h_grob_tbl_at_risk: Helper function to create patient-at-risk grobs

In tern: Create Common TLGs Used in Clinical Trials

Helper function to create patient-at-risk grobs

Description

Two graphical objects are obtained, one corresponding to row labeling and the second to the table of numbers of patients at risk. If title = TRUE, a third object corresponding to the table title is also obtained.

Usage

h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)

Arguments

data	(data.frame) survival data as pre-processed by h_data_plot.
annot_tbl	(data.frame) annotation as prepared by survival::summary.survfit() which includes the number of patients at risk at given time points.
xlim	(numeric(1)) the maximum value on the x-axis (used to ensure the at risk table aligns with the KM graph).
title	(flag) whether the "Patients at Risk" title should be added above the annot_at_risk table. Has no effect if annot_at_risk is FALSE. Defaults to TRUE.

Value

A named list of two gTree objects if title = FALSE: at_risk and label, or three gTree objects if title = TRUE: at_risk, label, and title.

Examples

library(dplyr)
library(survival)
library(grid)

fit_km <- tern_ex_adtte %>%
  filter(PARAMCD == "OS") %>%
  survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)

data_plot <- h_data_plot(fit_km = fit_km)

xticks <- h_xticks(data = data_plot)

gg <- h_ggkm(
  data = data_plot,
  censor_show = TRUE,
  xticks = xticks, xlab = "Days", ylab = "Survival Probability",
  title = "tt", footnotes = "ff", yval = "Survival"
)

# The annotation table reports the patient at risk for a given strata and
# times (`xticks`).
annot_tbl <- summary(fit_km, times = xticks)
if (is.null(fit_km$strata)) {
  annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = "All"))
} else {
  strata_lst <- strsplit(sub("=", "equals", levels(annot_tbl$strata)), "equals")
  levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]
  annot_tbl <- data.frame(
    n.risk = annot_tbl$n.risk,
    time = annot_tbl$time,
    strata = annot_tbl$strata
  )
}

# The annotation table is transformed into a grob.
tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks))

# For the representation, the layout is estimated for which the decomposition
# of the graphic element is necessary.
g_el <- h_decompose_gg(gg)
lyt <- h_km_layout(data = data_plot, g_el = g_el, title = "t", footnotes = "f")

grid::grid.newpage()
pushViewport(viewport(layout = lyt, height = .95, width = .95))
grid.rect(gp = grid::gpar(lty = 1, col = "purple", fill = "gray85", lwd = 1))
pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 2))
grid.rect(gp = grid::gpar(lty = 1, col = "orange", fill = "gray85", lwd = 1))
grid::grid.draw(tbl$at_risk)
popViewport()
pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 1))
grid.rect(gp = grid::gpar(lty = 1, col = "green3", fill = "gray85", lwd = 1))
grid::grid.draw(tbl$label)

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