Data Interfacing & Visualization in R

UNIT 14 DATA INTERFACING AND

VISUALISATION IN R
Structure Page Nos.
14.1 Introduction
14.2 Objectives
14.3 Reading Data From Files
14.3.1 CSV Files
14.3.2 Excel Files
14.3.3 Binary Files
14.3.4 XML Files
14.3.5 JSON Files
14.3.6 Interfacing with Databases
14.3.7 Web Data
14.4 Data Cleaning and Pre-processing
14.5 Visualizations in R
14.5.1 Bar Charts
14.5.2 Box Plots
14.5.3 Histograms
14.5.4 Line Graphs
14.5.5 Scatterplots
14.6 Summary
14.7 Answers
14.8. References and Further Readings

14.1 INTRODUCTION
In the previous unit, you have learnt about basic concepts of R programming.
This unit explains how to read and analyse data in R from various file types
including- CSV, Excel, binary, XML, JSON, etc. It also discusses how to extract
and work on data in R from databases and also web data. The unit also explains
in detail about data cleaning and pre-processing in R. In the later sections, the
unit explores the concept of visualisations in R. Various types of graphs and
charts, including - bar charts, box plots, histograms, line graphs and scatterplots,
are discussed.

14.2 OBJECTIVES
After going through this Unit, you will be able to:
• explain the various file types and their interface that can be processed for
data analysis in R;
• read, write and analyse data in R from different type of files including-
CSV, Excel, binary, XML and JSON;
• extract and use data from databases and web for analysis in R;
• explain the steps involved in data cleaning and pre-processing using R;
• Visualise the data using various types of graphs and charts using R and
explain their usage.

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14.3 READING DATA FROM FILES
In R, you can read data from files outside of the R environment. One
may also write data to files that the operating system can store and further
access. There is a wide range of file formats, including CSV, Excel,
binary, and XML, etc., R can read and write from.
14.3.1 CSV Files
Input as CSV File:
CSV file is a text file in which column values are separated by commas.
For example, you can create data with name, programme, phone of
students. By copying and pasting this data into Windows Notepad, you
can create the CSV file. Using notepad's Save As option, save the file as
input.csv.
Reading a CSV File:
Function used to read a CSV file: read.csv()

Figure 14.1: Reading data from a CSV file

Analysing the CSV File:

The read.csv() function returns a data frame as its default output. You
can use the following three print functions to:(1) verify if the read data
input from CSV file is in frame format or not; (2) find the number of
columns in the data; and (3) find the number of rows in the data.

Figure 14.2: Checking read data

Writing into a CSV File:

The write.csv() function of R can be used to generate a CSV file from a
data frame. For example, the following function will generate an
output.csv file. Please note that this output.csv will be created in the
present directory in which you are working.

14.3.2 Excel Files

Microsoft Excel is the most extensively used spreadsheet tool and it uses the.xls
or.xlsx file extension to store data. Using various Excel-specific packages, R
can read directly from these files. XLConnect, xlsx, and gdata are a few
examples of such packages. The xlsx package also allows R to write to an Excel
file.

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Install xlsx Package

• Command to install ‘xlsx’ package: install.packages("xlsx")

• To Load the library into R workspace: library("xlsx")

Reading the Excel File

The read.xlsx() function is used to read the input.xlsx file, as illustrated below.
In the R environment, the result is saved as a data frame.

Figure 14.3: Reading data from an Excel file

Writing the Excel File
For writing to a new Excel file, you use the write function, as shown below:

14.3.3 Binary Files

A binary file is one that solely includes data in the form of bits and bytes.
(0's and 1's). When you try to read a binary file, the sequence of bits is
translated as bytes or characters, which include numerous other non-
printable characters, that are not human readable. Any text editor that
tries to read a binary file will display characters like Ø , ð, printable
characters and many other characters including beeps.
R has two functions writeBin() and readBin() to create and read binary
files.

Syntax:
writeBin(object, con)
readBin(con, what, n )

where,
• The connection object con is used to read or write a binary file.
• The binary file to be written is the object.
• The mode that represents the bytes to be read, such as character,
integer, etc is what.
• The number of bytes to read from the binary file is given by n.

Writing the Binary File(You should read the comments for

explanation on each command.)

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Figure14.4: An example of Writing data to a Binary file

Reading the Binary File(You should read the comments for

explanation on each command.)

Figure14.5: An example of Reading data to a Binary file

14.3.4 XML Files

XML is an acronym for “extensible markup language”. It is a file format

that allows users to share the file format as well as the data over the
internet, intranet and other places, as standard ASCII text. XML uses
markup tags that describe the meaning of the data stored in the file. This
is similar to the markup tags used in HTML wherein the markup tag
describes the structure of the page instead.
The "XML" package in R can be used to read an xml file. The following
command can be used to install this package:

install.packages("XML")

Reading XML File

R reads the xml file using the function xmlParse(). In R, it is
saved as a list.

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Figure14.6: An example of reading data from a Binary file

XML to Data Frame

In order to manage the data appropriately in huge files, the data
in the xml file can be read as a data frame. The data frame should
then be processed for data analysis.

Figure14.7: converting the read data to a data frame

14.3.5 JSON Files

The data in a JSON file is stored as text in a human-readable

format. JavaScript Object Notation is abbreviated as JSON. The
rjson package in R can read JSON files.

Install rjson Package

To install the rjson package, type the following command in the
R console: install.packages("rjson")

Read the JSON File

R reads the JSON file using the function fromJSON(). In R, it is
saved as a list.

Figure14.8: An example of reading data from JSON file

Convert JSON to a Data Frame

Using the as.data.frame() function, you can turn the retrieved
data above into a R data frame for further study.

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Figure14.9: Converting read data to data frame

14.3.6 Databases

Data is stored in a normalised way in relational database systems. As a

result, you will require quite advanced and complex SQL queries to
perform statistical computing. However, R can readily connect to various
relational databases, such as MySQL, Oracle, and SQL Server, and
retrieve records as a data frame. Once the data is in the R environment,
it becomes a standard R data set that can be modified and analysed with
all of R's sophisticated packages and functions.

RMySQL Package
R contains a built-in package called "RMySQL" that allows you to
connect to a MySql database natively. The following command will
install this package in the R environment.

install.packages("RMySQL")

Connecting R to MySQL

Figure14.10: Connecting to MySQL database

Querying the Tables

Using the MySQL function dbSendQuery(), you can query the database
tables . The query is run in MySQL, and the results are returned with the
R fetch() function. Finally, it is saved in R as a data frame.

Figure 14.11: Querying the MySQL table

Updating Rows in the Tables

Figure 14.12: Updating rows in MySQL table

Inserting Data into the Tables

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Figure 14.13: Inserting data in a MySQL table

Creating Tables in MySQL

The function dbWriteTable() in MySQL can be used to create tables. It takes

a data frame as input and overwrites the table if it already exists.

Figure 14.14: Creating a table in MySQL

Dropping Tables in MySQL

Figure 14.15: Dropping a table in MySQL

14.3.7 Web Data

Many websites make data available for users to consume. The World
Health Organization (WHO), for example, provides reports on health and
medical information in CSV, txt, and XML formats. You can
programmatically extract certain data from such websites using R
applications. "RCurl," "XML," and "stringr" are some R packages that
are used to scrape data from the web. They are used to connect to URLs,
detect required file links, and download the files to the local
environment.

Install R Packages

For processing the URLs and links to the files, the following packages
are necessary.
install.packages("RCurl")
install.packages("XML")
install.packages("stringr")
install.packages("plyr")

14.4 DATA CLEANING AND PRE-PROCESSING

Data cleaning is the process of identifying, correcting and removing incorrect
raw data. The clean data is then fed to the models to build the logical
conclusions.
If the data is poorly prepped, unreliable results can destroy the assumptions and
insights.
Packages like tidy verse can make complex data manipulations easier.
The following is the checklist of cleaning and preparing data which is mainly
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considered among the best practices.
• Familiarization with the dataset: to get good domain knowledge so
that one is aware which variable represents what.
• Check for structural errors: You may check for mislabelled variables,
faulty Data types, non-unique (duplicated values) and string
inconsistencies or typing errors.
• Check for data irregularities: You may check for the invalid values and
outliers.
• Decide on how to deal missing values: Either delete the observations if
they are not providing any meaningful insights to our data or imputing
the data with some logical values like mean or median based on the
observations.
Check your Progress 1

1. What is the package used to use JSON Files in R?

………………………………………………………………………….
…………………………………………………………….
2. What are wb and rb mode while dealing with binary files?
………………………………………………………………………….
…………………………………………………………….
3. Mention any 2 checklist points used for cleaning/ preparing data?
………………………………………………………………………….
…………………………………………………………….

14.5 VISUALIZATION IN R
In the previous section, we have discussed about obtaining input from different
types of data. This section explains various types of graphs that can be drawn
using R. It may please be noted that only selected types of graphs have been
presented here.

14.5.1 Bar Charts

A bar chart depicts data as rectangular bars whose length is proportionate

to the variable's value. The function barplot() in R is used to make bar
charts. In a bar chart, R can create both vertical and horizontal bars. Each
of the bars in a bar chart can be coloured differently.

Syntax:
barplot(H,xlab,ylab,main, names.arg,col)

where,
• In a bar chart, H is a vector or matrix containing numeric values.
• The x axis label as xlab.
• The y axis label is ylab.
• The title of the bar chart is main.
• names.arg is a list of names that appear beneath each bar.
• col is used to color the graph's bars.

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Figure 14.16: Creating a Bar chart

Figure 14.17: A Bar Chart of data of Figure 14.16

Bar Chart Labels, Title and Colors

More parameters can be added to the bar chart to increase its capabilities.
The title is added using the main parameter. Colors are added to the bars
using the col parameter. To express the meaning of each bar, args.name
is a vector with the same number of values as the input vector.

Figure 14.18: Function for plotting Bar chart with labels and
colours

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Figure 14.19: A Bar Chart of with labels and colors

14.5.2 Box Plots

In order to determine how evenly the data is distributed in a dataset, you
can use boxplot, which is very effective tool. The dataset is split using
quartiles. This graph depicts the data set's minimum, first quartile,
median, third quartile and maximum. Drawing boxplots for each data set
allows you to compare the distribution of data across data sets.
The boxplot() function in R is used to make boxplots.
Syntax:
boxplot(x, data, notch, varwidth, names, main)
The parameters of the functions are as follows:
• Parameter x either can specify a formula or it can specify a vector.
• Parameter data is used to specify the data frame that contains the
data required to be plotted.
• Parameter notch represents a logical value. In case, you want to
draw a notch in the box plot, you may set its value to TRUE.
• Parameter varwidth is also logical. It can be set to TRUE, if you
want to make the box's width proportional to the sample size.
• Parameter names can be used to specify the group labels that will
be printed beneath each boxplot.
• main is used to give the graph a title.

Creating the Boxplot

Figure 14.20: Coding for Box plot

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Figure 14.21: A Box plot of Figure 14.20

14.5.3 Histograms

The frequency of values of a variable bucketed into ranges is represented

by a histogram. The difference between a histogram and a bar chart is
that a histogram groups the numbers into continuous ranges. The height
of each bar in a histogram represents the number of items present in that
range.

The hist() function in R is used to produce a histogram. This function

accepts a vector as an input and plots histograms using additional
parameters.

Syntax:
hist(v,main,xlab,xlim,ylim,breaks,col,border)

where,
• The parameter v is a vector that contains the numeric values for
which histogram is to be drawn.
• The title of the chart is shown by the main.
• The colour of the bars is controlled by col.
• Each bar's border colour is controlled by the border parameter.
• The xlab command is used to describe the x-axis.
• The x-axis range is specified using the xlim parameter.
• The y-axis range is specified with the ylim parameter.
• The term "breaks" refers to the breadth of each bar.

Figure 14.22: Creating a Histogram

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Figure 14.23: Histogram of data used in Figure 14.22

14.5.3 Line Graphs

A graph that uses line segments to connect a set of points is known as the
line graph. These points are sorted according to the value of one of their
coordinates (typically the x-coordinate). Line charts are commonly used
to identify data trends.
The line graph was created using R's plot() function.

Syntax:
plot(v,type,col,xlab,ylab)

where,
• The numeric values are stored in v, which is a vector.
• type takes values, "p","l","o". The value "p" is used to draw only
points, "l" is used to draw only lines, and "o" is used to draw both
points and lines.
• xlab specifies the label for the x axis.
• ylab specifies the label for the x axis..
• Main is used to specify the title of chart .
• col is used to specify the color of the points and/or the lines.

Figure 14.24: Function to draw a line chart

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Figure 14.25: A Line Chart for data of Figure 14.24

Multiple Lines in Line Chart & Axis Details

Figure 14.25: Function for Line Chart with multiple lines

Figure 14.27: A Line Chart with multiple lines for data of Figure
14.26

14.5.4 Scatterplots

Scatterplots are diagrams that display a large number of points shown in

the Cartesian plane. The values of two variables are represented by each
point.
One variable is chosen on the horizontal axis, while another is chosen on
the vertical axis. To create a simple scatterplot, use the plot() method.

Syntax:
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plot(x, y, main, xlab, ylab, xlim, ylim, axes)

The parameters of the plot functions are as follows:

• parameter x is the data values for x-axis.
• parameter y is the data values for y-axis
• parameter main is used for title of the grpah
• parameters xlab and ylab are used to specify the Labels for x-
axis and y-axis respectively.
• Parameters xlim and ylim used define the limits of values of x
and y respectively.
• axes specifies if the plot should include both axes.

Figure 14.28: Plot function to draw Scatter Plot

Figure 14.29: Scatter plot for the data of Figure 14.28

Scatterplot Matrices
The scatterplot matrix is used when there are more than two variables
and you want to identify the correlation between one variable and the
others. To make scatterplot matrices, we use pairs() function.

Syntax:
pairs(formula, data)
where,
• The formula represents a set of variables that are utilised in pairs.
• The data set from which the variables will be derived is referred
to as data.

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Figure 14.30: Function for Scatterplot matrix

Figure 14.31: A Scatterplot matrix

Check your Progress 2

1. What is scatter plot?

2. When you will use histogram and when you will use bar chart in R?
3. What type of chart you consider when trying to demonstrate
“relationship“ between variables/parameters?

14.6 Summary
In this unit you have gone though various file types that can be processed for
data analysis in R and further discussed their interfaces. R can read and write a
variety of file types outside the R environment, including CSV, Excel, binary,
XML and JSON. Further, R can readily connect to various relational databases,
such as MySQL, Oracle, and SQL Server, and retrieve records as a data frame
that can be modified and analysed with all of R's sophisticated packages and
functions. The data can also be programmatically extracted from websites using
R applications. "RCurl," "XML," and "stringr" are some R packages that are
used to scrape data from the web. The unit also explains the concept of data
cleaning and pre-processing which is the process of identifying, correcting and
removing incorrect raw data, familiarization with the dataset, checking data for
structural errors and data irregularities and deciding on how to deal with missing
values are the steps involved in cleaning and preparing data which is mainly
considered among the best practices. The unit finally explores the concept of
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Basics of R Programming
visualisations in R. There are various types of graphs and charts including- bar
charts, box plots, histograms, line graphs and scatterplots that can be used to
visualise the data effectively. The unit explained the usage and syntax for each
of the illustration with graphics.

14.7 Answers
Check your progress 1
1. Install.packages(“rjson”)
library(rjson)
2. rb mode opens the file in the binary format for reading and wb mode
opens the file in the binary format for writing.
3. The checklist points used for cleaning/ preparing data:
Check for data irregularities: You may check for the invalid values and
outliers.
Decide on how to deal missing values: Either delete the observations if
they are not providing any meaningful insights to our data or imputing
the data with some logical values like mean or median based on the
observations.
Check your progress 2
1. A scatter plot is a chart used to plot a correlation between two or more
variables at the same time
2. We use a histogram to plot the distribution of a continuous variable,
while we can use a bar chart to plot the distribution of a categorical
variable.
3. When you are trying to show “relationship” between two variables, you
will use a scatter plot or chart. When you are trying to show
“relationship” between three variables, you will have to use a bubble
chart.

14.8 REFERENCES AND FURTHER READINGS

1. De Vries, A., & Meys, J. (2015). R for Dummies. John Wiley & Sons.
2. Peng, R. D. (2016). R programming for data science (pp. 86-181). Victoria, BC, Canada:
Leanpub.
3. Schmuller, J. (2017). Statistical Analysis with R For Dummies. John Wiley & Sons.
4. Field, A., Miles, J., & Field, Z. (2012). Discovering statistics using R. Sage publications.
5. Lander, J. P. (2014). R for everyone: Advanced analytics and graphics. Pearson
Education.
6. Lantz, B. (2019). Machine learning with R: expert techniques for predictive modeling.
Packt publishing ltd.
7. Heumann, C., & Schomaker, M. (2016). Introduction to statistics and data analysis.
Springer International Publishing Switzerland.
8. Davies, T. M. (2016). The book of R: a first course in programming and statistics. No
Starch Press.
9. https://www.tutorialspoint.com/r/index.html

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