Styjun

I would like to use the script created by Thomas a couple of years ago to draw a forest plot. Unfortunately, the script is fitted to the data and need to be adjusted I case that treatment estimates and confidence interval are different.

To adapt the script to my data

1. I updated the data frame containing treatment estimates and
   standard errors


2. I changes the breaks of the x-axis to accommodate
   my data

But as you can see, the x-axis should be log-transformed. However, when I add log="x" to the plot() function, I get the following error message: Error in plot.window(...) : Logarithmic axis must have positive limits.
But the created plot did not fit on the panel if I change the xlim from xlim=c(-10,12) to xlim=c(1,12). Moreover, every x position of text on the left side of the plot need negative values.
Does anyone have an idea how to fix this?

Forest Plot

mydf <- data.frame(
 SubgroupH=c('LV-EF',NA,NA,'Sex',NA,NA),
 Subgroup=c(NA,'low','normal',NA,'female','male'),
 NoOfPatients=c(NA,2815,1935,NA,3843,908),
 HazardRatio=c(NA,1.07, 2.81,NA,1.69, 1.74),
 HazardLower=c(NA,0.42, 1.26,NA,0.41, 0.96),
 HazardUpper=c(NA,2.73, 6.26,NA,6.93, 3.16),
 Pvalue=c(NA,0.77,0.17,NA,0.47,0.21),
 PvalueI=c(0.46,NA,NA,0.46,NA,NA),
 stringsAsFactors=FALSE
)

#################

rowseq <- seq(nrow(mydf),1)
par(mai=c(1,0,0,0))
plot(mydf$HazardRatio, rowseq, pch=15,
 xlim=c(-10,12), ylim=c(0,7),
 xlab='', ylab='', yaxt='n', xaxt='n',
 bty='n')

axis(1, round(c(1/10, 1/5, 1, 5, 10),2), cex.axis=.5)

segments(1,-1,1,6.25, lty=3)
segments(mydf$HazardLower, rowseq, mydf$HazardUpper, rowseq)

mtext('Off-PumpnCABG Better',1, line=2.5, at=0, cex=.5, font=2)
mtext('On-PumpnCABG Better',1.5, line=2.5, at=2, cex=.5, font=2)

?text
text(-8,6.5, "Subgroup", cex=.75, font=2, pos=4)
t1h <- ifelse(!is.na(mydf$SubgroupH), mydf$SubgroupH, '')
text(-8,rowseq, t1h, cex=.75, pos=4, font=3)
t1 <- ifelse(!is.na(mydf$Subgroup), mydf$Subgroup, '')
text(-7.5,rowseq, t1, cex=.75, pos=4)

text(-5,6.5, "No. ofnPatients", cex=.75, font=2, pos=4)
t2 <- ifelse(!is.na(mydf$NoOfPatients), format(mydf$NoOfPatients,big.mark=","), '')
text(-3, rowseq, t2, cex=.75, pos=2)

text(-1,6.5, "Hazard Ratio (95%)", cex=.75, font=2, pos=4)
t3 <- ifelse(!is.na(mydf$HazardRatio), with(mydf, paste(HazardRatio,' (',HazardLower,'-',HazardUpper,')',sep='')), '')
text(3,rowseq, t3, cex=.75, pos=4)

text(7.5,6.5, "P Value", cex=.75, font=2, pos=4)
t4 <- ifelse(!is.na(mydf$Pvalue), mydf$Pvalue, '')
text(7.5,rowseq, t4, cex=.75, pos=4)

text(10,6.5, "P Value fornInteraction", cex=.75, font=2, pos=4)
t5 <- ifelse(!is.na(mydf$PvalueI), mydf$PvalueI, '')
text(10,rowseq, t5, cex=.75, pos=4)