Ultimate guide for Data Exploration in Python using NumPy, Matplotlib and Pandas

Introduction

Exploring data sets and developing deep understanding about the data is one of the most important skills every data scientist should possess. People estimate that the time spent on these activities can go as high as 80% of the project time in some cases.

Python has been gaining a lot of ground as preferred tool for data scientists lately, and for the right reasons. Ease of learning, powerful libraries with integration of C/C++, production readiness and integration with web stack are some of the main reasons for this move lately.

In this guide, I will use NumPy, Matplotlib, Seaborn, and Pandas to perform data exploration. These are powerful libraries to perform data exploration in Python. The idea is to create a ready reference for some of the regular operations required frequently. I am using an iPython Notebook to perform data exploration and would recommend the same for its natural fit for exploratory analysis.

In case you missed it, I would suggest you to refer to the baby steps series of Python to understand the basics of python programming.

• Learning Python for data analysis – with instructions on installation and creating the environment
• Libraries and data structures
• Exploratory analysis in Python (using Pandas)
• Data Munging in Python (using Pandas)

Contents – Data Exploration

Here are the operations I’ll cover in this article (Refer to this article for similar operations in SAS):

1. 1. How to load data file(s) using Pandas?

   2. How to convert a variable to different data type?

   3. How to transpose a table/Pandas dataframe?

   4. How to sort Data?

   5. How to create plots (Histogram, Scatter, Box Plot)?

   6. How to generate frequency tables?

   7. How to do sampling of Data set?

1. How to remove duplicate values of a variable?

2. How to group variables to calculate count, average, sum?

3. How to recognize and treat missing values and outliers?

4. How to merge / join data set or dataframes effectively in Pandas?

Part 1: How to load data file(s) using Pandas?

Input data sets can be in various formats (.XLS, .TXT, .CSV, JSON ). In Python, it is easy to load data from any source, due to its simple syntax and availability of predefined libraries, such as Pandas. Here I will make use of Pandas itself.

Pandas features a number of functions for reading tabular data as a Pandas DataFrame object. Below are the common functions that can be used to read data (including read_csv in Pandas):

Loading data from a CSV file(s):

Code

Loading data from excel file(s):

Code
df=pd.read_excel("E:/EMP.xlsx", "Data") # Load Data sheet of excel file EMP
Output
print df

Loading data from a txt file(s):

Code:

df=pd.read_csv("E:/Test.txt",sep='\t') # Load Data from text file having tab '\t' delimeter print df

Output

Part 2: How to convert a variable to a different data type?

Converting a variable data type to others is an important and common procedure we perform after loading data. Let’s look at some of the commands to perform these conversions:

• Convert numeric variables to string variables and vice versa

srting_outcome = str(numeric_input) #Converts numeric_input to string_outcome
integer_outcome = int(string_input) #Converts string_input to integer_outcome
float_outcome = float(string_input) #Converts string_input to integer_outcome

The later operations are especially useful when you input value from user using raw_input(). By default, the values are read at string.

• Convert character date to Date:

There are multiple ways to do this. The simplest would be to use the datetime library and strptime function. Here is the code:

from datetime import datetime
char_date = 'Apr 1 2015 1:20 PM' #creating example character date
date_obj = datetime.strptime(char_date, '%b %d %Y %I:%M%p')
print date_obj

Part 3: How to transpose a Data set or dataframe using Pandas?

Here, I want to transpose Table A into Table B on the variable Product. This task can be accomplished by using Pandas dataframe.pivot:

Code

#Transposing Pandas dataframe by a variable

df=pd.read_excel("E:/transpose.xlsx", "Sheet1") # Load Data sheet of excel file EMP 
print df 
result= df.pivot(index= 'ID', columns='Product', values='Sales') 
result

Output

Part 4: How to sort a Pandas DataFrame?

Sorting of data can be done using dataframe.sort(). It can be based on multiple variables and ascending or descending both orders.

Code

#Sorting Pandas Dataframe 
df=pd.read_excel("E:/transpose.xlsx", "Sheet1") #Add by variable name(s) to sort
print df.sort(['Product','Sales'], ascending=[True, False])

Above, we have a table with variables ID, Product and Sales. Now, we want to sort it by Product and Sales (in descending order) as shown in table 2.

Part 5: How to create plots (Histogram, Scatter, Box Plot)?

Data visualization always helps to understand the data easily. Python has libraries like matplotlib and seaborn to create multiple graphs effectively. Let’s look at the some of the visualizations to understand below behavior of variable(s) .

• The distribution of age
• Relation between age and sales; and
• If sales are normally distributed or not?

Histogram:

Code

#Plot Histogram

import matplotlib.pyplot as plt
import pandas as pd

df=pd.read_excel("E:/First.xlsx", "Sheet1")

#Plots in matplotlib reside within a figure object, use plt.figure to create new figure
fig=plt.figure()

#Create one or more subplots using add_subplot, because you can't create blank figure
ax = fig.add_subplot(1,1,1)

#Variable
ax.hist(df['Age'],bins = 5)

#Labels and Tit
plt.title('Age distribution')
plt.xlabel('Age')
plt.ylabel('#Employee')
plt.show()

Output

Scatter plot:

Code

#Plots in matplotlib reside within a figure object, use plt.figure to create new figure fig=plt.figure()

#Create one or more subplots using add_subplot, because you can't create blank figure
ax = fig.add_subplot(1,1,1)

#Variable
ax.scatter(df['Age'],df['Sales'])

#Labels and Tit
plt.title('Sales and Age distribution')
plt.xlabel('Age')
plt.ylabel('Sales')
plt.show()

Output

Box-plot:

Code

import seaborn as sns 
sns.boxplot(df['Age']) 
sns.despine()

Output

Part 6: How to generate frequency tables with Pandas?

Frequency Tables can be used to understand the distribution of a categorical variable or n categorical variables using frequency tables.

Code

import pandas as pd

df=pd.read_excel("E:/First.xlsx", "Sheet1") 
print df

test= df.groupby(['Gender','BMI'])
test.size()

Output

Part 7: How to do sample Data set in Python?

To select sample of a data set, we will use library numpy and random. Sampling of data set always helps to understand data quickly.

Let’s say, from EMP table, I want to select random sample of 5 employees.

Code

#Create Sample dataframe

import numpy as np
import pandas as pd
from random import sample

# create random index
rindex = np.array(sample(xrange(len(df)), 5))

# get 5 random rows from the dataframe df
dfr = df.ix[rindex]
print dfr

Output

Part 8: How to remove duplicate values of a variable in a Pandas Dataframe?

Often, we encounter duplicate observations. To tackle this in Python, we can use dataframe.drop_duplicates().

Code

#Remove Duplicate Values based on values of variables "Gender" and "BMI"

rem_dup=df.drop_duplicates(['Gender', 'BMI'])
print rem_dup

Output

Part 9: How to group variables in Pandas to calculate count, average, sum?

To understand the count, average and sum of variable, I would suggest you use dataframe.describe() with Pandas groupby().

Let’s look at the code:

Code

test= df.groupby(['Gender'])
test.describe()

Output

Part 10: How to recognize and Treat missing values and outliers in Pandas?

To identify missing values , we can use dataframe.isnull(). You can also refer article “Data Munging in Python (using Pandas)“, here we have done a case study to recognize and treat missing and outlier values.

Code

# Identify missing values of dataframe
df.isnull()

Output

To treat missing values, there are various imputation methods available. You can refer these articles for methods to detect Outlier and Missing values. Imputation methods for both missing and outlier values are almost similar. Here we will discuss general case imputation methods to replace missing values. Let’s do it using an example:

Code:

#Example to impute missing values in Age by the mean
import numpy as np
meanAge = np.mean(df.Age)     #Using numpy mean function to calculate the mean value
df.Age = df.Age.fillna(meanAge) #replacing missing values in the DataFrame

Part 11: How to merge / join data sets and Pandas dataframes?

Joining / merging is one of the common operation required to integrate datasets from different sources. They can be handled effectively in Pandas using merge function:

Code:

df_new = pd.merge(df1, df2, how = 'inner', left_index = True, right_index = True) # merges df1 and df2 on index
# By changing how = 'outer', you can do outer join.
# Similarly how = 'left' will do a left join
# You can also specify the columns to join instead of indexes, which are used by default.

End Notes:

In this comprehensive guide, we looked at the Python codes for various steps in data exploration and munging. We also looked at the python libraries like Pandas, Numpy, Matplotlib and Seaborn to perform these steps. In next article, I will reveal the codes to perform these steps in R.

Also See: If you have any doubts pertaining to Python, feel free to discuss with us.

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