• R Biplot Example
• R Biplot Examples

A biplot is plot which aims to represent both the observations and variables of a matrix of multivariate data on the same plot. There are many variations on biplots (see the references) and perhaps the most widely used one is implemented by biplot.princomp.The function biplot.default merely provides the underlying code to plot two sets of variables on the same figure. R offers two functions for doing PCA: princomp and prcomp, while plots can be visualised using the biplot function. However, the plots produced by biplot are often hard to read and the function lacks many of the options commonly available for customising plots.

In thistutorial you will learn how to read a csv file in R Programming with'read.csv' and 'read.csv2' functions. You will learn to import data inR from your computer or from a source on internet using url for readingcsv data.

R Biplot Example

Common methods for importingCSV data in R

1. Read a file from currentworking directory - using setwd.

2. Read a filefrom any location on your computer using file path.

• Title GGE Biplots with 'ggplot2' Version 0.1.1 Description Genotype plus genotype-by-environment (GGE) biplots rendered using 'ggplot2'. Pro-vides a command line interface to all of the functionality contained within 'GGEBiplotGUI'.
• 2 BiplotGUI: Interactive Biplots in R 1.1. Biplots Introduced byGabriel(1971), the biplot is described byGower and Hand(1996) in their authoritative monograph as the multivariate analogue of the ordinary scatter plot. As such, biplots are representations of multivariate data in which information on both the samples.

3. Usefile.choose() method to select a csv file to load in R.

4. Use fullurl to read a csv file from internet.

CSV files

CSV standsfor Comma Seperated Values. A CSV file is used to storedata. It is a plain text file with .csv extension. In these type offiles values are seperated by ',' (comma) or ';' (semi-colon)

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CSV fileshave many benefits, as they are simple text files consisting of linesand each line of data is represented by a line in csv file which helpsfor storing tabular data. Most applications support reading and writingcsv format.

An exampleof csv file is

Reading csv file with read.csvfunction

The function read.csv() isused to import data from a csv file. This function can take manyarguments, but the most important is file which is thename of file to be read. This function reads the data as a dataframe.If the values are seperated by a comma use read.csv() and if the valuesare seperated by ; (a semi-colon) use read.csv2() function. Otherwisethere is no difference between these two functions.

Read csv from working directory

In case youhave a folder with many csv files and want to read from this folderquite often then it is better to first set that folder as your currentworking directory so that you can easily read files of this folder. Forthat purpose first you will need to use getwd() function and then usesetwd() function. Lets say we want to make csvfiles folder onC: drive as our current working directory. We find our current workingdirectory

>getwd()

[1] 'd:/ProgramFiles/RStudio'

Then we setour working directory to csvfiles folder on c: drive

>setwd('c:/csvfiles')

Checkingagain for working directory

>getwd()

[1]'c:/csvfiles'

Now its timeto read the file testfile.csv

Analysisof csv file

Here data isa new variable or object which will store values read from csv file.read.csv is the name of function and we are providing only one argumentto this function which is the file name with extension. After importingdata in R you can check and see it with some common functions.

1. View():This function will show you the values of csv file in a table format.

R Biplot Examples

2. nrow():This function returns the total number of rows in your dataframe.

3.ncol(): Returnsthe total number of columns in your dataframe.

4.colnames(): This function returns the column headers or columnnames.

5.str(): Returns the structure of your dataframe. Column names with datatypes and factors.

RstudioOutput:

Readcsv with file path

If you have to read a singlecsv file or you don't want to change your working directory theninstead of using getwd and setwd for setting it, simply use file pathfor reading that file. Lets suppose your current working directory is 'd:/ProgramFiles/RStudio'. Andyou simply want to read csv file without changing it. First you willcreate a new variable file and assign the complete path of file withits name and extension to this variable. And then use it to import datain R.

>file <- 'c:/csvfiles/testfile.csv'

> data <-read.csv(file)

Readcsv with file.choose()

In case youdon't exactly know the file location or even not sure about name offile you may simply use file.choose option in read.csv function. Thiswill open a file dialog box to select the file you want to open in R.

Rread csv from internet source

To read a csvfile from a web resource for data analysis the same function i.eread.csv() will be used. In this case you need to have a complete urlor internet location of csv file. Lets support we want to read a filenamed advertising.csv from a website with this url'http://faculty.marshall.usc.edu/gareth-james/ISL/Advertising.csv'

This is asample file which contains four columns and about 200 rows. You canimport it in R and use the analysis methods describe earlier to have aview of this file contents. Then you may simply download this file onyour computer and use the earlier methods to open it as a practice forreinforcing what you learnt in this tutorial.

To read filefrom that location R code will be

> data <-read.csv('http://faculty.marshall.usc.edu/gareth-james/ISL/Advertising.csv')

or you canuse the file variable for storing url and then using it to import filein R

> file <-'http://faculty.marshall.usc.edu/gareth-james/ISL/Advertising.csv'

> data <-read.csv(file)

Biplot for Principal Components

Produces a biplot (in the strict sense) from the output of princomp or prcomp

Arguments

an object of class 'princomp'.

length 2 vector specifying the components to plot. Only the default is a biplot in the strict sense.

The variables are scaled by lambda ^ scale and the observations are scaled by lambda ^ (1-scale) where lambda are the singular values as computed by princomp. Normally 0 <= scale <= 1, and a warning will be issued if the specified scale is outside this range.

If true, use what Gabriel (1971) refers to as a 'principal component biplot', with lambda = 1 and observations scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner products between variables approximate covariances and distances between observations approximate Mahalanobis distance.

optional arguments to be passed to biplot.default.

Details

This is a method for the generic function biplot. There is considerable confusion over the precise definitions: those of the original paper, Gabriel (1971), are followed here. Gabriel and Odoroff (1990) use the same definitions, but their plots actually correspond to pc.biplot = TRUE.

Side Effects

a plot is produced on the current graphics device.

References

Gabriel, K. R. (1971). The biplot graphical display of matrices with applications to principal component analysis. Biometrika, 58, 453--467. 10.2307/2334381.

Gabriel, K. R. and Odoroff, C. L. (1990). Biplots in biomedical research. Statistics in Medicine, 9, 469--485. 10.1002/sim.4780090502.

See Also

biplot, princomp.

Aliases

• biplot.princomp
• biplot.prcomp

Examples