Kaplan-Meier Plot — g

From a survival model, a graphic is rendered along with tabulated annotation including the number of patient at risk at given time and the median survival per group.

Usage

g_km(
  df,
  variables,
  control_surv = control_surv_timepoint(),
  col = NULL,
  lty = NULL,
  lwd = 0.5,
  censor_show = TRUE,
  pch = 3,
  size = 2,
  max_time = NULL,
  xticks = NULL,
  xlab = "Days",
  yval = c("Survival", "Failure"),
  ylab = paste(yval, "Probability"),
  title = NULL,
  draw = TRUE,
  newpage = TRUE,
  gp = NULL,
  vp = NULL,
  name = NULL,
  font_size = 12,
  ci_ribbon = FALSE,
  ggtheme = nestcolor::theme_nest(),
  annot_at_risk = TRUE,
  annot_surv_med = TRUE,
  annot_coxph = FALSE,
  control_coxph_pw = control_coxph(),
  position_coxph = c(0, 0.05),
  position_surv_med = c(0.9, 0.9)
)

Arguments

df

(data frame)
data set containing all analysis variables.

variables

(named list) of variable names. Details are:

tte: variable indicating time-to-event duration values (numeric).
is_event: event variable (logical)
TRUE if event, FALSE if time to event is censored.
arm: the treatment group variable (factor).
strat: (character or NULL) variable names indicating stratification factors.

control_surv

a (list) of parameters for comparison details, specified by using
the helper function control_surv_timepoint. Some possible parameter options are:

conf_level: (proportion)
confidence level of the interval for survival rate.
conf_type: (string)
"plain" (default), "log", "log-log" for confidence interval type,
see more in survival::survfit(). Note that the option "none" is no longer supported.

col

(character)
lines colors. Length of a vector should be equal to number of strata from survival::survfit().

lty

(numeric)
line type. Length of a vector should be equal to number of strata from survival::survfit().

lwd

(numeric)
line width. Length of a vector should be equal to number of strata from survival::survfit().

censor_show

(flag)
whether to show censored.

pch

(numeric, string)
value or character of points symbol to indicate censored cases.

size

(numeric)
size of censored point, a class of unit.

max_time

(numeric)
maximum value to show on X axis. Only data values less than or up to to this threshold value will be plotted.(NULL for default)

xticks

(numeric, number, or NULL)
numeric vector of ticks or single number with spacing between ticks on the x axis. If NULL (default), labeling::extended() is used to determine an optimal tick position on the x axis.

xlab

(string)
label of x-axis.

yval

(string)
value of y-axis. Should be either Survival (default) or Failure probability.

ylab

(string)
label of y-axis.

title

(string)
title for plot.

draw

(flag)
whether the plot should be drawn.

newpage

(flag)
whether the plot should be drawn on a new page. Only considered if draw = TRUE is used.

gp

A "gpar" object, typically the output from a call to the function gpar. This is basically a list of graphical parameter settings.

vp

a viewport object (or NULL).

name

a character identifier for the grob. Used to find the grob on the display list and/or as a child of another grob.

font_size

(number)
font size to be used.

ci_ribbon

(flag)
draw the confidence interval around the Kaplan-Meier curve.

ggtheme

(theme)
a graphical theme as provided by ggplot2 to control outlook of the Kaplan-Meier curve.

annot_at_risk

(flag)
compute and add the annotation table reporting the number of patient at risk matching the main grid of the Kaplan-Meier curve.

annot_surv_med

(flag)
compute and add the annotation table on the Kaplan-Meier curve estimating the median survival time per group.

annot_coxph

(flag)
add the annotation table from a survival::coxph() model.

control_coxph_pw

(list)
parameters for comparison details, specified by using
the helper function control_coxph(). Some possible parameter options are:

pval_method: (string)
p-value method for testing hazard ratio = 1. Default method is "log-rank", can also be set to "wald" or "likelihood".
ties: (string)
specifying the method for tie handling. Default is "efron", can also be set to "breslow" or "exact". See more in survival::coxph()
conf_level: (proportion)
confidence level of the interval for HR.

position_coxph

numeric
x and y positions for plotting survival::coxph() model.

position_surv_med

numeric
x and y positions for plotting annotation table estimating median survival time per group

Value

a grob of class gTree.

Examples

if (FALSE) {
library(scda)
library(dplyr)
library(ggplot2)
library(survival)
library(grid)
library(nestcolor)

df <- synthetic_cdisc_data("latest")$adtte %>%
  filter(PARAMCD == "OS") %>%
  mutate(is_event = CNSR == 0)
variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD")
# 1. Example - basic option

res <- g_km(df = df, variables = variables)
res <- g_km(df = df, variables = variables, yval = "Failure")
res <- g_km(
  df = df,
  variables = variables,
  control_surv = control_surv_timepoint(conf_level = 0.9),
  col = c("grey25", "grey50", "grey75")
)
res <- g_km(df = df, variables = variables, ggtheme = theme_minimal())
res <- g_km(df = df, variables = variables, ggtheme = theme_minimal(), lty = 1:3)
res <- g_km(df = df, variables = variables, max = 2000)

# 2. Example - Arrange several KM curve on a single graph device

# 2.1 Use case: A general graph on the top, a zoom on the bottom.
grid.newpage()
lyt <- grid.layout(nrow = 2, ncol = 1) %>%
  viewport(layout = .) %>%
  pushViewport()

res <- g_km(
  df = df, variables = variables, newpage = FALSE, annot_surv_med = FALSE,
  vp = viewport(layout.pos.row = 1, layout.pos.col = 1)
)
res <- g_km(
  df = df, variables = variables, max = 1000, newpage = FALSE, annot_surv_med = FALSE,
  ggtheme = theme_dark(),
  vp = viewport(layout.pos.row = 2, layout.pos.col = 1)
)

# 2.1 Use case: No annotations on top, annotated graph on bottom
grid.newpage()
lyt <- grid.layout(nrow = 2, ncol = 1) %>%
  viewport(layout = .) %>%
  pushViewport()

res <- g_km(
  df = df, variables = variables, newpage = FALSE,
  annot_surv_med = FALSE, annot_at_risk = FALSE,
  vp = viewport(layout.pos.row = 1, layout.pos.col = 1)
)
res <- g_km(
  df = df, variables = variables, max = 2000, newpage = FALSE, annot_surv_med = FALSE,
  annot_at_risk = TRUE,
  ggtheme = theme_dark(),
  vp = viewport(layout.pos.row = 2, layout.pos.col = 1)
)

# Add annotation from a pairwise coxph analysis
g_km(
  df = df, variables = variables,
  annot_coxph = TRUE
)

g_km(
  df = df, variables = c(variables, list(strat = "SEX")),
  font_size = 15,
  annot_coxph = TRUE,
  control_coxph = control_coxph(pval_method = "wald", ties = "exact", conf_level = 0.99),
  position_coxph = c(0.4, 0.5)
)

# Change position of the treatment group annotation table.
g_km(
  df = df, variables = c(variables, list(strat = "SEX")),
  font_size = 15,
  annot_coxph = TRUE,
  control_coxph = control_coxph(pval_method = "wald", ties = "exact", conf_level = 0.99),
  position_surv_med = c(1, 0.7)
)
}