km_plot: Kaplan-Meier plot function

View source: R/km_plot.R

km_plotR 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.