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STATS 330: Lecture 4 Graphics: Doing it in R Housekeeping My contact details…. Plus much else on course web page www.stat.auckland.ac.nz/~lee/330/ Or via Cecil Today’s lecture: R for graphics Aim of the lecture:

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STATS 330: Lecture 4

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STATS 330: Lecture 4

Graphics:

Doing it in R

330 lecture 4


Housekeeping

My contact details….

Plus much else on course web page

www.stat.auckland.ac.nz/~lee/330/

Or via Cecil

330 lecture 1


330 lecture 1


Today’s lecture: R for graphics

Aim of the lecture:

To show you how to use R to produce the plots shown in the last few lectures

330 lecture 4


Getting data into R

  • In 330, as in most practice, data comes in 2 main forms

    • As a text file

    • As an Excel spreadsheet

  • Need to convert from these formats to R

  • Data in R is organized in data frames

    • Row by column arrangement of data (as in Excel)

    • Variables are columns

    • Rows are cases (individuals)

330 lecture 4


Text files to R

  • Suppose we have the data in the form of a text file

  • Edit the text file (use Notepad or similar) so that

    • The first row consists of the variable names

    • Each row of data (i.e. data on a complete case) corresponds to one line of the file

  • Suppose data fields are separated by spaces and/or tabs

  • Then, to create a data frame containing the data, we use the R function read.table

330 lecture 4


Example: the cherry tree data

Suppose we have a text file called cherry.txt (probably created using Notepad or maybe Word, but saved as a text file)

First line: variable names

Data for each tree on a separate line, separated by “white space” (spaces or tabs)

330 lecture 4


Creating the data frame

In R, type

cherry.df = read.table(file.choose(),

header=T)

and press the return key

Click here to select file

This brings up the dialog to select the file cherry.txt

containing the data.

Click here to load data

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Check all is OK!

330 lecture 4


Getting data from a spreadsheet (1)

Create the spreadsheet in Excel

Save it as Comma Delimited Text (CSV)

This is a text file with all cells separated by commas

File is called cherry.csv

330 lecture 4


Getting data from a spreadsheet (2)

In R, type

cherry.df = read.table(file.choose(),

header=T, sep=“,”)

and proceed as before

330 lecture 4


Data frames and variables

  • Suppose we have read in data and made a data frame

  • At this point R doesn’t know about the variables in the data frame, so we can’t use e.g. the variable diameter in R commands

  • We need to say

    attach(cherry.df)

    to make the variables in cherry.df visible to R.

  • Alternatively, say cherry.df$diameter

330 lecture 4


Scatterplots

In R, there are 2 distinct sets of functions for graphics, one for ordinary graphics, one for trellis.

Eg for scatterplots, we use either plot (ordinary R) or xyplot (Trellis)

In the next few slides, we discuss plot.

330 lecture 4


Simple plotting

plot(height,volume,

xlab=“Height (feet)”,

ylab=“Volume (cubic feet)”,

main = “Volume versus height for 31 black cherry trees”)

i.e. label axes (give units if possible), give a title

330 lecture 4


330 lecture 4


Alternative form of plot

plot(volume ~ height,

xlab=“Height (feet)”,

ylab=“Volume (cubic feet)”,

main = “Volume versus height for 31 black cherry trees”,

data = cherry.df)

Don’t need to attach with this form, note reversal of x,y

330 lecture 4


Colours, points, etc

Type

?par

for more info

par(bg="darkblue")

plot(height,volume,

xlab="Height (feet)",

ylab="Volume (cubic feet)",

main = "Volume versus height for 31 black cherry trees",

pch=19,fg="white",

col.axis=“lightblue",col.main="white",

col.lab=“white",col="white",cex=1.3)

330 lecture 4


330 lecture 4


Lines

  • Suppose we want to join up the rats on the rats plot. (see data next slide)

  • We could try

    plot(day, growth, type=“l”)but this won’t work

  • Points are plotted in order they appear in the data frame and each point is joined to the next

330 lecture 4


Rats: the data

  • > rats.df

  • growth group rat change day

  • 1 240 1 1 1 1

  • 2 250 1 1 1 8

  • 3 255 1 1 1 15

  • 4 260 1 1 1 22

  • 5 262 1 1 1 29

  • 6 258 1 1 1 36

  • 7 266 1 1 2 43

  • 8 266 1 1 2 44

  • 9 265 1 1 2 50

  • 10 272 1 1 2 57

  • 11 278 1 1 2 64

  • 12 225 1 2 1 1

  • 12 230 1 2 1 8

  • ... More data

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Don’t want this!

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Solution

Various solutions, but one is to plot each line separately, using subsetting

plot(day,growth,type="n")

lines (day[rat==1],growth[rat==1])

lines (day[rat==2],growth[rat==2])

and so on …. (boring!), or (better)

for(j in 1:16){

lines (day[rat==j],growth[rat==j])

}

Draw axes, labels only

330 lecture 4


Indicating groups

Want to plot the litters with different colours, add a legend: Rats 1-8 are litter 1, 9-12 litter 2, 13-16 litter 3

plot(day,growth,type="n")

for(j in 1:8)lines(day[rat==j],

growth[rat==j],col="white") # litter 1

for(j in 9:12)lines (day[rat==j], growth[rat==j],col="yellow") # litter 2

for(j in 13:16)lines (day[rat==j], growth[rat==j],col="purple") # litter 3

Set colour of line

330 lecture 4


legend

legend(13,380,

legend = c(“Litter 1”, “Litter 2”,

“Litter 3”),

col = c("white","yellow","purple"),

lwd = c(2,2,2),

horiz = T,

cex = 0.7)

(Type ?legend for a full explanation of these parameters)

330 lecture 4


330 lecture 4


Points and text

x=1:25

y=1:25

plot(x,y, type="n")

points(x,y,pch=1:25, col="red",

cex=1.2)


Points and text (3)

x=1:26

y=1:26

plot(x,y, type="n")

text(x,y, letters, col="blue", cex=1.2)


Trellis

  • Must load trellis library first

    library(lattice)

  • General form of trellis plots

    xyplot(y~x|W*Z, data=some.df)

  • Don’t need to attach data frame, trellis functions can pick out the variables, given the data frame

330 lecture 4


Main trellis functions

  • dotplotfor dotplots, use when X is categorical, Y is continuous

  • bwplotfor boxplots, use when X is categorical, Y is continuous

  • xyplotfor scatter plots, use when both x and y are continuous

  • equal.countuse to turn continuous conditioning variable into groups

330 lecture 4


Changing background colour

To change trellis background to white

trellis.par.set(background = list(col="white"))

To change plotting symbols

trellis.par.set(plot.symbol = list(pch=16, col="red", cex=1))

330 lecture 4


Equal.count

xyplot(volume~height|diameter, data=cherry.df)

330 lecture 4


Equal.count (2)

diam.gp<-equal.count(diameter,number=4,overlap=0)

xyplot(volume~height|diam.gp, data=cherry.df)

330 lecture 4


Changing plotting symbols

To change plotting symbols

trellis.par.set(plot.symbol = list(pch=16, col="red", cex=1))

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Non-trellis version

coplot(volume~height|diameter, data=cherry.df)

330 lecture 4


Non-trellis version (2)

coplot(volume~height|diameter,

data=cherry.df,number=4,overlap=0)

330 lecture 4


Other useful functions

  • Regular R

    • scatterplot3d (3d scatter plot, load library scatterplot3d)

    • contour, persp (draws contour plots, surfaces)

    • pairs

  • Trellis

    • cloud (3d scatter plot)

330 lecture 4


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