inst/examples/forestplot2_example.R

In raredd/Gmisc0: Collection of functions for plotting relations, generating tables, and more.

##############################################################
# Simple examples of how to do a forestplot with forestplot2 #
##############################################################

ask <- par(ask=TRUE)
library(grid)

# A basic example, create some fake data
row_names <- list(list("test = 1", expression(test >= 2)))
test_data <- data.frame(coef=c(1.59, 1.24),
  low=c(1.4, 0.78),
  high=c(1.8, 1.55))
forestplot2(row_names, 
            test_data$coef, 
            test_data$low, 
            test_data$high, 
            zero = 1, 
            cex  = 2,
            lineheight = "auto",
            xlab = "Lab axis txt",
            new_page = TRUE)

# Print two plots side by side using the grid 
# package's layout option for viewports
grid.newpage()
pushViewport(viewport(layout = grid.layout(1, 2)))
pushViewport(viewport(layout.pos.col = 1))
forestplot2(row_names, 
            test_data$coef, 
            test_data$low, 
            test_data$high, 
            zero = 1, 
            cex  = 2,
            lineheight = "auto",
            xlab = "Lab axis txt")
popViewport()
pushViewport(viewport(layout.pos.col = 2))
forestplot2(row_names, 
            test_data$coef, 
            test_data$low, 
            test_data$high, 
            zero = 1, 
            cex  = 2,
            lineheight = "auto",
            xlab = "Lab axis txt")
popViewport()
popViewport()


# An advanced test
test_data <- data.frame(coef1=c(1, 1.59, 1.3, 1.24),
  coef2=c(1, 1.7, 1.4, 1.04),
  low1=c(1, 1.3, 1.1, 0.99),
  low2=c(1, 1.6, 1.2, 0.7),
  high1=c(1, 1.94, 1.6, 1.55),
  high2=c(1, 1.8, 1.55, 1.33))

col_no <- grep("coef", colnames(test_data))
row_names <- list(
  list("Category 1", "Category 2", "Category 3", expression(Category >= 4)),
  list("ref", 
    substitute(expression(bar(x) == val), 
               list(val = round(rowMeans(test_data[2, col_no]), 2))), 
    substitute(expression(bar(x) == val), 
               list(val = round(rowMeans(test_data[3, col_no]), 2))), 
    substitute(expression(bar(x) == val), 
               list(val = round(rowMeans(test_data[4, col_no]), 2))))
)

coef <- with(test_data, cbind(coef1, coef2))
low <- with(test_data, cbind(low1, low2))
high <- with(test_data, cbind(high1, high2))
forestplot2(row_names, coef, low, high, 
            main="Cool study",
            zero = 1, boxsize=0.5,
            col=fpColors(box=c("royalblue", "gold"),
                         line=c("darkblue", "orange"),
                         summary=c("darkblue", "red")),
            xlab="The estimates",
            new_page = TRUE, 
            legend.title="Group",
            legend=c("Treatment", "Placebo"),
            legend.pos=list("topright"),
            legend.r = unit(.1, "snpc"),
            legend.gp = gpar(col="#CCCCCC", lwd=1.5))

# An example of how the exponential works
test_data <- data.frame(coef=c(2.45, 0.43),
  low=c(1.5, 0.25),
  high=c(4, 0.75),
  boxsize=c(0.5, 0.5))
row_names <- cbind(c("Name", "Variable A", "Variable B"),
                   c("HR", test_data$coef))
test_data <- rbind(rep(NA, 3), test_data)

forestplot2(labeltext = row_names, 
            is.summary=c(TRUE, FALSE, FALSE),
            mean      = test_data$coef, 
            lower     = test_data$low, 
            upper     = test_data$high, 
            boxsize   = test_data$boxsize,
            zero      = 1,
            xlog      = TRUE,
            col = fpColors(lines="red", box="darkred"),
            new_page = TRUE)


par(ask=ask)