Microbial Informatics

• Homework 2 due today
• Homework 3 is out
• Read Introduction to Statistics with R (Chapter 8)

• Histograms
• Box plots
• Bar plots
• Strip charts

• Graphics
  • Dot plots
  • Legends
  • Line segments
• Random variables

metadata <- read.table(file="wild.metadata.txt", header=T)

## Warning: cannot open file 'wild.metadata.txt': No such file or directory

## Error: cannot open the connection

rownames(metadata) <- metadata$Group

## Error: object 'metadata' not found

metadata <- metadata[,-1]

## Error: object 'metadata' not found

• The above methods generally involve plotting a numerical value against a categorical value
• We'd also like to plot numerical variables against each other

    plot(metadata$Weight)               # what is this using as an x-axis?

## Error: object 'metadata' not found

    plot(metadata$Weight, metadata$Ear)         # what is this using as an x-axis?          

## Error: object 'metadata' not found

    plot(metadata$Ear~metadata$Weight)          # what is this using as an x-axis?

## Error: object 'metadata' not found

• Be sure to see ?plot and ?plot.default

    plot(metadata$Ear~metadata$Weight, col="blue", pch=18)

## Error: object 'metadata' not found

    plot(metadata$Ear~metadata$Weight, col="blue", pch=20)

## Error: object 'metadata' not found

    plot(metadata$Ear~metadata$Weight, col="blue", pch=20, cex=2)

## Error: object 'metadata' not found

    plot(metadata[metadata$Sex=="M","Ear"]~metadata[metadata$Sex=="M","Weight"], col="blue", pch=18)

## Error: object 'metadata' not found

    points(metadata[metadata$Sex=="F","Ear"]~metadata[metadata$Sex=="F","Weight"], col="pink", pch=20)

## Error: object 'metadata' not found

m.hist <- hist(metadata$Weight[metadata$Sex=="F"], breaks=10, ylim=c(0,20), xlim=c(0,30), col="pink")

## Error: object 'metadata' not found

f.hist <- hist(metadata$Weight[metadata$Sex=="M"], breaks=10, col="blue", add=T)

## Error: object 'metadata' not found

plot(m.hist$density~m.hist$mids, type="h", col="blue", ylim=c(0,0.2))

## Error: object 'm.hist' not found

points(f.hist$density~f.hist$mids, type="h", col="red")

## Error: object 'f.hist' not found

plot(m.hist$density~m.hist$mids, type="l", col="blue", ylim=c(0,0.2))

## Error: object 'm.hist' not found

points(f.hist$density~f.hist$mids, type="l", col="red")

## Error: object 'f.hist' not found

legend(x=20, y=0.18, legend=c("Female", "Male"), col=c("red", "blue"), lty=1, lwd=2)

## Error: plot.new has not been called yet

location <- locator(1)

## Error: plot.new has not been called yet

legend(location, legend=c("Female", "Male"), col=c("red", "blue"), lty=1, lwd=2)

## Error: object 'location' not found

location

## Error: object 'location' not found

abline(a=0.01, b=0.01)

## Error: plot.new has not been called yet

abline(v=20, col="red", lwd=3)

## Error: plot.new has not been called yet

abline(h=0.05, col="blue", lty=2, lwd=3)

## Error: plot.new has not been called yet

segments(x0=10, x1=15, y0=0.20, y1=0.15)

## Error: plot.new has not been called yet

segments(x0=c(10, 21), x1=c(15, 25), y0=c(0.20, 0.15), y1=c(0.15, 0.12))

## Error: plot.new has not been called yet

• In science, much of what we do assumes that samples are observed randomly
• We live in a probabilistic world where everything has a probability, even if it is very small

• Pick a number between 1 and 10 and write it down
• What would you expect a random sampling of the numbers from 1 to 10 to look like?
• What would it depend on?
• Mean?
• Min?
• Max?
• What type of plot would we use?