batch_sig_surv_plot: Batch Signature Survival Plot

In IOBR: Immune Oncology Biological Research

Batch Signature Survival Plot

Description

Generates Kaplan-Meier survival plots for multiple projects or cohorts based on signature scores. Automatically determines optimal cutpoints for signature stratification and creates publication-ready survival curves.

Usage

batch_sig_surv_plot(
  input_pdata,
  signature,
  id = "ID",
  column_of_project = "ProjectID",
  project = NULL,
  time = "time",
  status = "status",
  time_type = "day",
  break_month = "auto",
  palette = "jama",
  cols = NULL,
  mini_sig = "score",
  save_path = NULL,
  show_col = TRUE,
  fig_type = "pdf"
)

Arguments

input_pdata	Data frame containing survival data and signature scores.
signature	Character string specifying the column name of the target signature for survival analysis.
id	Character string specifying the column name containing unique identifiers. Default is '"ID"'.
column_of_project	Character string specifying the column name containing project identifiers. Default is '"ProjectID"'.
project	Character string or vector specifying project name(s) to analyze. If 'NULL', all projects are analyzed. Default is 'NULL'.
time	Character string specifying the column name containing time-to-event data. Default is '"time"'.
status	Character string specifying the column name containing event status. Default is '"status"'.
time_type	Character string specifying the time unit. Options are '"day"' or '"month"'. Default is '"day"'.
break_month	Numeric value or '"auto"' specifying the interval for time axis breaks in months. Default is '"auto"'.
palette	Character string specifying the color palette. Default is '"jama"'.
cols	Character vector of custom colors. If 'NULL', palette is used. Default is 'NULL'.
mini_sig	Character string for the signature label in the legend. Default is '"score"'.
save_path	Character string or 'NULL'. Directory path for saving plots. If 'NULL', plots are not saved. Default is 'NULL'.
show_col	Logical indicating whether to display color information. Default is 'TRUE'.
fig_type	Character string specifying the output file format ('"pdf"', '"png"', etc.). Default is '"pdf"'.

Value

Data frame containing combined survival analysis results from all projects.

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
test_pdata <- data.frame(
  ID = paste0("S", 1:20),
  ProjectID = rep("P1", 20),
  OS_time = runif(20, 1, 60),
  OS_status = sample(c(0, 1), 20, replace = TRUE),
  Marker = rnorm(20)
)
result <- batch_sig_surv_plot(
  input_pdata = test_pdata, signature = "Marker",
  id = "ID", column_of_project = "ProjectID",
  time = "OS_time", status = "OS_status", time_type = "month"
)
if (!is.null(result)) head(result)

IOBR documentation built on May 30, 2026, 5:07 p.m.