 have heart disease and 24 do not have heart disease.

Similarly, out of 207 males - 93 have heart disease and 114 do not have heart disease.

We can visualize this information below.

We can visualize the value counts of the sex variable wrt target as follows -

In [20]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="sex", hue="target", data=df)

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plt.show()

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---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[20], line 2
1 f, ax = plt.subplots(figsize=(8, 6))
----> 2 ax = sns.countplot(x="sex", hue="target", data=df)
3 plt.show()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:2955, in countplot(data, x, y, hue, order, hue_order, orient, color,

palette, saturation, width, dodge, ax, **kwargs)
2952 if ax is None:
2953 ax = plt.gca()
-> 2955 plotter.plot(ax, kwargs)
2956 return ax

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:1587, in _BarPlotter.plot(self, ax, bar_kws)

1585 """Make the plot."""
1586 self.draw_bars(ax, bar_kws)
-> 1587 self.annotate_axes(ax)
1588 if self.orient == "h":
1589 ax.invert_yaxis()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:767, in _CategoricalPlotter.annotate_axes(self, ax)

764 ax.set_ylim(-.5, len(self.plot_data) - .5, auto=None)
766 if self.hue_names is not None:
--> 767 ax.legend(loc="best", title=self.hue_title)

File ~\anaconda3\Lib\site-packages\matplotlib\axes\_axes.py:322, in Axes.legend(self, *args, **kwargs)

204 @_docstring.dedent_interpd
205 def legend(self, *args, **kwargs):
206 """
207 Place a legend on the Axes.
208
(...)
320 .. plot:: gallery/text_labels_and_annotations/legend.py
321 """
--> 322 handles, labels, kwargs = mlegend._parse_legend_args([self], *args, **kwargs)
323 self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
324 self.legend_._remove_method = self._remove_legend

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1361, in _parse_legend_args(axs, handles, labels, *args, **kwargs)

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1357 handles = [handle for handle, label

1358 in zip(_get_legend_handles(axs, handlers), labels)]
1360 elif len(args) == 0: # 0 args: automatically detect labels and handles.
-> 1361 handles, labels = _get_legend_handles_labels(axs, handlers)
1362 if not handles:
1363 log.warning(
1364 "No artists with labels found to put in legend. Note that "
1365 "artists whose label start with an underscore are ignored "
1366 "when legend() is called with no argument.")

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1291, in _get_legend_handles_labels(axs, legend_handler_map)

1289 for handle in _get_legend_handles(axs, legend_handler_map):
1290 label = handle.get_label()
-> 1291 if label and not label.startswith('_'):
1292 handles.append(handle)
1293 labels.append(label)

AttributeError: 'numpy.int64' object has no attribute 'startswith'

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Interpretation
We can see that the values of target variable are plotted wrt sex : (1 = male; 0 = female).

target variable also contains two integer values 1 and 0 : (1 = Presence of heart disease; 0 = Absence of heart disease)

The above plot confirms our findings that -

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Out of 96 females - 72 have heart disease and 24 do not have heart disease.

Similarly, out of 207 males - 93 have heart disease and 114 do not have heart disease.

Alternatively, we can visualize the same information as follows :

In [21]: ax = sns.catplot(x="target", col="sex", data=df, kind="count", height=5, aspect=1)

Comment
The above plot segregate the values of target variable and plot on two different columns labelled as (sex = 0, sex = 1).

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I think it is more convinient way of interpret the plots.

We can plot the bars horizontally as follows :

In [22]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(y="target", hue="sex", data=df)
plt.show()

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---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[22], line 2
1 f, ax = plt.subplots(figsize=(8, 6))
----> 2 ax = sns.countplot(y="target", hue="sex", data=df)
3 plt.show()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:2955, in countplot(data, x, y, hue, order, hue_order, orient, color,

palette, saturation, width, dodge, ax, **kwargs)
2952 if ax is None:
2953 ax = plt.gca()
-> 2955 plotter.plot(ax, kwargs)
2956 return ax

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:1587, in _BarPlotter.plot(self, ax, bar_kws)

1585 """Make the plot."""
1586 self.draw_bars(ax, bar_kws)
-> 1587 self.annotate_axes(ax)
1588 if self.orient == "h":
1589 ax.invert_yaxis()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:767, in _CategoricalPlotter.annotate_axes(self, ax)

764 ax.set_ylim(-.5, len(self.plot_data) - .5, auto=None)
766 if self.hue_names is not None:
--> 767 ax.legend(loc="best", title=self.hue_title)

File ~\anaconda3\Lib\site-packages\matplotlib\axes\_axes.py:322, in Axes.legend(self, *args, **kwargs)

204 @_docstring.dedent_interpd
205 def legend(self, *args, **kwargs):
206 """
207 Place a legend on the Axes.
208
(...)
320 .. plot:: gallery/text_labels_and_annotations/legend.py
321 """
--> 322 handles, labels, kwargs = mlegend._parse_legend_args([self], *args, **kwargs)
323 self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
324 self.legend_._remove_method = self._remove_legend

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1361, in _parse_legend_args(axs, handles, labels, *args, **kwargs)

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1357 handles = [handle for handle, label

1358 in zip(_get_legend_handles(axs, handlers), labels)]
1360 elif len(args) == 0: # 0 args: automatically detect labels and handles.
-> 1361 handles, labels = _get_legend_handles_labels(axs, handlers)
1362 if not handles:
1363 log.warning(
1364 "No artists with labels found to put in legend. Note that "
1365 "artists whose label start with an underscore are ignored "
1366 "when legend() is called with no argument.")

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1291, in _get_legend_handles_labels(axs, legend_handler_map)

1289 for handle in _get_legend_handles(axs, legend_handler_map):
1290 label = handle.get_label()
-> 1291 if label and not label.startswith('_'):
1292 handles.append(handle)
1293 labels.append(label)

AttributeError: 'numpy.int64' object has no attribute 'startswith'

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We can use a different color palette as follows :

In [23]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="target", data=df, palette="Set3")
plt.show()

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We can use plt.bar keyword arguments for a different look :

In [24]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="target", data=df, facecolor=(0, 0, 0, 0), linewidth=5, edgecolor=sns.color_palette("dark", 3))
plt.show()

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Comment
I have visualize the target values distribution wrt sex .

We can follow the same principles and visualize the target values distribution wrt fbs (fasting blood sugar) and exang
(exercise induced angina) .

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In [25]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="target", hue="fbs", data=df)
plt.show()

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---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[25], line 2
1 f, ax = plt.subplots(figsize=(8, 6))
----> 2 ax = sns.countplot(x="target", hue="fbs", data=df)
3 plt.show()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:2955, in countplot(data, x, y, hue, order, hue_order, orient, color,

palette, saturation, width, dodge, ax, **kwargs)
2952 if ax is None:
2953 ax = plt.gca()
-> 2955 plotter.plot(ax, kwargs)
2956 return ax

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:1587, in _BarPlotter.plot(self, ax, bar_kws)

1585 """Make the plot."""
1586 self.draw_bars(ax, bar_kws)
-> 1587 self.annotate_axes(ax)
1588 if self.orient == "h":
1589 ax.invert_yaxis()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:767, in _CategoricalPlotter.annotate_axes(self, ax)

764 ax.set_ylim(-.5, len(self.plot_data) - .5, auto=None)
766 if self.hue_names is not None:
--> 767 ax.legend(loc="best", title=self.hue_title)

File ~\anaconda3\Lib\site-packages\matplotlib\axes\_axes.py:322, in Axes.legend(self, *args, **kwargs)

204 @_docstring.dedent_interpd
205 def legend(self, *args, **kwargs):
206 """
207 Place a legend on the Axes.
208
(...)
320 .. plot:: gallery/text_labels_and_annotations/legend.py
321 """
--> 322 handles, labels, kwargs = mlegend._parse_legend_args([self], *args, **kwargs)
323 self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
324 self.legend_._remove_method = self._remove_legend

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1361, in _parse_legend_args(axs, handles, labels, *args, **kwargs)

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1357 handles = [handle for handle, label

1358 in zip(_get_legend_handles(axs, handlers), labels)]
1360 elif len(args) == 0: # 0 args: automatically detect labels and handles.
-> 1361 handles, labels = _get_legend_handles_labels(axs, handlers)
1362 if not handles:
1363 log.warning(
1364 "No artists with labels found to put in legend. Note that "
1365 "artists whose label start with an underscore are ignored "
1366 "when legend() is called with no argument.")

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1291, in _get_legend_handles_labels(axs, legend_handler_map)

1289 for handle in _get_legend_handles(axs, legend_handler_map):
1290 label = handle.get_label()
-> 1291 if label and not label.startswith('_'):
1292 handles.append(handle)
1293 labels.append(label)

AttributeError: 'numpy.int64' object has no attribute 'startswith'

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In [26]: f, ax = plt.subplots(figsize=(8, 6))

ax = sns.countplot(x="target", hue="exang", data=df)
plt.show()

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---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[26], line 2
1 f, ax = plt.subplots(figsize=(8, 6))
----> 2 ax = sns.countplot(x="target", hue="exang", data=df)
3 plt.show()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:2955, in countplot(data, x, y, hue, order, hue_order, orient, color,

palette, saturation, width, dodge, ax, **kwargs)
2952 if ax is None:
2953 ax = plt.gca()
-> 2955 plotter.plot(ax, kwargs)
2956 return ax

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:1587, in _BarPlotter.plot(self, ax, bar_kws)

1585 """Make the plot."""
1586 self.draw_bars(ax, bar_kws)
-> 1587 self.annotate_axes(ax)
1588 if self.orient == "h":
1589 ax.invert_yaxis()

File ~\anaconda3\Lib\site-packages\seaborn\categorical.py:767, in _CategoricalPlotter.annotate_axes(self, ax)

764 ax.set_ylim(-.5, len(self.plot_data) - .5, auto=None)
766 if self.hue_names is not None:
--> 767 ax.legend(loc="best", title=self.hue_title)

File ~\anaconda3\Lib\site-packages\matplotlib\axes\_axes.py:322, in Axes.legend(self, *args, **kwargs)

204 @_docstring.dedent_interpd
205 def legend(self, *args, **kwargs):
206 """
207 Place a legend on the Axes.
208
(...)
320 .. plot:: gallery/text_labels_and_annotations/legend.py
321 """
--> 322 handles, labels, kwargs = mlegend._parse_legend_args([self], *args, **kwargs)
323 self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
324 self.legend_._remove_method = self._remove_legend

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1361, in _parse_legend_args(axs, handles, labels, *args, **kwargs)

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1357 handles = [handle for handle, label

1358 in zip(_get_legend_handles(axs, handlers), labels)]
1360 elif len(args) == 0: # 0 args: automatically detect labels and handles.
-> 1361 handles, labels = _get_legend_handles_labels(axs, handlers)
1362 if not handles:
1363 log.warning(
1364 "No artists with labels found to put in legend. Note that "
1365 "artists whose label start with an underscore are ignored "
1366 "when legend() is called with no argument.")

File ~\anaconda3\Lib\site-packages\matplotlib\legend.py:1291, in _get_legend_handles_labels(axs, legend_handler_map)

1289 for handle in _get_legend_handles(axs, legend_handler_map):
1290 label = handle.get_label()
-> 1291 if label and not label.startswith('_'):
1292 handles.append(handle)
1293 labels.append(label)

AttributeError: 'numpy.int64' object has no attribute 'startswith'

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Findings of Univariate Analysis

Findings of univariate analysis are as follows:-

Our feature variable of interest is target .

It refers to the presence of heart disease in the patient.

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It is integer valued as it contains two integers 0 and 1 - (0 stands for absence of heart disease and 1 for presence of heart disease).

1 stands for presence of heart disease. So, there are 165 patients suffering from heart disease.

Similarly, 0 stands for absence of heart disease. So, there are 138 patients who do not have any heart disease.

There are 165 patients suffering from heart disease, and

There are 138 patients who do not have any heart disease.

Out of 96 females - 72 have heart disease and 24 do not have heart disease.

Similarly, out of 207 males - 93 have heart disease and 114 do not have heart disease.

8. Bivariate Analysis
Back to Table of Contents

Estimate correlation coefficients

Our dataset is very small. So, I will compute the standard correlation coefficient (also called Pearson's r) between every pair of attributes. I will
compute it using the df.corr() method as follows:-

In [27]: correlation = df.corr()

The target variable is target . So, we should check how each attribute correlates with the target variable. We can do it as follows:-

In [28]: correlation['target'].sort_values(ascending=False)

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Out[28]: target 1.000000

cp 0.433798
thalach 0.421741
slope 0.345877
restecg 0.137230
fbs -0.028046
chol -0.085239
trestbps -0.144931
age -0.225439
sex -0.280937
thal -0.344029
ca -0.391724
oldpeak -0.430696
exang -0.436757
Name: target, dtype: float64

Interpretation of correlation coefficient

The correlation coefficient ranges from -1 to +1.

When it is close to +1, this signifies that there is a strong positive correlation. So, we can see that there is no variable which has strong
positive correlation with target variable.

When it is clsoe to -1, it means that there is a strong negative correlation. So, we can see that there is no variable which has strong
negative correlation with target variable.

When it is close to 0, it means that there is no correlation. So, there is no correlation between target and fbs .

We can see that the cp and thalach variables are mildly positively correlated with target variable. So, I will analyze the interaction
between these features and target variable.

Analysis of target and cp variable

Explore cp variable

cp stands for chest pain type.

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First, I will check number of unique values in cp variable.

In [ ]: df['cp'].nunique()

So, there are 4 unique values in cp variable. Hence, it is a categorical variable.

Now, I will view its frequency distribution as follows :

In [ ]: df['cp'].value_counts()

Comment
It can be seen that cp is a categorical variable and it contains 4 types of values - 0, 1, 2 and 3.

Visualize the frequency distribution of cp variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.countplot(x="cp", data=df)
plt.show()

Frequency distribution of target variable wrt cp

In [ ]: df.groupby('cp')['target'].value_counts()

Comment
cp variable contains four integer values 0, 1, 2 and 3.

target variable contains two integer values 1 and 0 : (1 = Presence of heart disease; 0 = Absence of heart disease)

So, the above analysis gives target variable values categorized into presence and absence of heart disease and groupby cp variable
values.

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We can visualize this information below.

We can visualize the value counts of the cp variable wrt target as follows -

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.countplot(x="cp", hue="target", data=df)
plt.show()

Interpretation
We can see that the values of target variable are plotted wrt cp .

target variable contains two integer values 1 and 0 : (1 = Presence of heart disease; 0 = Absence of heart disease)

The above plot confirms our above findings,

Alternatively, we can visualize the same information as follows :

In [ ]: ax = sns.catplot(x="target", col="cp", data=df, kind="count", height=8, aspect=1)

Analysis of target and thalach variable

Explore thalach variable

thalach stands for maximum heart rate achieved.

I will check number of unique values in thalach variable as follows :

In [ ]: df['thalach'].nunique()

So, number of unique values in thalach variable is 91. Hence, it is numerical variable.

I will visualize its frequency distribution of values as follows :

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Visualize the frequency distribution of thalach variable

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
ax = sns.distplot(x, bins=10)
plt.show()

Comment
We can see that the thalach variable is slightly negatively skewed.

We can use Pandas series object to get an informative axis label as follows :

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
x = pd.Series(x, name="thalach variable")
ax = sns.distplot(x, bins=10)
plt.show()

We can plot the distribution on the vertical axis as follows:-

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
ax = sns.distplot(x, bins=10, vertical=True)
plt.show()

Seaborn Kernel Density Estimation (KDE) Plot

The kernel density estimate (KDE) plot is a useful tool for plotting the shape of a distribution.

The KDE plot plots the density of observations on one axis with height along the other axis.

We can plot a KDE plot as follows :

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In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
x = pd.Series(x, name="thalach variable")
ax = sns.kdeplot(x)
plt.show()

We can shade under the density curve and use a different color as follows:

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
x = pd.Series(x, name="thalach variable")
ax = sns.kdeplot(x, shade=True, color='r')
plt.show()

Histogram
A histogram represents the distribution of data by forming bins along the range of the data and then drawing bars to show the number of
observations that fall in each bin.

We can plot a histogram as follows :

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['thalach']
ax = sns.distplot(x, kde=False, rug=True, bins=10)
plt.show()

Visualize frequency distribution of thalach variable wrt target

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.stripplot(x="target", y="thalach", data=df)
plt.show()

Interpretation

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We can see that those people suffering from heart disease (target = 1) have relatively higher heart rate (thalach) as compared to people
who are not suffering from heart disease (target = 0).

We can add jitter to bring out the distribution of values as follows :

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.stripplot(x="target", y="thalach", data=df, jitter = 0.01)
plt.show()

Visualize distribution of thalach variable wrt target with boxplot

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x="target", y="thalach", data=df)
plt.show()

Interpretation
The above boxplot confirms our finding that people suffering from heart disease (target = 1) have relatively higher heart rate (thalach) as
compared to people who are not suffering from heart disease (target = 0).

Findings of Bivariate Analysis

Findings of Bivariate Analysis are as follows –

There is no variable which has strong positive correlation with target variable.

There is no variable which has strong negative correlation with target variable.

There is no correlation between target and fbs .

The cp and thalach variables are mildly positively correlated with target variable.

We can see that the thalach variable is slightly negatively skewed.

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The people suffering from heart disease (target = 1) have relatively higher heart rate (thalach) as compared to people who are not
suffering from heart disease (target = 0).

The people suffering from heart disease (target = 1) have relatively higher heart rate (thalach) as compared to people who are not
suffering from heart disease (target = 0).

9. Multivariate analysis
Back to Table of Contents

The objective of the multivariate analysis is to discover patterns and relationships in the dataset.

Discover patterns and relationships

An important step in EDA is to discover patterns and relationships between variables in the dataset.

I will use heat map and pair plot to discover the patterns and relationships in the dataset.

First of all, I will draw a heat map .

Heat Map
In [ ]: plt.figure(figsize=(16,12))
plt.title('Correlation Heatmap of Heart Disease Dataset')
a = sns.heatmap(correlation, square=True, annot=True, fmt='.2f', linecolor='white')
a.set_xticklabels(a.get_xticklabels(), rotation=90)
a.set_yticklabels(a.get_yticklabels(), rotation=30)
plt.show()

Interpretation
From the above correlation heat map, we can conclude that :-

target and cp variable are mildly positively correlated (correlation coefficient = 0.43).

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target and thalach variable are also mildly positively correlated (correlation coefficient = 0.42).

target and slope variable are weakly positively correlated (correlation coefficient = 0.35).

target and exang variable are mildly negatively correlated (correlation coefficient = -0.44).

target and oldpeak variable are also mildly negatively correlated (correlation coefficient = -0.43).

target and ca variable are weakly negatively correlated (correlation coefficient = -0.39).

target and thal variable are also waekly negatively correlated (correlation coefficient = -0.34).

Pair Plot
In [ ]: num_var = ['age', 'trestbps', 'chol', 'thalach', 'oldpeak', 'target' ]
sns.pairplot(df[num_var], kind='scatter', diag_kind='hist')
plt.show()

Comment
I have defined a variable num_var . Here age , trestbps , chol`, `thalach` and `oldpeak are numerical variables and target
is the categorical variable.

So, I wll check relationships between these variables.

Analysis of age and other variables

Check the number of unique values in age variable

In [ ]: df['age'].nunique()

View statistical summary of age variable

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In [ ]: df['age'].describe()

Interpretation
The mean value of the age variable is 54.37 years.

The minimum and maximum values of age are 29 and 77 years.

Plot the distribution of age variable

Now, I will plot the distribution of age variable to view the statistical properties.

In [ ]: f, ax = plt.subplots(figsize=(10,6))
x = df['age']
ax = sns.distplot(x, bins=10)
plt.show()

Interpretation
The age variable distribution is approximately normal.

Analyze age and target variable

Visualize frequency distribution of age variable wrt target

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.stripplot(x="target", y="age", data=df)
plt.show()

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Interpretation
We can see that the people suffering from heart disease (target = 1) and people who are not suffering from heart disease (target = 0)
have comparable ages.

Visualize distribution of age variable wrt target with boxplot

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x="target", y="age", data=df)
plt.show()

Interpretation
The above boxplot tells two different things :

The mean age of the people who have heart disease is less than the mean age of the people who do not have heart disease.

The dispersion or spread of age of the people who have heart disease is greater than the dispersion or spread of age of the people
who do not have heart disease.

Analyze age and trestbps variable

I will plot a scatterplot to visualize the relationship between age and trestbps variable.

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.scatterplot(x="age", y="trestbps", data=df)
plt.show()

Interpretation
The above scatter plot shows that there is no correlation between age and trestbps variable.

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In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.regplot(x="age", y="trestbps", data=df)
plt.show()

Interpretation
The above line shows that linear regression model is not good fit to the data.

Analyze age and chol variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.scatterplot(x="age", y="chol", data=df)
plt.show()

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.regplot(x="age", y="chol", data=df)
plt.show()

Interpretation
The above plot confirms that there is a slighly positive correlation between age and chol variables.

Analyze chol and thalach variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.scatterplot(x="chol", y = "thalach", data=df)
plt.show()

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
ax = sns.regplot(x="chol", y="thalach", data=df)
plt.show()

Interpretation

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The above plot shows that there is no correlation between chol and thalach variable.

10. Dealing with missing values

Back to Table of Contents

In Pandas missing data is represented by two values:

None: None is a Python singleton object that is often used for missing data in Python code.

NaN : NaN (an acronym for Not a Number), is a special floating-point value recognized by all systems that use the standard IEEE
floating-point representation.

There are different methods in place on how to detect missing values.

Pandas isnull() and notnull() functions

Pandas offers two functions to test for missing data - isnull() and notnull() . These are simple functions that return a boolean
value indicating whether the passed in argument value is in fact missing data.

Below, I will list some useful commands to deal with missing values.

Useful commands to detect missing values

df.isnull()

The above command checks whether each cell in a dataframe contains missing values or not. If the cell contains missing value, it returns True
otherwise it returns False.

df.isnull().sum()

The above command returns total number of missing values in each column in the dataframe.

df.isnull().sum().sum()

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It returns total number of missing values in the dataframe.

df.isnull().mean()

It returns percentage of missing values in each column in the dataframe.

df.isnull().any()

It checks which column has null values and which has not. The columns which has null values returns TRUE and FALSE otherwise.

df.isnull().any().any()

It returns a boolean value indicating whether the dataframe has missing values or not. If dataframe contains missing values it returns TRUE and
FALSE otherwise.

df.isnull().values.any()

It checks whether a particular column has missing values or not. If the column contains missing values, then it returns TRUE otherwise FALSE.

df.isnull().values.sum()

It returns the total number of missing values in the dataframe.

In [ ]: # check for missing values

df.isnull().sum()

Interpretation
We can see that there are no missing values in the dataset.

11. Check with ASSERT statement

Back to Table of Contents

We must confirm that our dataset has no missing values.

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We can write an assert statement to verify this.

We can use an assert statement to programmatically check that no missing, unexpected 0 or negative values are present.

This gives us confidence that our code is running properly.

Assert statement will return nothing if the value being tested is true and will throw an AssertionError if the value is false.

Asserts

assert 1 == 1 (return Nothing if the value is True)

assert 1 == 2 (return AssertionError if the value is False)

In [ ]: #assert that there are no missing values in the dataframe

assert pd.notnull(df).all().all()

In [ ]: #assert all values are greater than or equal to 0

assert (df >= 0).all().all()

Interpretation
The above two commands do not throw any error. Hence, it is confirmed that there are no missing or negative values in the dataset.

All the values are greater than or equal to zero.

12. Outlier detection

Back to Table of Contents

I will make boxplots to visualise outliers in the continuous numerical variables : -

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age , trestbps , chol , thalach and oldpeak variables.

age variable

In [ ]: df['age'].describe()

Box-plot of age variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x=df["age"])
plt.show()

trestbps variable

In [ ]: df['trestbps'].describe()

Box-plot of trestbps variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x=df["trestbps"])
plt.show()

chol variable

In [ ]: df['chol'].describe()

Box-plot of chol variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x=df["chol"])
plt.show()

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thalach variable

In [ ]: df['thalach'].describe()

Box-plot of thalach variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x=df["thalach"])
plt.show()

oldpeak variable

In [ ]: df['oldpeak'].describe()

Box-plot of oldpeak variable

In [ ]: f, ax = plt.subplots(figsize=(8, 6))
sns.boxplot(x=df["oldpeak"])
plt.show()

Findings
The age variable does not contain any outlier.

trestbps variable contains outliers to the right side.

chol variable also contains outliers to the right side.

thalach variable contains a single outlier to the left side.

oldpeak variable contains outliers to the right side.

Those variables containing outliers needs further investigation.

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13. Conclusion
Back to Table of Contents

So, friends, our EDA journey has come to an end.

In this kernel, we have explored the heart disease dataset. In this kernel, we have implemented many of the strategies presented in the book
Think Stats - Exploratory Data Analysis in Python by Allen B Downey . The feature variable of interest is target variable. We have
analyzed it alone and check its interaction with other variables. We have also discussed how to detect missing data and outliers.

I hope you like this kernel on EDA journey.

Thanks

14. References
Back to Table of Contents

The following references are used to create this kernel

Think Stats - Exploratory Data Analysis in Python by Allen B Downey

Seaborn API reference

My other kernel

Go to Top

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