TOmicsVis (version 2.0.0)

survival_plot: Survival plot for analyzing and visualizing survival data.

Description

Survival plot for analyzing and visualizing survival data.

Usage

survival_plot(
  data,
  curve_function = "pct",
  conf_inter = TRUE,
  interval_style = "ribbon",
  risk_table = TRUE,
  num_censor = TRUE,
  sci_palette = "aaas",
  ggTheme = "theme_light",
  x_start = 0,
  y_start = 0,
  y_end = 100,
  x_break = 10,
  y_break = 10
)

Value

Plot: survival plot for analyzing and visualizing survival data.

Arguments

data

Dataframe: survival record data (1st-col: Time, 2nd-col: Status, 3rd-col: Group).

curve_function

Character: an arbitrary function defining a transformation of the survival curve. Often used transformations can be specified with a character argument: "event" plots cumulative events (f(y) = 1-y), "cumhaz" plots the cumulative hazard function (f(y) = -log(y)), and "pct" for survival probability in percentage.

conf_inter

Logical: confidence interval. Default: TRUE, options: TRUE, FALSE.

interval_style

Character: confidence interval style. Default: "ribbon", options: "ribbon", "step".

risk_table

Logical: show cumulative risk table. Default: TRUE, options: TRUE, FALSE.

num_censor

Logical: show cumulative number of censoring. Default: TRUE, options: TRUE, FALSE.

sci_palette

Character: ggsci color palette. Default: "aaas", options: "aaas", "npg", "lancet", "jco", "ucscgb", "uchicago", "simpsons", "rickandmorty".

ggTheme

Character: ggplot2 themes. Default: "theme_light", options: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"

x_start

Numeric: x-axis start value. Default: 0, min: 0, max: null.

y_start

Numeric: y-axis start value. Default: 0, min: 0, max: 100.

y_end

Numeric: y-axis end value. Default: 100, min: 0, max: 100.

x_break

Numeric: x-axis break value. Default: 10, min: 0, max: null.

y_break

Numeric: y-axis break value. Default: 10, min: 0, max: 100.

Author

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(survival_data)
head(survival_data)

# 3. Default parameters
survival_plot(survival_data)

# 4. Set conf_inter = FALSE
survival_plot(survival_data, conf_inter = FALSE)

# 5. Set sci_palette = "jco"
survival_plot(survival_data, sci_palette = "jco")