P01. Introduction to R, part 3

A. Read in the same data as before

This file can be downloaded from here.

myTBdata <- read.table("TB_stats.txt", header=TRUE)

B. Plot the mortality in HIV negative against HIV positive check the plot function help file

?plot

plot is a generic function, and depending on what type of data you pass the function R will use different sub-functions (you dont need to worry about how it handles this!).

# make the plot
plot(x=myTBdata$HIV_neg_TB_mortality, y=myTBdata$HIV_pos_TB_mortality)

C. Add meaningful axes labels

plot(x=myTBdata$HIV_neg_TB_mortality, 
     y=myTBdata$HIV_pos_TB_mortality,
     xlab="Mortality in HIV negative people",
     ylab="Mortality in HIV positive people")

D. Add a meaningful title

plot(x=myTBdata$HIV_neg_TB_mortality, 
     y=myTBdata$HIV_pos_TB_mortality,
     xlab="Mortality in HIV negative people",
     ylab="Mortality in HIV positive people",
     main="Comparison of mortality in HIV negative and positive")

E. Change the colour of the points to red

plot(x=myTBdata$HIV_neg_TB_mortality, 
     y=myTBdata$HIV_pos_TB_mortality,
     xlab="Mortality in HIV negative people",
     ylab="Mortality in HIV positive people",
     main="Comparison of mortality in HIV negative and positive",
     col="red")

F. It’s hard to see the numbers because some are small and some very large Using a log scale is useful for that.You can either log the values and re-plot, or use the log option in plot()

plot(x=myTBdata$HIV_neg_TB_mortality, 
     y=myTBdata$HIV_pos_TB_mortality,
     xlab="Mortality in HIV negative people",
     ylab="Mortality in HIV positive people",
     main="Comparison of mortality in HIV negative and positive",
     col="red",
     log="xy")

G. Now let’s make a different kind of plot Show the distribution of Total_TB_mortality in a histogram and then change the x axis label. Note, same options as before.

hist(myTBdata$Total_TB_mortality)

hist(myTBdata$Total_TB_mortality,
     xlab="Number")

Now add a meaningful title to the plot

# Add your code here

H. Check what other aspects of the histogram you can change

?hist

Then change the color to “blue” in the last plot

hist(myTBdata$Total_TB_mortality,
     xlab="Number",
     main="Total TB mortality",
     col="blue")

I. Now let’s plot a histogram of mortality per 1000

Hint: calculate it as in the previous practical

# Add your code here

And add a title, and x axis label

# Add your code here

change the color to something different hint: to find more colours, run “colors()” or google “Colors in R”

# Add your code here

J. Now let’s show both histograms at the same time you need to make a call to “par”, short for parameters, setting the plot parameter “mfrow” (Multi-Figure ROW-wise) gives 1 row, and 2 columns of plot

par(mfrow=c(1,2))
hist(myTBdata$Total_TB_mortality,
     xlab="Number",
     main="Total TB mortality",
     col="blue")

cut and paste your plot code from I. here and run it. Then resize the plot window and see what happens

K. Export the figure and save it as a PNG with a useful name

Hint: use the Export button in the plot window

L. R has functions for every kind of plot for example:

?barplot
?boxplot
?contour

and stackoverflow.com has a lot of comments and help on every kind of plot

Advanced plotting exercises
Make a plot where:

# Add your code here

add HIV_neg_TB_mortality on the same y axis, in a different colour.

Hint: use points(). see ?points for information

# Add your code here

do you need to change the y axis label? i.e. does it still make sense now that it shows negative and positive mortality?

Answer:

Some of the points no longer fit on the graph. Why is this? You need to alter the y limit (ylim), which is an option of plot. What value will you choose?

Hint: the maximum value that the data go to change the ylim of the plot.

# Add your code here

The plot now has 2 data sets in different colours, so it needs a legend check the help of legend (there’s a lot of options!)

Hint: use x=“topright” instead of setting the x and y values for location.

Hint: use the option “fill” to change the colours

# Add your code here

The solutions can be accessed here.