km_plot: Kaplan-Meier plot function
In swehip/shprplotfun: R functions for SHPR annual report

km_plot

R Documentation

Kaplan-Meier plot function

Description

Kaplan-Meier plot using ggplot2.

Usage

km_plot(
  survfit_obj,
  make_step = NULL,
  first_point = 1,
  one_level = FALSE,
  y_lim = NULL,
  percent_accuracy = 1,
  y_breaks = 5,
  x_lim = NULL,
  x_breaks = 1,
  n_points = NULL,
  n_risk_break = 50,
  title = NULL,
  subtitle = NULL,
  title_size = 14,
  subtitle_size = 10,
  title_margin = 1,
  y_lab = NULL,
  x_lab = NULL,
  background_color = "moccasin",
  panel_grid_color = "grey",
  panel_grid_size = 0.3,
  axis_size = 0.3,
  text_size = 8,
  line_size = 0.5,
  show_ci = TRUE,
  ribbon_ci = TRUE,
  ribbon_alpha = 0.5,
  ci_line_size = 0.2,
  line_colors = c("#377EB8", "#E41A1C", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33",
    "#A65628", "#F781BF"),
  legend_pos = c(0, 0),
  legend_labels = ggplot2::waiver(),
  label_breaks = ggplot2::waiver(),
  legend_key_height_mult = 1
)

Arguments

`survfit_obj`	Object returned from survfit function in survival package. Also works with data frame if year and surv variable exist. lower and upper variable needed if show_ci = TRUE. Specify strata variable needed if several curves wanted.
`make_step`	If TRUE, step data will be created.
`first_point`	If make_step = TRUE, first_point for KM is 1 and for competing risk 0.
`one_level`	Boolean indicating if there is only one level in the strata.
`y_lim`	Limit on y-axis.
`percent_accuracy`	Set accuracy for `percent_format`.
`y_breaks`	Length between each break on y-axis.
`x_lim`	Limit on x-axis.
`x_breaks`	Length between each break on x-axis.
`n_points`	Number of points to be plotted, useful to change if file is large because of too many points!
`n_risk_break`	Minimum number at risk to include
`title`	Plot title, NULL for no title.
`subtitle`	Small text under title, NULL for no subtitle.
`title_size`	Text size of title in pt.
`subtitle_size`	Text size of subtitle in pt.
`title_margin`	Space between title and subtitle in pt.
`y_lab`	Y-axis label.
`x_lab`	X-axis label.
`background_color`	Color of the panel background.
`panel_grid_color`	Color of the panel grid lines.
`panel_grid_size`	Size of the panel grid lines in plot, useful to change if large dpi!
`axis_size`	Size of the axis lines, useful to change if large dpi!
`text_size`	Size of the text in pt.
`line_size`	Size of the head lines.
`show_ci`	If TRUE, show confidence interval lines.
`ribbon_ci`	Show confidence interval
`ribbon_alpha`	Degree of transparency for confidence interval
`ci_line_size`	Size of the confidence interval lines.
`line_colors`	Color of the different curves.
`legend_pos`	Position of the legend in plot.
`legend_labels`	Label for each legend key, default order as they appear in names(survfit_obj$strata).
`label_breaks`	Order of the legend keys.
`legend_key_height_mult`	Increase space between legend keys with a multiple.

Value

ggplot object containing Kaplan-Meier plot.

Examples


# KM-plot with 2 levels
survfit_obj <-
  survival::survfit(survival::Surv(time/365.24, status) ~ sex,
  data = survival::colon
)
km_plot(survfit_obj, y_lim = c(40,100), y_breaks = 10, x_lim = c(0,9))

# KM-plot with 6 levels
survfit_obj <-
  survival::survfit(survival::Surv(time/365.24, status) ~ sex + differ,
  data = survival::colon
)
km_plot(survfit_obj, y_lim = c(30,100), y_breaks = 10,
x_lim = c(0,9), line_colors =
  c('dodgerblue', 'red', 'green', 'black', 'yellow', 'chocolate'))

swehip/shprplotfun documentation built on Oct. 21, 2022, 8:26 a.m.