aubagnac: Amount of viral RNA

In kbroman/labstat: Statistics for Lab Scientists

Description

Amount of viral RNA in the central nervous systems of mice with three different genotypes at 6, 21 and 45 days after infection with Theiler's virus.

Usage

data(aubagnac)

Format

A data frame with four columns: mouse strain (genotype), days post infection, and amount of viral RNA in spinal cord and brain.

Source

Jean-Francois Bureau, Institut Pasteur, France

References

Aubagnac, S., Brahic, M. and Bureau, J.-F. (2001) Viral load increases in SJL/J mice persistently infected by Theiler's virus after inactivation of the B2m gene. J. Virol. 75, 7723-7726. (See Figure 1.)

Examples

data(aubagnac)
me.s <- tapply(aubagnac[,3],list(aubagnac[,1],aubagnac[,2]),mean,na.rm=TRUE)
me.b <- tapply(aubagnac[,4],list(aubagnac[,1],aubagnac[,2]),mean,na.rm=TRUE)
se.s <- tapply(aubagnac[,3],list(aubagnac[,1],aubagnac[,2]),sem)
se.b <- tapply(aubagnac[,4],list(aubagnac[,1],aubagnac[,2]),sem)

# barplots
par(mfrow=c(3,1),las=1)
# day 6
me <- as.numeric(rbind(me.s[,1],me.b[,1]))
se <- as.numeric(rbind(se.s[,1],se.b[,1]))
barplot(me,width=1,space=c(0,0,rep(c(1,0),2)),xlab="Mouse Group",
        ylab="Amount of viral RNA (score)", ylim=c(0,4),xlim=c(-0.5,8.5),
        col=c("white","black"),main="6 days post-infection")
abline(h=0)
x <- c(-0.5,2.5,5.5,8.5)
segments(x,0,x,-0.1,xpd=TRUE)
text(c(1,4,7),-0.3,as.character(levels(aubagnac[,1])),xpd=TRUE)
legend(-0.5,4,c("Spinal cord","Brain"),pch=15,cex=1.15,
       col=c("white","black"))
legend(-0.5,4,c("",""),pch=0,bty="n",cex=1.15)
x <- c(0:1,3:4,6:7)+0.5
segments(x,me,x,me+se,lwd=2)
segments(x-0.1,me+se,x+0.1,me+se,lwd=2)

# day 21
me <- as.numeric(rbind(me.s[,2],me.b[,2]))
se <- as.numeric(rbind(se.s[,2],se.b[,2]))
barplot(me,width=1,space=c(0,0,rep(c(1,0),2)),xlab="Mouse Group",
        ylab="Amount of viral RNA (score)", ylim=c(0,4),xlim=c(-0.5,8.5),
        col=c("white","black"),main="21 days post-infection")
abline(h=0)
x <- c(-0.5,2.5,5.5,8.5)
segments(x,0,x,-0.1,xpd=TRUE)
text(c(1,4,7),-0.3,as.character(levels(aubagnac[,1])),xpd=TRUE)
x <- c(0:1,3:4,6:7)+0.5
segments(x,me,x,me+se,lwd=2)
segments(x-0.1,me+se,x+0.1,me+se,lwd=2)

# day 45
me <- me.s[,3];names(me) <- NULL
se <- se.s[,3]
barplot(me,width=1,space=c(0,1,1),xlab="Mouse Group",
        ylab="Amount of viral RNA (score)", ylim=c(0,4),xlim=c(-0.5,5.5),
        col="white",main="45 days post-infection")
abline(h=0)
x <- c(-0.5,1.5,3.5,5.5)
segments(x,0,x,-0.1,xpd=TRUE)
x <- c(0,2,4)+0.5
text(x,-0.3,as.character(levels(aubagnac[,1])),xpd=TRUE)
segments(x,me,x,me+se,lwd=2)
segments(x-0.1,me+se,x+0.1,me+se,lwd=2)

kbroman/labstat documentation built on Jan. 6, 2021, 4:51 a.m.