Introduction to R for Life Sciences - Plotting

1. Plotting
Day 3 - Introduction to R for Life Sciences

2. Graphics
Very powerful
Exploration
Publishing
Three systems:
‘base’
lattice
ggplot2

3. Graphics
Anscombe's quartet
importance of graphing data
before analyzing it
Mind the effect of outliers on
statistical properties

4. Devices
device is "graphics destination": a window, or a file
Must be created and closed
win.graph(); X11() # window
pdf(); postscript(); svg(); # vector-graphics file (preferred)
png(); jpeg(); tiff() # bitmap file (for speed)
dev.off() # write the file
Multiple can exist at the same time, output goes to active device
dev.list(); dev.set()

5. Image formats
jpeg png pdf

6. plot()
plot() is a generic function, see ?plot.default for help
Common arguments: main; x/ylab; x/ylim; type; pch; cex; col; lty; lwd
> x <- -100:100
> plot(x, x^2)

7. plot()
> plot(main="the title",
x=avg, y=M[,1]-avg,
xlim=c(-0.5,0.5), ylim=c(-1, 1),
xlab="mean", ylab="deviation")
> points(x=avg, y=M[,2], col="red", pch="x")
> points(x=avg, y=M[,3], col="blue", pch=19)
> lines(x=avg, y=M[,4], col="green4")
> abline(h=0,v=0,col="grey")
> abline(h=c(-0.5, 0.5), col="purple", lty=2)

8. plot()
plot() is a generic function, see ?plot.default for help
Common arguments: main; x/ylab; x/ylim; type; pch; cex; col; lty; lwd
Many graphics aspects are controlled by par(), the graphics context
See ?par for meaning of additional parameters passed as '...'
Change with par(key1=value1, key2=value2, ...)
Common parameters:
cex.{main,lab,etc} # character scaling
mar # margin sizes
pty # "s" for square plots; "m" otherwise
mfrow(c(2,3)) # plotting several panels

9. Example
par(mfrow=c(2,3) # 2 rows, 3 columns
par(pty="s") # square plots

10. plot types

11. Pie charts: don’t use them!