tests/forestplot2_vtests.R

In forestplot: Advanced Forest Plot Using 'grid' Graphics

library(forestplot)
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
forestplot(row_names, coef, low, high,
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  ),
  legend = c("Treatment", "Placebo")
)

# Check colgap
forestplot(row_names, coef, low, high,
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  colgap = unit(2, "mm"),
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  ),
  legend = c("Treatment", "Placebo")
)

forestplot(row_names, coef, low, high,
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  colgap = unit(20, "mm"),
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  ),
  legend = c("Treatment", "Placebo")
)

# Change first to diamonds
forestplot(row_names, coef, low, high,
  fn.ci_norm = c(
    "fpDrawDiamondCI",
    rep("fpDrawNormalCI",
      times = nrow(coef) - 1
    )
  ),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    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]]
forestplot(row_names, coef, low, high,
  fn.ci_norm = list(
    list(fpDrawDiamondCI, fpDrawCircleCI),
    list(fpDrawNormalCI, fpDrawNormalCI),
    list(fpDrawNormalCI, fpDrawCircleCI),
    list(fpDrawNormalCI, fpDrawNormalCI)
  ),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)


# Check with pch=1
forestplot(row_names, coef, low, high,
  pch = 1,
  fn.ci_norm = c("fpDrawDiamondCI", "fpDrawPointCI"),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)
# Check with pch = 2
forestplot(row_names, coef, low, high,
  pch = 2,
  fn.ci_norm = c("fpDrawDiamondCI", "fpDrawPointCI"),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright"),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)

# Check xlab
forestplot(row_names, coef, low, high,
  cex = 1.5,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(title = "Group", pos = "top")
)

forestplot(row_names, coef, low, high,
  cex = 1,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates"
)


# Check line-height
forestplot(row_names, coef, low, high,
  lineheight = "lines",
  cex = 1, # Base cex height
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates"
)

forestplot(row_names, coef, low, high,
  line.margin = .1,
  lineheight = "lines",
  cex = 1.5, # Larger line height
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  new_page = TRUE
)


my_cex <- 1.4
forestplot(row_names, coef, low, high,
  line.margin = .1,
  lineheight = unit(1.5 * my_cex, "lines"),
  cex = my_cex, # Larger line height
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  new_page = TRUE
)


my_cex <- 1.4
forestplot(row_names, coef, low, high,
  line.margin = .1,
  lineheight = unit(1.5 * my_cex, "lines"),
  cex = my_cex, # Larger line height
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  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))
forestplot(row_names, coef, low, high,
  new_page = FALSE,
  lineheight = unit(1.5 * my_cex, "lines"),
  cex = my_cex, # Larger line height
  fn.ci_norm = 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()
pushViewport(viewport(layout.pos.row = 2))
grid.rect(gp = gpar(col = "blue", fill = NA, lwd = 4))
forestplot(row_names, coef, low, high,
  new_page = FALSE,
  lineheight = unit(1.5 * my_cex, "lines"),
  cex = my_cex, # Larger line height
  fn.ci_norm = 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()

row_names <- list(list("test = 1", expression(test >= 2)))

test_data <- data.frame(
  coef = c(1.8, .8),
  low = c(1.4, 0.4),
  high = c(5, 1.55)
)

forestplot(row_names,
           test_data$coef,
           test_data$low,
           test_data$high,
           zero = 1,
           cex = 1,
           lineheight = "auto",
           xlab = "Odds",
           xlog = TRUE,
           xticks = c(1, 2, 5, 10))

#####################
# Check square data #
#####################
test_data <- data.frame(
  coef1 = c(1, 1.59, 1.24),
  coef2 = c(1, 1.7, 1.04),
  coef3 = c(1, 1.8, .94)
)
test_data$low1 <- test_data$coef1 - 1.96 * c(0, .2, .15)
test_data$high1 <- test_data$coef1 + 1.96 * c(0, .2, .15)

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

test_data$low3 <- test_data$coef3 - 1.96 * c(0, .1, .2)
test_data$high3 <- test_data$coef3 + 1.96 * c(0, .1, .2)

coef <- with(test_data, cbind(coef1, coef2, coef3))
low <- with(test_data, cbind(low1, low2, low3))
high <- with(test_data, cbind(high1, high2, high3))

forestplot(1:3, coef, low, high,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  fn.ci_norm = c(
    "fpDrawDiamondCI",
    rep("fpDrawNormalCI",
      times = nrow(coef) - 1
    )
  ),
  col = fpColors(
    box = c("royalblue", "gold", "gold"),
    line = c("darkblue", "orange", "orange")
  ),
  xlab = "The estimates"
)

# Single row test - issue #57
tt <- data.frame(
  mean = 3, upper = 4, lower = 2, P = 0.01, gene = "XX"
)
tt |>
  forestplot(labeltext = c(gene,P),
             xlog = TRUE,
             xlab = "OR",boxsize = 0.25) |>
  fp_set_style(box = "royalblue",
               line = "darkblue",
               summary = "royalblue") |>
  fp_add_header(gene = c("gene"),
                P = c("P")) |>
  fp_set_zebra_style("#EFEFEF")

# From issue #59
data(dfHRQoL)

dfHRQoL |>
  dplyr::group_by(.data$group) |>
  forestplot::forestplot(
    legend_args = forestplot::fpLegend(
      pos = list("top", "align" = "horizontal")
    )
  )