NumPy, Matplotlib and Pandas for Data Exploration

Introduction

Exploring data sets and developing deep understanding about the data is one of the most important skill every data scientist should possess. People estimate that 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 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 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 operation I’ll cover in this article (Refer to this article for similar operations in SAS):

How to load data file(s)?

How to convert a variable to different data type?

How to transpose a table?

How to sort Data?

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

How to generate frequency tables?

How to do sampling of Data set?

How to remove duplicate values of a variable?

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

How to recognize and treat missing values and outliers?

How to merge / join data set effectively?

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

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. Here I will make use of Pandas. It features a number of functions for reading tabular data as a DataFrame object. Below are the common functions that can be used to read data.

Loading data from CSV file(s):

Code

import pandas as pd #Import Library Pandas df = pd.read_csv("E:/train.csv") #I am working in Windows environment #Reading the dataset in a dataframe using Pandas print df.head(3) #Print first three observations

Output

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 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 different data type?

Converting a variable data type to other is 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 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?

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

Code

#Transposing 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 DataFrame?

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

Code

#Sorting 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 library like matplotlib and seaborn to create multiple graphs effectively. Let’s look at the some of the visualization 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 Histogramimport matplotlib.pyplot as plt import pandas as pddf=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 pddf=pd.read_excel("E:/First.xlsx", "Sheet1") print dftest= 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 employee.

Code

#Create Sample dataframeimport 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 df dfr = df.ix[rindex] print dfr

Output

 

 

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

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 Python to calculate count, average, sum?

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

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?

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

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.