g_forest: Create a forest plot from an 'rtable'

In tern: Create Common TLGs Used in Clinical Trials

Create a forest plot from an rtable

Description

Usage

g_forest(
  tbl,
  col_x = attr(tbl, "col_x"),
  col_ci = attr(tbl, "col_ci"),
  vline = 1,
  forest_header = attr(tbl, "forest_header"),
  xlim = c(0.1, 10),
  logx = TRUE,
  x_at = c(0.1, 1, 10),
  width_row_names = lifecycle::deprecated(),
  width_columns = NULL,
  width_forest = lifecycle::deprecated(),
  lbl_col_padding = 0,
  rel_width_forest = 0.25,
  font_size = 12,
  col_symbol_size = attr(tbl, "col_symbol_size"),
  col = getOption("ggplot2.discrete.colour")[1],
  ggtheme = NULL,
  as_list = FALSE,
  gp = lifecycle::deprecated(),
  draw = lifecycle::deprecated(),
  newpage = lifecycle::deprecated()
)

Arguments

tbl	(VTableTree) rtables table with at least one column with a single value and one column with 2 values.
col_x	(integer(1) or NULL) column index with estimator. By default tries to get this from tbl attribute col_x, otherwise needs to be manually specified. If NULL, points will be excluded from forest plot.
col_ci	(integer(1) or NULL) column index with confidence intervals. By default tries to get this from tbl attribute col_ci, otherwise needs to be manually specified. If NULL, lines will be excluded from forest plot.
vline	(numeric(1) or NULL) x coordinate for vertical line, if NULL then the line is omitted.
forest_header	(character(2)) text displayed to the left and right of vline, respectively. If vline = NULL then forest_header is not printed. By default tries to get this from tbl attribute forest_header. If NULL, defaults will be extracted from the table if possible, and set to "Comparison\nBetter" and "Treatment\nBetter" if not.
xlim	(numeric(2)) limits for x axis.
logx	(flag) show the x-values on logarithm scale.
x_at	(numeric) x-tick locations, if NULL, x_at is set to vline and both xlim values.
width_row_names	Please use the lbl_col_padding argument instead.
width_columns	(numeric) a vector of column widths. Each element's position in colwidths corresponds to the column of tbl in the same position. If NULL, column widths are calculated according to maximum number of characters per column.
width_forest	Please use the rel_width_forest argument instead.
lbl_col_padding	(numeric) additional padding to use when calculating spacing between the first (label) column and the second column of tbl. If colwidths is specified, the width of the first column becomes colwidths[1] + lbl_col_padding. Defaults to 0.
rel_width_forest	(proportion) proportion of total width to allocate to the forest plot. Relative width of table is then 1 - rel_width_forest. If as_list = TRUE, this parameter is ignored.
font_size	(numeric(1)) font size.
col_symbol_size	(numeric or NULL) column index from tbl containing data to be used to determine relative size for estimator plot symbol. Typically, the symbol size is proportional to the sample size used to calculate the estimator. If NULL, the same symbol size is used for all subgroups. By default tries to get this from tbl attribute col_symbol_size, otherwise needs to be manually specified.
col	(character) color(s).
ggtheme	(theme) a graphical theme as provided by ggplot2 to control styling of the plot.
as_list	(flag) whether the two ggplot objects should be returned as a list. If TRUE, a named list with two elements, table and plot, will be returned. If FALSE (default) the table and forest plot are printed side-by-side via cowplot::plot_grid().
gp	g_forest is now generated as a ggplot object. This argument is no longer used.
draw	g_forest is now generated as a ggplot object. This argument is no longer used.
newpage	g_forest is now generated as a ggplot object. This argument is no longer used.

Details

Given a rtables::rtable() object with at least one column with a single value and one column with 2 values, converts table to a ggplot2::ggplot() object and generates an accompanying forest plot. The table and forest plot are printed side-by-side.

Value

ggplot forest plot and table.

Examples

library(dplyr)
library(forcats)
library(nestcolor)

adrs <- tern_ex_adrs
n_records <- 20
adrs_labels <- formatters::var_labels(adrs, fill = TRUE)
adrs <- adrs %>%
  filter(PARAMCD == "BESRSPI") %>%
  filter(ARM %in% c("A: Drug X", "B: Placebo")) %>%
  slice(seq_len(n_records)) %>%
  droplevels() %>%
  mutate(
    # Reorder levels of factor to make the placebo group the reference arm.
    ARM = fct_relevel(ARM, "B: Placebo"),
    rsp = AVALC == "CR"
  )
formatters::var_labels(adrs) <- c(adrs_labels, "Response")
df <- extract_rsp_subgroups(
  variables = list(rsp = "rsp", arm = "ARM", subgroups = c("SEX", "STRATA2")),
  data = adrs
)
# Full commonly used response table.

tbl <- basic_table() %>%
  tabulate_rsp_subgroups(df)
g_forest(tbl)

# Odds ratio only table.

tbl_or <- basic_table() %>%
  tabulate_rsp_subgroups(df, vars = c("n_tot", "or", "ci"))
g_forest(
  tbl_or,
  forest_header = c("Comparison\nBetter", "Treatment\nBetter")
)

# Survival forest plot example.
adtte <- tern_ex_adtte
# Save variable labels before data processing steps.
adtte_labels <- formatters::var_labels(adtte, fill = TRUE)
adtte_f <- adtte %>%
  filter(
    PARAMCD == "OS",
    ARM %in% c("B: Placebo", "A: Drug X"),
    SEX %in% c("M", "F")
  ) %>%
  mutate(
    # Reorder levels of ARM to display reference arm before treatment arm.
    ARM = droplevels(fct_relevel(ARM, "B: Placebo")),
    SEX = droplevels(SEX),
    AVALU = as.character(AVALU),
    is_event = CNSR == 0
  )
labels <- list(
  "ARM" = adtte_labels["ARM"],
  "SEX" = adtte_labels["SEX"],
  "AVALU" = adtte_labels["AVALU"],
  "is_event" = "Event Flag"
)
formatters::var_labels(adtte_f)[names(labels)] <- as.character(labels)
df <- extract_survival_subgroups(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM", subgroups = c("SEX", "BMRKR2")
  ),
  data = adtte_f
)
table_hr <- basic_table() %>%
  tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1])
g_forest(table_hr)

# Works with any `rtable`.
tbl <- rtable(
  header = c("E", "CI", "N"),
  rrow("", 1, c(.8, 1.2), 200),
  rrow("", 1.2, c(1.1, 1.4), 50)
)
g_forest(
  tbl = tbl,
  col_x = 1,
  col_ci = 2,
  xlim = c(0.5, 2),
  x_at = c(0.5, 1, 2),
  col_symbol_size = 3
)

tbl <- rtable(
  header = rheader(
    rrow("", rcell("A", colspan = 2)),
    rrow("", "c1", "c2")
  ),
  rrow("row 1", 1, c(.8, 1.2)),
  rrow("row 2", 1.2, c(1.1, 1.4))
)
g_forest(
  tbl = tbl,
  col_x = 1,
  col_ci = 2,
  xlim = c(0.5, 2),
  x_at = c(0.5, 1, 2),
  vline = 1,
  forest_header = c("Hello", "World")
)

tern documentation built on Sept. 24, 2024, 9:06 a.m.