survminer (version 0.1.1)

ggsurvplot: Drawing survival curves using ggplot2

Description

Drawing survival curves using ggplot2

Usage

ggsurvplot(fit, fun = NULL, color = NULL, palette = NULL,
  break.time.by = NULL, surv.scale = c("default", "percent"),
  conf.int = FALSE, conf.int.fill = "gray", censor = TRUE, pval = FALSE,
  pval.size = 5, pval.coord = c(NULL, NULL), main = NULL, xlab = "Time",
  ylab = "Survival probability", xlim = NULL, ylim = NULL,
  legend = c("top", "bottom", "left", "right", "none"),
  legend.title = "strata", legend.labs = NULL, risk.table = FALSE,
  risk.table.col = "black", risk.table.adj = NULL,
  risk.table.height = 0.25, surv.plot.adj = NULL, surv.plot.height = 2,
  ggtheme = ggplot2::theme_classic(), ...)

Arguments

fit

an object of class survfit.

fun

an arbitrary function defining a transformation of the survival curve. For example use function(y){y*100}. Often used transformations can be specified with a character argument instead: "event" plots cumulative events (f(y) = 1-y), "cumhaz" plots the cumu

color

color to be used for the survival curves. This argument is ignored when the number of strata (groups > 1). In this case, use the argument palette.

palette

the color palette to be used. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red").

break.time.by

numeric value controlling time axis breaks. Default value is NULL.

surv.scale

scale transformation of survival curves. Allowed values are "default" or "percent".

conf.int

logical value. If TRUE, plots confidence interval.

conf.int.fill

fill color to be used for confidence interval.

censor

logical value. If TRUE, censors will be drawn.

pval

logical value. If TRUE, the p-value is added on the plot.

pval.size

numeric value specifying the p-value text size. Default is 5.

pval.coord

numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL.

main, xlab, ylab

main title and axis labels

xlim, ylim

x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).

legend

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). Default is "top" side position. to remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); se

legend.title

legend title.

legend.labs

character vector specifying legend labels.

risk.table

logical value specifying whether to show risk table. Default is FALSE.

risk.table.col

color to be used for risk table. Default value is "black". If you want to color by strata (i.e. groups), use risk.table.col = "strata".

risk.table.adj

numeric value, used to adjust the location of the risk table. Negative value will shift the table to the left and positive value will shift the table to the right side. Ignored when risk.table = FALSE.

risk.table.height

the height of the risk table on the grid. Increase the value when you have many strata. Default is 0.25. Ignored when risk.table = FALSE.

surv.plot.adj

numeric value, used to adjust survival plot (like risk.table.adj). Ignored when risk.table = FALSE.

surv.plot.height

the height of the survival plot on the grid. Default is 2. Ignored when risk.table = FALSE.

ggtheme

function, ggplot2 theme name. Default value is theme_classic(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

other arguments to be passed to ggplot2 geom_*() functions such as linetype, size, ...

Value

• return a ggplot2 (when risk.table = FALSE).

Details

legend position: The argument legend can be also a numeric vector c(x,y). In this case it is possible to position the legend inside the plotting area. x and y are the coordinates of the legend box. Their values should be between 0 and 1. c(0,0) corresponds to the "bottom left" and c(1,1) corresponds to the "top right" position. For instance use legend = c(0.8, 0.2).

Examples

#\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%
# Example 1: Survival curves with two groups
#\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%

# Fit survival curves
#++++++++++++++++++++++++++++++++++++
require("survival")
fit<- survfit(Surv(time, status) ~ sex, data = lung)

# Drawing survival curves
ggsurvplot(fit)

# Legend: title, labels and position
#++++++++++++++++++++++++++++++++++++

# Change the legend title and labels
ggsurvplot(fit, legend = "bottom",
          legend.title = "Sex",
          legend.labs = c("Male", "Female"))

# Specify legend position by its coordinates
ggsurvplot(fit, legend = c(0.2, 0.2))


# format
#++++++++++++++++++++++++++++++++++++
# change line size --> 1
# Change line types by groups (i.e. "strata")
# and change color palette
ggsurvplot(fit,  size = 1,  # change line size
          linetype = "strata", # change line type by groups
          break.time.by = 250, # break time axis by 250
          palette = c("#E7B800", "#2E9FDF"), # custom color palette
          conf.int = TRUE, # Add confidence interval
          pval = TRUE # Add p-value
)

# Use brewer color palette "Dark2"
ggsurvplot(fit, linetype = "strata",
          conf.int = TRUE, pval = TRUE,
          palette = "Dark2")


# Add risk table
#++++++++++++++++++++++++++++++++++++

# Add Risk table
ggsurvplot(fit, pval = TRUE, conf.int = TRUE,
          risk.table = TRUE)

# Change color, linetype by strata, risk.table color by strata
ggsurvplot(fit,
          pval = TRUE, conf.int = TRUE,
          risk.table = TRUE, # Add risk table
          risk.table.col = "strata", # Change risk table color by groups
          lienetype = "strata", # Change line type by groups
          ggtheme = theme_bw(), # Change ggplot2 theme
          palette = c("#E7B800", "#2E9FDF"))

# Survival curve transformation
#++++++++++++++++++++++++++++++++++++
# Plot cumulative events
ggsurvplot(fit, conf.int = TRUE,
          palette = c("#FF9E29", "#86AA00"),
          risk.table = TRUE, risk.table.col = "strata",
          fun = "event")


# Arbitrary function
ggsurvplot(fit, conf.int = TRUE,
          palette = c("#FF9E29", "#86AA00"),
          risk.table = TRUE, risk.table.col = "strata",
          pval = TRUE,
          fun = function(y) y*100)


#\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%
# Example 3: Survival curve with multiple group
#\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%\%

# Fit (complexe) survival curves
#++++++++++++++++++++++++++++++++++++

require("survival")
fit2 <- survfit( Surv(time, status) ~ rx + adhere,
                data = colon )

# Visualize
#++++++++++++++++++++++++++++++++++++

# Visualize: add p-value, chang y limits
# change color using brewer palette
ggsurvplot(fit2, pval = TRUE,
          break.time.by = 400,
          risk.table = TRUE)

# Adjust risk table and survival plot locations
# ++++++++++++++++++++++++++++++++++++
# Adjust risk table location, shift to the left

ggsurvplot(fit2, pval = TRUE,
          break.time.by = 400,
          risk.table = TRUE,
          risk.table.col = "strata",
          risk.table.adj = -2, # risk table location adj
          palette = "Dark2")

# Adjust survival plot location, shift to the right
# Change Risk table height
ggsurvplot(fit2, pval = TRUE,
          break.time.by = 400,
          risk.table = TRUE,
          risk.table.col = "strata",
          risk.table.height = 0.5, # Useful when you have multiple groups
          surv.plot.adj = 4.9, # surv plot location adj
          palette = "Dark2")


# Change legend labels
# ++++++++++++++++++++++++++++++++++++
ggsurvplot(fit2, pval = TRUE,
          break.time.by = 400,
          risk.table = TRUE,
          risk.table.col = "strata",
          ggtheme = theme_bw(),
          legend.labs = c("A", "B", "C", "D", "E", "F"))