Plots in R

Simple Plots in R

There are varieties of plots in R, lets try some of them

Simple scatter plot import data from sheet 2 of  demo data.xls,

read.table('clipboard',header=T) ->a.df

names (a.df)

attach(a.df)

a.df

plot (year,temp)                                # scatter plot

plot (year,pcpn)                        # scatter plot

There are different types of plots

Boxplot, Histogram, Bar plot, Line,......

Changing parameters in plot command

Now work with sheet 1 data in demodata.xls file

To plot in new window (keep the previous)

X11()                 # give new blank window to plot

# Notice comma (,) and inverted codes ('  ')

In about commands, the circled functions right side of '=' is changeable. 
Practice with sheet 2, demo data excel file

temp.df<- read.table ('clipboard', header=T)

attach (temp.df)

plot (year, temp, xlab='Year', ylab='Temperature', main='Annual Average Temperature', pch=18 , col='blue')

plot (year, temp, xlab='Year', ylab='Temperature',  main='Annual Average Temperature', type='s' , col='blue')

Practice changing the 'pch' values (eg. 15, 11, 21), colour (eg. yellow, red, green), type (eg. S, l, h, b)

Multiple chart in a window

par(mfrow=c(1,3))

par = the graphics parameter,

mfrow = mf (make fragment?)

row (number of rows),

c(nr, nc) = [c (concentrate or concatenate), nr =number for rows), c =number of columns)]

Subsequent figures will be drawn in an nr-by-nc array on the device by columns (mfcol), or rows (mfrow), respectively.

x<-0:10

x1<-0:15

x2<-0:20

par(mfrow=c(1,3))

boxplot(x,x1,x2)

barplot(x1,x2)

plot(x)

Defining graphical parameters

par(mfrow=c(1,3), bg='gray’)   # bg= Background Colour

par(mfrow=c(1,3), bg='light yellow', cex=.8)       # cex= define font size, but it doesn’t match with mother programmes as here font size is relative

par(bg='green', cex=.8, mar=c(4,3,2,2))              # mar= margin, it goes clockwise from bottom, left, top and right

Plot and Legends

Legend components

Creating vector for Matplot

y60<-c(316.27, 316.81, 317.42, 318.87, 319.87, 319.43, 318.01, 315.74, 314.00, 313.68, 314.84, 316.03)

y70<-c(324.89, 325.82, 326.77, 327.97, 327.91, 327.50, 326.18, 324.53, 322.93, 322.90, 323.85, 324.96)

y80<-c(337.84, 338.19, 339.91, 340.60, 341.29, 341.00, 339.39, 337.43, 335.72, 335.84, 336.93, 338.04)

y90<-c(353.50, 354.55, 355.23, 356.04, 357.00, 356.07, 354.67, 352.76, 350.82, 351.04, 352.69, 354.07)

CO2<-data.frame (y60, y70, y80, y90)                    # making matrix from 4 vectors

CO2                                                                                                    # there is no row names

row.names(CO2)<-c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec") # adding row names

CO2

row.names(CO2)                                                                            # check values

matplot(CO2)                                                                           # mat plot

Note: here the observations labeled '1' represents the monthly CO2 levels for 1960, '2' represents those for 1970, and so on.

colnames(CO2) <- c("1960", "1970", '1980','1990')

CO2

We can enhance the plot by changing the line types and adding axis labels and titles:

x11()

matplot(CO2,axes=F, frame=T, type='b', ylab="", col=1:4)

    #axes =F:                               Initially do not draw axis, try changing F and T

    #frame =T:                             Box around the plot is drawn; try changing F instead T

    #type =b:                               Both line and character represent a seris;

    #ylab ="":                               No label for y-axis is shown;

    #ylim =c(310,400):                Specify the y-axis range

    #col =1:4                               Is define colors from colour 1 to 4, try changing it

axis(2)                                # put numerical annotations at the tick marks in y-axis;

axis(1, 1:12, row.names(CO2))

    # use the Monthly names for the tickmarks in x-axis; length is 12;

title(xlab="Month")                       #label for x-axis;

title(ylab="CO2 (ppm)")     #label for y-axis;

title("Monthly CO2 Concentration \n for 1960, 1970, 1980 and 1990")                      # '\n' is line break (like enter)

legend('topleft',c('1960','1970','1980','1990'),pch=c('1','2','3','4'),col=1:4,bty='o')

Try changing different parameters by yourself.

Pie chart

piechart<-read.table('E:R Exercise/R class/piedata.txt',header=T)

piechart

attach(piechart)

pie(score, label=rank, clockwise=TRUE, col= c("red", "orange", "yellow", "green", "blue", "purple"),  border=NA)

title(main="Clockwise Pie Chart with custom colours", font.main= 4)

Matplot

Plot the columns of one matrix against the columns of another

a<-seq(1:10)

b<-seq(10:1)

c<-seq(1:10)^2

matplot(a,b,type='l', lwd=1)

matplot(a,c)

matpoints(a, b, type = "p")

matlines (a, b, type = "l",lwd=3)

matlines (a, c, type = "l")

High Quality plot export

tiff(filename = "D:/pie.tiff", pointsize=7, width = 8.5, height = 8.5,units = "cm", res = 400, restoreConsole = TRUE)   # to starting graphics command, filename = the drive/folder location and the desired file name, with extenstion

The command 'tiff' can be jpeg, ping, pdf but you need to change the parameters in in parenthesis 

pie(score, label=rank, clockwise=TRUE, col= c("red", "orange", "yellow", "green", "blue", "purple"),  border=NA) # you can give any type of plots you want

dev.off()                 # to end graphics command, then the plot will be saved in above given location

Working with plot and legends

data.df<-read.table('E:/R Exercise/R class/regression.txt', header=T)

data.df; names(data.df); attach(data.df)

par(mfrow = c(1,1), col='green', bg='6', col.axis='red', col.lab= 'white', fg='blue') # setting different parameters in 'par' command

here,       col =                        colour of plot (eg points in plot)

              bg =                         background colour

              col.axis =                 colour of axis

              col.lab =                   colour of axis labels

              fg =                          foreground label                                    

It is not necessary to state if you want to plot only one plot in a plot window

plot(growth, pch=20, col='yellow')                                         

Plot for only one variable

lines(growth,lty=3, col=3)

lines(lowess(growth), col=2, lty=2,lwd=2)

Find help file for more on 'lowess', it a kind of polynomial regression

legend(5.5,12, c('growth', 'Line join', 'Polynomial regression'),

       lty=c(0,3,1),col=c(1,3,2),pch=c(20,NA,NA))

Try with more parameters and changed location of legend

legend('topright',c('growth','Line join', 'Polynomial regression'), pch=c(20,NA,NA), lty=c(0,3,1), col=c(1,3,2), bty='n',cex=0.8)

# 0.9, 4                                  - position of top left corner or legend to place

# bottomright                          - is position of legend

# c('growth','Line join', 'Polynomial regression') -text to describe legends

# pch=c(20,NA,NA)             - is to give legend types that are used in plot, hence must be the same as above command

# lty=c(0,3,1)                      - is line types that are used above in line command

# col=c(1,3,2)                     - colour types used in plot respectively to the commands

# bty=n                               - do not plot the legend box      

# cex=0.8                             - changes legend font size

Work yourself: add another variable 'tannin' and display in legend as well

points(tannin,pch=18)

legend('topright', c('growth', 'Line join', 'Polynomial regression', 'tannin'), pch=c(20,NA,NA,18),lty=c(0,3,1,0),col=c(1,3,2,1), bty='n')

Adding Text in plot

plot(growth, xlab='', ylab='',  type='n')       # here, type='n' means blank plot or nothing to display

mtext('Text on side 1, cex=1', side=1, cex=1)

mtext('Text on side 2, cex=1.2', side=2,cex=1.2)

mtext('Text on side 3, cex=1.3', side=3,cex=1.5)

mtext('Text on side 4, cex=2', side=4,cex=2)

text(5,5, "TESTING")

text(5,10,'CHEKCING')

Adding symbols to plots

abline()                                                        # can be used to draw a straight line to a plot.

abline(a,b)                                        # a= y-intercept, b=slope.

plot(growth,xlim=c(0,25),ylim=c(0,30))

abline(h=30, lwd=2)                         # draws a horizontal line at y=30.

abline(v=12)                                    # draws a vertical line at x=12.

abline(h=12,lwd=3)

abline(v=4,lty=5)

let's try with changing parameters

plot(growth,tannin)

abline(a=3,b=.2)

abline(v=5)

plot(growth)

abline(a=2,b=.3)

Adding arrow and line segment

plot(growth, tannin)

arrows(5,2,6,4)                                      # (start.x,start.y, end.x,end.y)

segments(5,2,10,1,lty=3)                        # (start.x,start.y, end.x,end.y)

title("arrow and segment")     

text(6,4.2,"This the point", cex=0.7)

Identifying plotted points

# While examining a plot, identifying a data point such as possible outliers can be achieved using identify() function.

plot(growth,pch=16,col=2,cex=2)                   # pch= point type, col= colour type, cex = size

identify(data.df$growth, n=8)          # work for single variable plot only

# After pressing return, R waits for you to identify (n=8) points with the mouse.

# Moving the mouse cursor over the graphics window and click on a data point.

# Then the observation number appears next to the point, thus making the point identifiable.