km.plot: KM plotting function

In sjacobson94/clinicaltrials: A Collection of Functions for use in CCS

Description

This is a function to consistently plot aesthetically pleasing KM plots using survminer::ggsurvplot() that include risk table below and survival table within.

Usage

km.plot(
  data,
  stat,
  time,
  arm = "arm",
  x.lab = "Time (Months)",
  x.time = NULL,
  y.lab = "% Event-Free",
  ref = as.character(levels(data2$arm)[1]),
  x.max = max(data2$time),
  x.by = 12,
  surv.legend.labs = levels(data2$arm2),
  table.legend.labs = levels(data2$arm2),
  color = RColorBrewer::brewer.pal(8, "Set1"),
  lty = 1,
  table.font.size = 9,
  y.scale = "percent",
  one.sided = FALSE,
  risk.table = TRUE,
  table.include = TRUE,
  pval.include = TRUE,
  pval = NULL,
  pval.loc = NULL,
  size = 0.5,
  risk.table.height = 0.175,
  surv.plot.height = 0.825,
  table.x.min = x.max/5,
  table.x.max = x.max/1.5,
  x.scale = 1,
  surv.order = NULL,
  surv.legend.title = "Arm: ",
  legend.font = 9,
  theme = survminer::theme_survminer(),
  table.loc = "topright",
  ...
)

Arguments

data	The data.
stat	The survival status variable used in survfit()
time	The survival time variable used in survfit()
arm	By variable used in survfit()
x.lab	Label for x-axis of KM plot
x.time	Specific unit for the survival time variable in x-axis label, character (eg. "Days", "Months", "Years").
y.lab	Label for y-axis of KM plot
ref	Specify reference arm for HR values in survival table.
x.max	Max value for the x-axis
x.by	By value for tick marks on the x-axis based on the scaled time variable.
surv.legend.labs	KM plot legend arm labels
table.legend.labs	Survival table arm labels
color	Color for KM plot lines
lty	Type of lines for KM plot
table.font.size	Font size for the survival table
y.scale	Scale for y-axis. Options are "default" (decimals, 0.20) and "percent" (percent, 20%)
one.sided	TRUE for one-sided p-value, FALSE for two-sided p-value
risk.table	Include risk table (TRUE/FALSE)
table.include	Include survival table (TRUE/FALSE)
pval.include	Include p-value. if TRUE and pval = NULL, logrank p-value from survfit() is included
pval	User specified p-value. This can be used to specify p-value used if something different than logrank is desired. Can be character or numeric.
pval.loc	Vector of length 2 to specify the position for the p-value if necessary.
size	Overall size of the plot?
risk.table.height	Percent of plot size taken up by the risk table.
surv.plot.height	Percent of plot size taken up by the KM plot.
table.x.min	Minimum x-axis value for the survival table if table.loc = "topright".
table.x.max	Maximum x-axis value for the survival table if table.loc = "bottomleft".
x.scale	Numeric variable to allow for scaling of the time variable. Will divide the time variable by the value given.
surv.order	Character vector. Allows for the display order of the variables in the legend, plot, survival table, and risk table to be specified. Must include all levels of the "arm" variable.
surv.legend.title	Legend title to appear at the top of the plot (i.e. "Arm: ", "Strata: ').
legend.font	Font size for the legend.
theme	Desired theme for the KM plot and risk table.
table.loc	Character. Specify where the survival table should go inside the plot. Currently support "topright" and "bottomleft".
...	Additional arguments passed onto ggsurvplot()

Value

This function returns a publication quality KM curve.

Examples

library(arsenal)
data(mockstudy)
mockstudy %>% 
    km.plot(data = ., stat = "fu.stat", time = "fu.time", arm = "arm", 
            table.loc = "topright", x.scale = 30.44)

sjacobson94/clinicaltrials documentation built on Oct. 27, 2020, 6:43 p.m.