Misplaced grid lines with xlog=TRUE - Forestplot - R

Question

Please, I need some help about using the xlog=TRUE option.

It is requested to provide the mean, lower, upper, zero, grid and clip already as exponentials, but I find the package is drawing the grid lines at the exponential of the numbers I am already providing as exponentials. As a consequence, the grid lines are in the wrong place.

metaan <- 
  structure(list(
    mean  = c(NA, NA, NA, 0.27, 0.47, 0.33, 0.69, 0.86, 0.37, 0.08, 0.44, 0.54, 0.41, NA), 
    lower = c(NA, NA, NA, 0.13, 0.12, 0.19, 0.12, 0.54, 0.17, 0.03, 0.16, 0.06, 0.29, NA),
    upper = c(NA, NA, NA, 0.58, 1.81, 0.60, 3.97, 1.36, 0.81, 0.21, 1.25, 4.50, 0.58, NA)),
    .Names = c("mean", "lower", "upper"), 
    row.names = c(NA, -27L), 
    class = "data.frame")

tabletext<-cbind(
  c("", "AB class", "", "     Aminoglycosides", "     B-lactams", "     Cephalosporins", "     Fenicoles", "     Fluoroquinolones", "     Multiresistance", "     Sulphamides", "     Tetracyclines", "     Tri/Sulpha", "     Subtotal", ""),  
  c("", "OR", "", "0.27", "0.47", "0.33", "0.69", "0.86", "0.37", "0.08", "0.44", "0.54", "0.41", ""),
  c("", "n", "", "4", "3", "2", "3", "4", "2", "3", "4", "3", "5", ""))

xticks <- c(0.1, 0.25, 0.5, 1, 1.5, 2, 3)

forestplot(tabletext,
           graph.pos = 3,
           txt_gp = fpTxtGp(label = gpar(fontsize=10)),
           hrzl_lines = list("3" = gpar(lty=1)),
           zero = 1,
           line.margin = .05,
           mean = cbind(metaan[,"mean"]),
           lower = cbind(metaan[,"lower"]),
           upper = cbind(metaan[,"upper"]),
           is.summary=c(FALSE, TRUE, rep(FALSE, 9)),
           col=fpColors(box=c("blue"), summary=c("blue")),
           grid = structure(0.41, 
                            gp = gpar(lty = 2, col = "#CCCCFF")),
           clip=c(0.1, 3),
           xlog=T,
           xticks=xticks,
           xlab="Odds ratio")

The grid line is at the exponential of OR=0.41, instead of at OR=0.41

When provided the log to get the grid lines at the correct place (e.g. -0.38, or log(0.41)), I get the error message that I should provide all parameters already as exponential.

forestplot(tabletext,
           graph.pos = 3,
           txt_gp = fpTxtGp(label = gpar(fontsize=10)),
           hrzl_lines = list("3" = gpar(lty=1)),
           zero = 1,
           line.margin = .05,
           mean = cbind(metaan[,"mean"]),
           lower = cbind(metaan[,"lower"]),
           upper = cbind(metaan[,"upper"]),
           is.summary=c(FALSE, TRUE, rep(FALSE, 9)),
           col=fpColors(box=c("blue"), summary=c("blue")),
           grid = structure(-0.39, 
                            gp = gpar(lty = 2, col = "#CCCCFF")),
           clip=c(0.1, 3),
           xlog=T,
           xticks=xticks,
           xlab="Odds ratio")

Error in forestplot.default(tabletext, graph.pos = 3, txt_gp = fpTxtGp(label = gpar(fontsize = 10)),  : 
  All argument values (mean, lower, upper, zero, grid and clip) should be provided as exponentials when using the log scale. This is an intentional break with the original forestplot function in order to simplify other arguments such as ticks, clips, and more.

I have tried including the grid numbers as lists, but I always encounter the same error message either if I provide the numbers as exponentials (grid misplaced) or as log (error message).

I am wondering what I am doing wrong and if there is any other way to get the grid lines in the correct place.

Thanks in advance,

Magda.

Answer 1

Solved. Updated to 1.8 package version from GitHub and got the correct figure. :)