Bar Plots with Error Bars in R

I've given up on Sigmaplot and dove back into plotting my results in R. This is a document of a process to plot means + standard error of the means (SEM).

First off, here's an example data set (FreeF.csv) in .csv format:

Sample,FreeF,State

1,63.46,A

2,0.5,B

3,0.33,C

4,0.16,B

5,0.45,C

6,0.1,C

7,0.18,B

8,0.6,A

9,2.01,A

10,16.84,C

11,1.27,C

12,0.14,B

13,1.75,C

14,5.13,B

15,0.84,A

16,0.82,A

17,3.52,A

18,0.4,C

19,0.12,B

I'll read this file into R:

> freef = read.csv(file="FreeF.csv",head=T,sep=",")

Next, we'll enter a function that I've borrowed and altered that will plot error bars for me from Monkey's Uncle. This function will plot a positive error bar only, unlike the original function.

> error.bar = function(x, y, upper, length=0.1,...){

+ arrows(x,y+upper, x, y, angle=90, code=1, length=length, ...) 

+ }

For this example data set, I have 3 states: A, B, and C. We'll have to calculate and store the FreeF means and standard errors for each state. We'll use the aggregate() function to do so:

> freef.mean = aggregate(freef$FreeF,by=list(freef$State),FUN=mean)

> freef.sd = aggregate(freef$FreeF,by=list(freef$State),FUN=sd)

> freef.n = aggregate(freef$FreeF,by=list(freef$State),FUN=length)

> freef.sem = freef.sd$x / sqrt(freef.n$x)

 We can now plot the data. First, we plot the means:

> freef.bp = barplot(freef.mean$x, main="FreeF By State", ylab="FreeF", xlab="State", ylim=range(0,25),  names.arg=freef.mean$Group.1, axis.lty=1)

This will plot a vertical bar plot for the FreeF means aggregated by State. I'll explain the arguments in the command:

main: Sets the title of the plot

ylab: Sets the y-axis label

xlab: Sets the x-axis label

ylim: Sets the y-axis limits

names.arg: Sets the x-axis labels for each State (A, B, and C)

axis.lty=1: Displays the x-axis in the same style as the y-axis (otherwise, it won't show the x-axis at all)

 Now to add the error bars:

> error.bar(freef.bp,freef.mean$x,freef.sem)

 Those are some massive-looking error bars. Oh well, back to lab.