tests/visual_tests/forestplot2_vtests.R

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

library(grid)
test_data <- data.frame(coef1=c(1, 1.59, 1.3, 1.24),
                        coef2=c(1, 1.7, 1.4, 1.04))

test_data$low1 <- test_data$coef1 - 1.96*c(0, .2, .1, .15)
test_data$high1 <- test_data$coef1 + 1.96*c(0, .2, .1, .15)

test_data$low2 <- test_data$coef2 - 1.96*c(0, .1, .15, .2)
test_data$high2 <- test_data$coef2 + 1.96*c(0, .1, .15, .2)

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))

# Change all to diamonds
forestplot2(row_names, coef, low, high, 
            confintNormalFn=fpDrawDiamondCI,
            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))

# Change first to diamonds
forestplot2(row_names, coef, low, high, 
            confintNormalFn=c("fpDrawDiamondCI", 
                              rep("fpDrawNormalCI", 
                                  times=nrow(coef)-1)),
            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))

# You can also use a list with the actual functions
# as long as it is formatted [[row]][[column]]
# Note: if you have a non-square input then
# the software will reformat [[col]][[row]]
# to [[row]][[col]]
forestplot2(row_names, coef, low, high, 
            confintNormalFn=list(list(fpDrawDiamondCI, fpDrawCircleCI),
                                 list(fpDrawNormalCI, fpDrawNormalCI),
                                 list(fpDrawNormalCI, fpDrawCircleCI),
                                 list(fpDrawNormalCI, fpDrawNormalCI)),
            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))


# Check with pch=1
forestplot2(row_names, coef, low, high, 
            pch=1,
            confintNormalFn=c("fpDrawDiamondCI", "fpDrawPointCI"),
            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))

# Check with pch = 2
forestplot2(row_names, coef, low, high, 
            pch=2,
            confintNormalFn=c("fpDrawDiamondCI", "fpDrawPointCI"),
            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))

# Check xlab
forestplot2(row_names, coef, low, high, 
            cex=1.5,
            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="top")

forestplot2(row_names, coef, low, high, 
            cex=1,
            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="top")


# Check line-height
forestplot2(row_names, coef, low, high, 
            lineheight="lines",
            cex=1, # Base cex height
            confintNormalFn=fpDrawDiamondCI,
            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="top")



forestplot2(row_names, coef, low, high, 
            lineheight="lines",
            cex=1.5, # Larger line height
            confintNormalFn=fpDrawDiamondCI,
            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="top")


my_cex <- 1.4
forestplot2(row_names, coef, low, high, 
            lineheight=unit(1.5*my_cex, "lines"),
            cex=my_cex, # Larger line height
            confintNormalFn=fpDrawDiamondCI,
            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="top")


my_cex <- 1.4
forestplot2(row_names, coef, low, high, 
            lineheight=unit(1.5*my_cex, "lines"),
            cex=my_cex, # Larger line height
            confintNormalFn=fpDrawDiamondCI,
            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)


# Check if you can stack the plots in a grid
grid.newpage()
lv <- grid.layout(nrow=2, heights=unit(c(.6,.4), "npc"))
pushViewport(viewport(layout=lv))
pushViewport(viewport(layout.pos.row=1))
grid.rect(gp=gpar(col="blue", fill=NA, lwd=4))
forestplot2(row_names, coef, low, high, 
            lineheight=unit(1.5*my_cex, "lines"),
            cex=my_cex, # Larger line height
            confintNormalFn=fpDrawDiamondCI,
            zero = 1, boxsize=0.5,
            col=fpColors(box=c("royalblue", "gold"),
                         line=c("darkblue", "orange"),
                         summary=c("darkblue", "red")),
            xlab="The estimates",
            legend.title="Group",
            legend=c("Treatment", "Placebo"),
            legend.pos="top")
grid.rect(gp=gpar(col="red", fill=NA, lwd=2))
popViewport()
pushViewport(viewport(layout.pos.row=2))
grid.rect(gp=gpar(col="blue", fill=NA, lwd=4))
forestplot2(row_names, coef, low, high, 
            lineheight=unit(1.5*my_cex, "lines"),
            cex=my_cex, # Larger line height
            confintNormalFn=fpDrawDiamondCI,
            zero = 1, boxsize=0.5,
            col=fpColors(box=c("royalblue", "gold"),
                         line=c("darkblue", "orange"),
                         summary=c("darkblue", "red")),
            xlab="The estimates")
grid.rect(gp=gpar(col="red", fill=NA, lwd=2))
popViewport()