###################################################################### # R code Statistics for Laboratory Scientists # Lab 3 Johns Hopkins University ###################################################################### # This file contains the miscellaneous R commands that appear in the # lab handout/pdf file. # # Lines beginning with the symbol '#' are comments in R. All other # lines contain code. # # In R for Windows, you may wish to open this file from the menu bar # (File:Display file); you can then copy commands into the command # window. (Use the mouse to highlight one or more lines; then # right-click and select "Paste to console".) ###################################################################### ###################################################################### # dotplot # This function plots the data for two samples # If includeCI=TRUE, it also includes t-based confidence intervals ###################################################################### dotplot <- function(x,y,includeCI=TRUE) { # Arrange the data X <- c(x,y) Y <- rep(1:0,c(length(x),length(y))) # jitter the Y positions Y <- Y + runif(length(Y),-0.1,0.1) # If requested, calculate the CI's # and make sure x-limits allow plot of CI's if(includeCI) { xci <- t.test(x)\$conf.int yci <- t.test(y)\$conf.int xlimits <- range(c(x,y,xci,yci)) } else xlimits <- range(c(x,y)) # make plot plot(X,Y,ylim=c(-0.5,1.5),yaxt="n",lwd=2,xlab="",ylab="", xlim=xlimits) abline(h=0:1,lty=2,col="gray") # add Y-axis labels u <- par("usr") segments(u[1],0:1,u[1]-diff(u[1:2])*0.03,0:1,xpd=TRUE) text(u[1]-diff(u[1:2])*0.08,1:0,c("A","B"),xpd=TRUE,cex=1.3) # add confidence intervals, if requested if(includeCI) { segments(xci[1],1.2,xci[2],1.2,lwd=2,col="blue") segments(xci,1.18,xci,1.22,lwd=2,col="blue") segments(mean(x),1.15,mean(x),1.25,lwd=2,col="blue") segments(yci[1],0.2,yci[2],0.2,lwd=2,col="red") segments(yci,0.18,yci,0.22,lwd=2,col="red") segments(mean(y),0.15,mean(y),0.25,lwd=2,col="red") } } ############################## # Hummer et al. (2001) data ############################## hummer <- read.csv("http://www.biostat.jhsph.edu/~kbroman/teaching/data/hummer.csv") x <- hummer[4:6,3] y <- hummer[1:3,3] x <- hummer[hummer[,1]=="IFN" & hummer[,2]=="--", 3] y <- hummer[hummer[,1]=="IFN" & hummer[,2]=="++", 3] dotplot(x,y) x2 <- hummer[hummer[,1]=="SV" & hummer[,2]=="--", 3] y2 <- hummer[hummer[,1]=="SV" & hummer[,2]=="++", 3] dotplot(x2,y2) t.test(x) t.test(y) t.test(x2) t.test(y2) ?t.test t.test(x, conf.level=0.99) t.test(x, y) t.test(y, x) t.test(x, y, var.equal=TRUE) t.test(x2, y2) t.test(x2, y2, alternative="two.sided") t.test(x2, y2, alternative="less") t.test(x2, y2, alternative="greater") t.test(activity ~ p53, data=hummer, subset=(medium=="IFN")) t.test(activity ~ p53, data=hummer, subset=(medium=="SV")) ############################## # Berrios et al. (2001) data ############################## # The following line will need to be revised, # according to the location of the file. berrios <- read.csv("http://www.biostat.jhsph.edu/~kbroman/teaching/data/berrios.csv") x <- berrios[berrios[,1]==1,2] y <- berrios[berrios[,1]==4,2] dotplot(x,y) ############### # End of lab3.R ###############